| HOME | HELP | FEEDBACK | SUBSCRIPTIONS | ARCHIVE | SEARCH | TABLE OF CONTENTS |
|
|
|
|||||||
|
|||||||||
1 Department of Chemistry, University of Missouri–Columbia, Columbia, MO 65211, USA
2 Department of Biochemistry, Kansas State University, Manhattan, KS 66506-3702, USA
Reprint requests to: John J. Tanner, Department of Chemistry, University of Missouri–Columbia, 125 Chemistry Building, Columbia, MO 65211, USA; e-mail: tannerjj{at}missouri.edu; fax: (573) 882-2754.
(RECEIVED May 2, 2002; FINAL REVISION June 4, 2002; ACCEPTED June 6, 2002)
Article and publication are at http://www.proteinscience.org/cgi/doi/10.1110/ps.0213502.
 |
Abstract |
|---|
 TOP Abstract IntroductionResultsDiscussionMaterials and methodsElectronic supplemental materialReferences |
|---|
1.90 Å) enzyme-dinucleotide (NAD, NADP, FAD) complexes was performed to investigate the role of solvent in dinucleotide recognition by Rossmann fold domains. The typical binding site contains about 9–12 water molecules, and about 30% of the hydrogen bonds between the protein and the dinucleotide are water mediated. Detailed inspection of the structures reveals a structurally conserved water molecule bridging dinucleotides with the well-known glycine-rich phosphate-binding loop. This water molecule displays a conserved hydrogen-bonding pattern. It forms hydrogen bonds to the dinucleotide pyrophosphate, two of the three conserved glycine residues of the phosphate-binding loop, and a residue at the C-terminus of strand four of the Rossmann fold. The conserved water molecule is also present in high-resolution structures of apo enzymes. However, the water molecule is not present in structures displaying significant deviations from the classic Rossmann fold motif, such as having nonstandard topology, containing a very short phosphate-binding loop, or having 
-helix "A" oriented perpendicular to the ß-sheet. Thus, the conserved water molecule appears to be an inherent structural feature of the classic Rossmann dinucleotide-binding domain. Keywords: NAD; NADP; FAD; dinucleotide-protein interactions; Rossmann fold; structurally conserved water molecule; molecular recognition
Abbreviations: A, adenine • ACP, acyl carrier protein • ADH, alcohol dehydrogenase • CNS, crystallography and NMR system • CoA, coenzyme A • dh, dehydrogenase • dTDP, deoxythymidine diphosphate • EBI-MSD, European Bioinformatics Institute Macromolecular Structure Database • FAD, flavin adenine dinucleotide • GAPDH, d-glyceraldehyde-3-phosphate dehydrogenase • GDP, Guanosine diphosphate • N, nicotinamide • NAD, nicotinamide adenine dinucleotide • NADP, nicotinamide adenine dinucleotide phosphate • NMN, nicotinamide adenine mononucleotide • P, pyrophosphate • PDB, Protein Data Bank • Ra, adenine ribose • rd, reductase • RMSD, root-mean-square deviation • Rn, nicotinamide ribose • UDP-galactose, uridine 5`-diphosphate galactose
|
Introduction |
|---|
|
TOPAbstractIntroductionResultsDiscussionMaterials and methodsElectronic supplemental materialReferences |
|---|
).
|
The Rossmann fold was first identified in dinucleotide-binding proteins (Rossmann et al. 1974) and remains one of the most thoroughly studied dinucleotide-binding folds. The Rossmann fold, or mononucleotide-binding motif, is a single ßßß motif that binds a mononucleotide. The fold that binds NAD and NADP consists of two mononucleotide-binding motifs that are structurally related by a pseudo twofold rotation, with the most N-terminal strands adjacent to each other (Fig. 2). Together, the two ßßß motifs form a six-stranded parallel ß-sheet flanked by -helices, with relative strand order 321456. The fold that binds FAD typically contains one mononucleotide-binding motif with two additional parallel ß-strands, giving a relative strand order of 32145 (Murzin et al. 1995).
|
A (Wierenga et al. 1985) (Fig. 2
). Typically, this loop contains three conserved glycine residues arranged in patterns such as GXGXXG. Mutations in the conserved glycine residues of the loop have been correlated with attenuation or elimination of enzyme activity (Rescigno and Perham 1994; Nishiya and Imanaka 1996; Eschenbrenner et al. 2001) and also with disease (van Grunsven et al. 1998). The second feature is a side chain interaction with the adenine ribose group of the dinucleotide. In NAD- and FAD-binding Rossmann fold proteins, the carboxylate of Asp or Glu interacts with the adenine ribose hydroxyls. In contrast, NADP-binding proteins typically have Arg interacting with the monophosphate at the O2` position of adenine ribose (Branden and Tooze 1991).
The conserved characteristics of dinucleotide-binding proteins have been described in several studies (Rossmann et al. 1974; Lesk 1995); however, the role that structural water plays in dinucleotide recognition has not been extensively analyzed. Five years ago, Carugo and Argos (1997) reported a study of NAD(P)–protein interactions using a data set of 32 NAD(P)–enzyme complexes representing 19 enzymes. The resolution of these structures ranged from 1.6 to 3.20 Å, averaging 2.30 Å, and only eight structures had 1.9 Å resolution or better. Since their work, many high-resolution (1.90 Å) structures have become available for study. Here we describe the results of a survey of 102 high-resolution enzyme/dinucleotide complexes that display the Rossmann dinucleotide-binding fold. These higher resolution structures allow an accurate description of the role of solvent in dinucleotide recognition. We find that bridging water molecules contributes significantly to the dinucleotide-binding interface in all of the enzymes studied. Moreover, we identified a structurally conserved water molecule that links, through hydrogen bonding, the glycine-rich loop and the dinucleotide pyrophosphate moiety. We assert that this conserved water molecule is an integral characteristic of dinucleotide-binding Rossmann fold domains, and thus it contributes significantly to dinucleotide recognition.
|
Results |
|---|
|
TOPAbstractIntroductionResultsDiscussionMaterials and methodsElectronic supplemental materialReferences |
|---|
) bound to a Rossmann fold motif and having a resolution of 1.9 Å or better were selected for analysis. The resulting data set consists of 102 structures, and represents 43 enzymes and 40 species (Tables 1, 2, and 3). The crystallographic resolution ranges from 1.15 to 1.90 Å, averaging 1.70 Å. Notwithstanding our conservative resolution cutoff, this study is one of the largest comparisons of dinucleotide-binding proteins performed to date.
|
|
|
show alignments of the glycine-rich pyrophosphate-binding sequences for the enzymes studied. The majority of enzymes in our data set display the pyrophosphate-binding loop sequence patterns GXGXXG, GXXGXXG, or GXXXGXG, where G is Gly and X is any amino acid residue. Two enzymes have the sequence pattern GXXXXXG, and two have the pattern GXXXXXXXG. Note that sometimes Ala substitutes for the last Gly, and, in one case, dihydropyrimidine dehydrogenase, Ser substitutes for the last Gly. Note that all the FAD-binding proteins in our data set except one have the phosphate-binding loop sequence GXGXXG. Quinone reductase does not have a glycine-rich loop, although it is still classified as a Rossmann fold protein.
Identification of a structurally conserved water molecule
All the structures in our database have several water molecules in the interface between the dinucleotide and the protein. On average, FAD-, NADP-, and NAD-binding proteins accommodate about 12, 11, and 9 interfacial (within 3.75Å of the protein and dinucleotide) water molecules per dinucleotide-binding site, respectively. As expected, many of these interfacial water molecules hydrogen bond to both the dinucleotide and the protein, thus forming water-mediated hydrogen bonds. Figure 3 shows the average numbers of direct and water-mediated hydrogen bonds formed between the protein and the five groups of each of the dinucleotides. Water-mediated hydrogen bonds comprise 29, 32, and 29% of the protein/dinucleotide hydrogen bonds for NAD, NADP, and FAD, respectively. The pyrophosphate group forms almost as many water-mediated hydrogen bonds (2.7 for NAD, 2.4 for NADP, and 3.5 for FAD) as direct hydrogen bonds (2.8 for NAD, 3.2 for NADP, and 4.1 for FAD) to the protein. The remaining groups average one or fewer water-mediated hydrogen bonds, with the exception of adenine ribose in NADP. This group averages more than two water-mediated hydrogen bonds, a result due to its monophosphate. Thus, bridging water molecules are concentrated around the pyrophosphate and monophosphate groups, although they are commonly found associated with the rest of the dinucleotide as well.
|
A) in 77 structures, which represents 37 of 43 enzymes studied. The structures displaying the conserved water molecule are indicated by the checkmark in Tables 1–3. Figure 4A shows the superimposed phosphate binding loops, cofactors, and structurally conserved water molecules of these 37 enzymes. Note the almost perfect superimposition of the phosphate moiety, the glycine-rich loop, and the structurally conserved water molecule of these different structures. In contrast, adenine, nicotinamide, and flavin do not superimpose as well. Figure 4B shows the structurally conserved water molecule from 77 structures after superposition onto the alcohol dehydrogenase structure 1HET, as described in Materials and Methods. Also shown are secondary structurally elements and NADH of 1HET. These water molecules have an RMSD of 0.5 Å from a reference water molecule, which indicates that the water molecules occupy essentially the same location in their respective structures. As will be discussed below, the six enzymes that do not bind this water molecule show significant deviations from the classic Rossmann fold motif.
|
, and an example of this hydrogen bond coordination is shown in Figure 5B. A table detailing the hydrogen bonding partners of the structurally conserved water molecule in each dinucleotide-binding site is provided in the electronic supplement.
|
). Thus, the water molecule always links the pyrophosphate to the glycine-rich loop. Moreover, the interaction with the pyrophosphate is stereospecific. Although the pyrophosphate is not chiral, the oxygen atoms are distinct stereochemically (Schultze and Feigon 1997). Almost without exception, the pyrophosphate atom that interacts with the structurally conserved water molecule is O2N in the case of NAD- or NADP-binding proteins. In FAD-binding proteins, however, it is always O1P (i.e., equivalent to O1N of NAD[P]), which interacts with the structurally conserved water molecule. Interestingly, the only two structures in our study that have both FAD and NADP bound are also the only ones in which NADP binds to the structurally conserved water molecule via its pyrophosphate atom O1N (see 1E1M and 1GRB).
The partners for the other two hydrogen bonds formed by the conserved water molecule depend upon the sequence of the glycine-rich loop. One sequence-dependent hydrogen bond involves either the first or second conserved Gly. This bond occurs in structures with the sequence patterns GXGXXG, GXXGXXG, and GXXXXXXXG. It also occurs in seven of the eight structures with the sequence pattern GXXXGXG, but does not occur in structures with the sequence pattern GXXXXXG. In structures with the sequence GXGXXG, the water molecule forms a hydrogen bond with the amino group of the second conserved Gly. An example of this hydrogen-bonding pattern is shown in Figure 5B. In structures with the sequence patterns GXXGXXG, GXXXGXG, and GXXXXXXXG, the water molecule instead forms a hydrogen bond with the carbonyl group of the first conserved Gly.
The second sequence-dependent hydrogen bond involves a C-terminal residue of ß4. In structures with the pattern GXGXXG and GXXGXXG, this hydrogen bond usually involves the backbone carbonyl of either a small residue or a hydrophobic residue (i.e., Ala, Cys, Gly, Leu, Phe, Ser, or Val for the structures studied). However, occasionally it will involve the hydroxyl of Ser or Thr. In structures with the sequence pattern GXXXGXG, the C-terminal residue of ß4 usually donates a hydrogen bond via the side chain of an Asn. In structures with the sequence pattern GXXXXXXXG, the C-terminal residue of ß4 donates a hydrogen bond via a Ser hydroxyl.
The hydrogen bonding patterns observed in structures with the sequence GXXXXXG are minor variations of the paradigm described above. There are two such structures in our data set, 1A4I (human methylenetetrahydrofolate dehydrogenase) and 1E7W (Leishmania major pteridine reductase). The water molecule of 1A4I does not superimpose as well as the others, as is evident from its 1.1-Å separation from the others in Figure 4. The conserved water molecule of 1A4I displays a hydrogen-bonding pattern identical to that of GXGXXG structures, with Ser of its GRSKIVG sequence playing the role of the second conserved Gly. On the other hand, the hydrogen bond coordination in 1E7W is very similar to that of proteins with the sequence GXXXGXG. The only exception is that the first conserved glycine residue interacts with the structurally conserved water molecule via another water molecule inside the phosphate-binding loop. To our knowledge, this is the only case in which the structurally conserved water molecule forms a hydrogen bond with another water molecule.
Finally, the conserved water molecule sometimes forms a fifth hydrogen bond. For example, in structures with the sequence pattern GXXXGXG, the conserved water molecule forms a fifth hydrogen bond with the carbonyl of the third "X" residue. It is also common to see the methylene of the second or third conserved Gly within hydrogen bonding distance of the structurally conserved water molecule. Several studies have mentioned the presence of CH . . . O hydrogen bonds in NAD(P) interfaces (Carugo and Argos 1997; Chu and Hwang 1998). Although CH . . . O hydrogen bonds are somewhat unconventional, the methylene of glycine can theoretically form a significant hydrogen bond. Such a bond would have about half the energy of a typical hydrogen bond from water (Scheiner et al. 2001).
Structures lacking the conserved water molecule
Six enzymes (3-dehydroquinate synthase, NMN adenylyltransferase, NADP[H] transhydrogenase, nitric-oxide synthase, dihydrofolate reductase, quinone reductase) lack the structurally conserved water molecule (Tables 1–3). These enzymes show significant deviations from the standard Rossmann fold motif in terms of their sequence and/or structure. Thus, the conserved water molecule is found only in classic Rossmann fold structures.
Some of the unusual features of these enzymes are obvious. For example, 3-dehydroquinate synthase has a nonstandard topology in which the phosphate-binding loop connects ß4 and D instead of ß1 and A. No other enzyme in our data set has this unusual topology. In NADP(H) transhydrogenase and dihydrofolate reductase, the long axis of A runs perpendicular to the ß-sheet rather than parallel to it as in all the other structures. NMN adenylyltransferase differs from the other enzymes in our data set because NAD is a product of catalysis rather than a redox cofactor. The pyrophosphate binds near the beginning of the phosphate-binding loop rather than at the end of the loop near the N-terminus of A as occurs in the classic Rossmann fold structures. Thus, the pyrophosphate interacts with the Rossmann fold in a fundamentally unique way that is related to the nature of the reaction catalyzed.
3-Dehydroquinate synthase, NADP(H) transhydrogenase, and nitric-oxide synthase show a subtle, but very important, deviation from the standard Rossmann fold structure concerning the hydrogen bonding potential of the last residue of their phosphate-binding sequences. In the classic Rossmann fold, this residue occurs at the beginning of A (Fig. 2) and its amino group donates one of the invariant hydrogen bonds to the structurally conserved water molecule (Fig. 5A). However, in 3-dehydroquinate synthase, NADP(H) transhydrogenase, and nitric-oxide synthase, this residue cannot hydrogen bond to a water molecule because it is the fifth or later residue of the helix, and its amino group must form an "n + 4" -helix hydrogen bond with the carbonyl four residues preceding it in the sequence.
Lastly, dihydrofolate reductase and quinone reductase deviate from the classic Rossmann fold because of the length and sequence, respectively, of their phosphate binding loops. The dihydrofolate reductases have short phosphate-binding loops. Their loops consist of four to five residues compared to six to nine residues in the other structures (Tables 1–3). The resulting loop between ß1 and A is not wide enough to accommodate a water molecule. Quinone reductase, on the other hand, has no glycine residues in its phosphate-binding loop. This is a critical feature, because, in the classic Rossmann fold motif, the first Gly of the phosphate-binding loop always occupies the first quadrant (i.e., 
> 0, 
> 0) of the Ramachandran plot. This region of – space is typically inaccessible to nonglycine residues. Thus, the phosphate-binding loop of quinone reductase cannot adopt the backbone conformations typically observed in classic Rossmann fold proteins.
|
Discussion |
|---|
|
TOPAbstractIntroductionResultsDiscussionMaterials and methodsElectronic supplemental materialReferences |
|---|
More generally, our results demonstrate a pitfall of ignoring water molecules when analyzing protein crystal structures. In the present case, neglecting water molecules would have given the incorrect impression that Rossmann fold domains greatly underutilize the hydrogen bonding potential of dinucleotides. This issue is critical for ligand docking calculations and structure-based drug design and optimization (Marrone et al. 1997; Raymer et al. 1997).
The result that water molecules are important in dinucleotide recognition is perhaps not surprising, because solvent is important in protein recognition of small molecules, DNA, and protein. For example, about 40% of all protein–DNA hydrogen bonds are water mediated (Luscombe et al. 2001), and protein–protein interfaces contain an average of about 22 water molecules and 11 water-mediated hydrogen bonds (Janin 1999).
Structurally conserved water molecule
We discovered a water molecule that bridges the glycine-rich loop and the pyrophosphate in 77 of the 102 structures studied. The structurally conserved water molecule binds at the N-terminus of A and it displays a conserved hydrogen-bonding pattern (Fig. 4). Structurally conserved water molecules have also been identified in fatty acid binding proteins (Likic et al. 2000) and serine proteases (Sreenivasan and Axelsen 1992). Water molecules of ligand-binding sites have also been found to be conserved between pairs of homologous proteins from different species (Poornima and Dean 1995). Several authors have noted the presence of a water molecule that we refer to as the structurally conserved water molecule, but they did not realize its ubiquity in Rossmann fold domains or its conserved hydrogen-bonding pattern (Lamzin et al. 1994; Dessen et al. 1995; Rafferty et al. 1995; Dengler et al. 1997; Adolph et al. 2000; Thoden et al. 2000; Horer et al. 2001; Pantano et al. 2002). In NAD-binding proteins, we found the water molecule to be more highly conserved than the carboxylate interaction with the adenine-ribose diol. Not only do the structures in our data set represent a significant cross section of enzymes, but they also represent a variety of species and even biologic kingdoms. Such structural conservation argues strongly for an important functional role.
The structurally conserved water molecule typically forms hydrogen bonds with two of the three conserved glycine residues, a C-terminal residue of ß4, and the dinucleotide pyrophosphate. The water molecule always forms hydrogen bonds to both the pyrophosphate and the last conserved Gly, which is part of helix A. This water-mediated hydrogen bond is significant, because previous studies have noted that direct hydrogen bonding between A and the pyrophosphate is not optimal. Based on this observation, a favorable electrostatic interaction between the helix dipole of A and the pyrophosphate has been considered an important factor in dinucleotide recognition (Wierenga et al. 1985). This conclusion, however, was based on analyses of crystal structures that generally lacked water molecules; therefore, water-mediated hydrogen bonds could not be considered. Including water-mediated hydrogen bonds almost doubles the number of observed hydrogen bonds between the protein and pyrophosphate. Due to the high solvent content about the pyrophosphate and the several water-mediated hydrogen bonds, we wonder if the helix dipole would be an important contributing factor to pyrophosphate binding. Additional studies would be needed to resolve this issue.
Structures that exhibit the classic Rossmann fold motif bind the structurally conserved water molecule, whereas structures that have major deviations from the standard Rossmann fold do not. The following classic features are shared by all the structures bearing the conserved water molecule. The ß-sheet topology is 321456 for NAD(P)- and 32145 for FAD-binding domains, and A is parallel to the ß-sheet. The phosphate-binding loop is at least six residues long, and it contains Gly at the first position. The last residue of the phosphate-binding sequence is located at the beginning of A where its amino group is available to hydrogen bond to the water.
The conserved water molecule appears to be a structural feature inherent to the classic Rossmann dinucleotide-binding fold itself, because this water molecule is also present in apo structures. Examples of such apo structures include the FAD utilizing enzyme L-aspartate oxidase, 1CHU (Mattevi et al. 1999), the NAD enzyme malate dehydrogenase, 1MLD (Gleason et al. 1994), and the NADP enzyme secondary alcohol dehydrogenase, 1PED (Korkhin et al. 1998). Some of the FAD-containing structures in our study also contained NADP-binding domains that lacked NADP. All of these apo-NADP domains also contained the structurally conserved water molecule.
There are several potential functional roles for the conserved water molecule in dinucleotide recognition. First, it could help maintain the unique conformation of the glycine-rich phosphate-binding loop. This role is suggested by the presence of the water molecule in apo structures of dinucleotide-binding enzymes, and by the fact that at least two residues of the glycine-rich loop hydrogen bond to the water molecule (Fig. 5A). These residues interact with the water molecule through their backbone carbonyl or amide groups; thus, these protein–water hydrogen bonds appear to stabilize the backbone conformation of the loop by maintaining these residues in specific phi and psi ranges. A second functional role for the water molecule is that it helps to maintain the cofactor in an extended conformation. Experimental (Zens et al. 1976) and computational studies (Smith and Tanner 1999Smith and Tanner 2000) of NAD+ in various solvents suggest that NAD+ is folded in aqueous solution such that the two bases stack against each other at a distance of about 4–5 Å. Thus, NAD+ must unfold into an extended conformation during complexation to the enzyme. The extent to which the enzyme facilitates the unfolding of the cofactor is unknown; however, the protein presumably provides interactions that encourage and maintain the extended geometry. The hydrogen bonding and steric interactions provided by the conserved water molecule could help constrain the dihedral angles of the pyrophosphate group to the values observed in enzyme/dinucleotide complexes. A third possible functional role for the conserved water molecule is that the sequence independent hydrogen bond between the dinucleotide pyrophosphate and the water molecule (Fig. 5) presumably provides a favorable enthalpic contribution to the free energy of binding. Future studies will explore these potential roles to evaluate their possible contributions to dinucleotide recognition and binding.
|
Materials and methods |
|---|
|
TOPAbstractIntroductionResultsDiscussionMaterials and methodsElectronic supplemental materialReferences |
|---|
). Some of the proteins had representatives in multiple species. To ensure an accurate accounting of interactions, including those involving solvent positions near subunit interfaces, the biologically relevant oligomeric forms of the enzyme were used. Typically, we used the "Likely Quaternary Structure" obtained from the European Bioinformatics Institute Macromolecular Structure Database (EBI-MSD) via the OCA-browser interface (http://oca.ebi.ac.uk/oca-bin/ocamain). Using symmetry operators, the EBI generates oligomeric structures from coordinates deposited in the PDB. Each structure downloaded from the EBI-MSD was superimposed onto its parent structure from the PDB using CNS (Brunger et al. 1998) and visualized in O (Jones et al. 1991) to verify the accuracy of the symmetry expansion and to inspect the dinucleotide binding site. In a few cases, the symmetry expansion was incorrect or incomplete, and CNS was used to create the correct quaternary structures from the corresponding PDB structures. In other cases, visual inspection revealed that a few subunits contained incompletely modeled NAD+ molecules. These subunits were omitted from the subsequent analysis. Bound sulfate ions present due to the crystallization medium were removed.
To facilitate comparison, all the structures were superimposed onto a common structure using CNS. Each protein was superimposed onto the ADH structure of Meijers et al. (2001) (1HET) using the -carbon coordinates of the first, third from last, and last residue of the phosphate-binding loop. The molecular visualization programs O and Protein Explorer (Martz 2001) were used to examine the structures.
Hydrogen bonding calculations
Hydrogen bonds found in biologic molecules typically have an acceptor–donor distance of 2.7–3.2 Å (Jeffrey 1997). For the purposes of our study, the functional definition of a hydrogen bond was the presence of an acceptor and a donor within 3.2 Å of each other. Only nitrogen and oxygen atoms were considered for our hydrogen bonding calculations (i.e., CH. . .O hydrogen bonds were not included in Fig. 3). Due to the difficult nature of assigning hydrogen atom positions for water molecules and hydroxyl groups, as well as the absence of explicit hydrogen atoms in the crystal structures under study, an angle cutoff was not included in our definition of a hydrogen bond. Based on our functional definition, X-PLOR (Brunger 1992) was used to identify hydrogen bonds.
The data set of structures used in this study contains some redundancy; therefore, hydrogen-bonding calculations for each structure were weighted to avoid biasing the results toward enzymes heavily represented in our data set. Each enzyme contributed equally to the overall average by assigning each structure a weight equal to the inverse of the product of the number of sources per enzyme and the number of structures per source. For example, Table 1 lists three structures of UDP-galactose-4-epimerase from Homo sapiens and six structures from Escherichia coli. Thus, each H. sapiens UDP-galactose-4-epimerase structure would receive a weight of 1/6, while each E. coli UDP-galactose-4-epimerase structure would receive a weight of 1/12. Likewise, because there is only one source and one structure representing 7-hydroxysteroid dehydrogenase (1FMC), it would receive a weight of 1. In addition, most of the structures used in this analysis are oligomers; therefore, the hydrogen bonding data were averaged over all the subunits within each structure. Each subunit contributed equally to the average for its structure.
|
Electronic supplemental material |
|---|
|
TOPAbstractIntroductionResultsDiscussionMaterials and methodsElectronic supplemental materialReferences |
|---|
|
Acknowledgments |
|---|
The publication costs of this article were defrayed in part by payment of page charges. This article must therefore be hereby marked "advertisement" in accordance with 18 USC section 1734 solely to indicate this fact.
|
References |
|---|
|
TOPAbstractIntroductionResultsDiscussionMaterials and methodsElectronic supplemental materialReferences |
|---|
Al-Karadaghi, S., Cedergren-Zeppezauer, E.S., Petratos, K., Hovmoeller, S., Terry, H., Dauter, Z., and Wilson, K.S. 1994. Refined crystal structure of liver alcohol dehydrogenase-NADH complex at 1.8 Å resolution. Acta Crystallogr. D Biol. Crystallogr. 50: 793–807.
Allaire, M., Li, Y., MacKenzie, R.E., and Cygler, M. 1998. The 3-D structure of a folate-dependent dehydrogenase/cyclohydrolase bifunctional enzyme at 1.5 Å resolution. Structure 6: 173–182.[Medline]
Aronov, A.M., Verlinde, C.L., Hol, W.G., and Gelb, M.H. 1998. Selective tight binding inhibitors of trypanosomal glyceraldehyde-3-phosphate dehydrogenase via structure-based drug design. J. Med. Chem. 41: 4790–4799.[CrossRef][Medline]
Auerbach, G., Herrmann, A., Gutlich, M., Fischer, M., Jacob, U., Bacher, A., and Huber, R. 1997. The 1.25 Å crystal structure of sepiapterin reductase reveals its binding mode to pterins and brain neurotransmitters. EMBO J. 16: 7219–7230.[CrossRef][Medline]
Barycki, J.J., O'Brien, L.K., Strauss, A.W., and Banaszak, L.J. 2000. Sequestration of the active site by interdomain shifting. Crystallographic and spectroscopic evidence for distinct conformations of L-3-hydroxyacyl-CoA dehydrogenase. J. Biol. Chem. 275: 27186–27196.
Becker, K., Savvides, S.N., Keese, M., Schirmer, R.H., and Karplus, P.A. 1998. Enzyme inactivation through sulfhydryl oxidation by physiologic NO-carriers. Nat. Struct. Biol. 5: 267–271.[CrossRef][Medline]
Berman, H.M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T.N., Weissig, H., Shindyalov, I.N., and Bourne, P.E. 2000. The Protein Data Bank (http://www.rcsb.org/). Nucleic Acids Res. 28: 235–242.
Bieger, B. and Essen, L.O. 2001. Crystal structure of the catalytic core component of the alkylhydroperoxide reductase AhpF from Escherichia coli. J. Mol. Biol. 307: 1–8.[CrossRef][Medline]
Binda, C., Angelini, R., Federico, R., Ascenzi, P., and Mattevi, A. 2001. Structural bases for inhibitor binding and catalysis in polyamine oxidase. Biochemistry 40: 2766–2776.[CrossRef][Medline]
Binda, C., Coda, A., Angelini, R., Federico, R., Ascenzi, P., and Mattevi, A. 1999. A 30 Å long U-shaped catalytic tunnel in the crystal structure of polyamine oxidase. Struct. Fold. Des. 7: 265–276.[Medline]
Biou, V., Dumas, R., Cohen-Addad, C., Douce, R., Job, D., and Pebay-Peyroula, E. 1997. The crystal structure of plant acetohydroxy acid isomeroreductase complexed with NADPH, two magnesium ions and a herbicidal transition state analog determined at 1.65 Å resolution. EMBO J. 16: 3405–3415.[CrossRef][Medline]
Bolin, J.T., Filman, D.J., Matthews, D.A., Hamlin, R.C., and Kraut, J. 1982. Crystal structures of Escherichia coli and Lactobacillus casei dihydrofolate reductase refined at 1.7 Å resolution. I. General features and binding of methotrexate. J. Biol. Chem. 257: 13650–13662.
Branden, C. and Tooze, J. 1991. Chapter 10: Enzymes that bind nucleotides. In Introduction to protein structure, 1st ed., pp. 141–159. Garland Publishing, New York.
Bressi, J.C., Verlinde, C.L., Aronov, A.M., Shaw, M.L., Shin, S.S., Nguyen, L.N., Suresh, S., Buckner, F.S., Van Voorhis, W.C., Kuntz, I.D., Hol, W.G., and Gelb, M.H. 2001. Adenosine analogues as selective inhibitors of glyceraldehyde-3-phosphate dehydrogenase of Trypanosomatidae via structure-based drug design. J. Med. Chem. 44: 2080–2093.[CrossRef][Medline]
Brunger, A.T. 1992. X-PLOR, version 3.1: A system for X-ray crystallography and NMR. Yale University Press, New Haven, CT.
Brunger, A.T., Adams, P.D., Clore, G.M., DeLano, W.L., Gros, P., Grosse-Kunstleve, R.W., Jiang, J.S., Kuszewski, J., Nilges, M., Pannu, N.S., Read, R.J., Rice, L.M., Simonson, T., and Warren, G.L. 1998. Crystallography & NMR system: A new software suite for macromolecular structure determination. Acta Crystallogr. D Biol. Crystallogr. 54: 905–921.[CrossRef][Medline]
Brunhuber, N.M., Thoden, J.B., Blanchard, J.S., and Vanhooke, J.L. 2000. Rhodococcus L-phenylalanine dehydrogenase: Kinetics, mechanism, and structural basis for catalytic specificity. Biochemistry 39: 9174–9187.[CrossRef][Medline]
Carpenter, E.P., Hawkins, A.R., Frost, J.W., and Brown, K.A. 1998. Structure of dehydroquinate synthase reveals an active site capable of multistep catalysis. Nature 394: 299–302.[CrossRef][Medline]
Carugo, O. and Argos, P. 1997. NADP-dependent enzymes. I: Conserved stereochemistry of cofactor binding. Proteins 28: 10–28.[CrossRef][Medline]
Champness, J.N., Achari, A., Ballantine, S.P., Bryant, P.K., Delves, C.J., and Stammers, D.K. 1994. The structure of Pneumocystis carinii dihydrofolate reductase to 1.9 Å resolution. Structure 2: 915–924.[Medline]
Cho, H., Ramaswamy, S., and Plapp, B.V. 1997. Flexibility of liver alcohol dehydrogenase in stereoselective binding of 3-butylthiolane 1-oxides. Biochemistry 36: 382–389.[CrossRef][Medline]
Chu, P.Y. and Hwang, M.J. 1998. New insights for dinucleotide backbone binding in conserved C5`-H . . . O hydrogen bonds. J. Mol. Biol. 279: 695–701.[CrossRef][Medline]
Cody, V., Galitsky, N., Rak, D., Luft, J.R., Pangborn, W., and Queener, S.F. 1999. Ligand-induced conformational changes in the crystal structures of Pneumocystis carinii dihydrofolate reductase complexes with folate and NADP+. Biochemistry 38: 4303–4312.[CrossRef][Medline]
Dengler, U., Niefind, K., Kiess, M., and Schomburg, D. 1997. Crystal structure of a ternary complex of D-2-hydroxyisocaproate dehydrogenase from Lactobacillus casei, NAD+ and 2-oxoisocaproate at 1.9 Å resolution. J. Mol. Biol. 267: 640–660.[CrossRef][Medline]
Dessen, A., Quemard, A., Blanchard, J.S., Jacobs, W.R., Jr., and Sacchettini, J.C. 1995. Crystal structure and function of the isoniazid target of Mycobacterium tuberculosis. Science 267: 1638–1641.
Dobritzsch, D., Schneider, G., Schnackerz, K.D., and Lindqvist, Y. 2001. Crystal structure of dihydropyrimidine dehydrogenase, a major determinant of the pharmacokinetics of the anti-cancer drug 5-fluorouracil. EMBO J. 20: 650–660.[CrossRef][Medline]
Duee, E., Olivier-Deyris, L., Fanchon, E., Corbier, C., Branlant, G., and Dideberg, O. 1996. Comparison of the structures of wild-type and a N313T mutant of Escherichia coli glyceraldehyde 3-phosphate dehydrogenases: Implication for NAD binding and cooperativity. J. Mol. Biol. 257: 814–838.[CrossRef][Medline]
Dunn, C.R., Banfield, M.J., Barker, J.J., Higham, C.W., Moreton, K.M., Turgut-Balik, D., Brady, R.L., and Holbrook, J.J. 1996. The structure of lactate dehydrogenase from Plasmodium falciparum reveals a new target for anti-malarial design. Nat. Struct. Biol. 3: 912–915.[CrossRef][Medline]
Eschenbrenner, M., Chlumsky, L.J., Khanna, P., Strasser, F., and Jorns, M.S. 2001. Organization of the multiple coenzymes and subunits and role of the covalent flavin link in the complex heterotetrameric sarcosine oxidase. Biochemistry 40: 5352–5367.[CrossRef][Medline]
Faig, M., Bianchet, M.A., Talalay, P., Chen, S., Winski, S., Ross, D., and Amzel, L.M. 2000. Structures of recombinant human and mouse NAD(P)H: quinone oxidoreductases: Species comparison and structural changes with substrate binding and release. Proc. Natl. Acad. Sci. 97: 3177–3182.
Faig, M., Bianchet, M.A., Winski, S., Hargreaves, R., Moody, C.J., Hudnott, A.R., Ross, D., and Amzel, L.M. 2001. Structure-based development of anticancer drugs: Complexes of NAD(P)H:quinone oxidoreductase 1 with chemotherapeutic quinones. Structure (Camb.) 9: 659–667.[Medline]
Franchetti, P., Cappellacci, L., Perlini, P., Jayaram, H.N., Butler, A., Schneider, B.P., Collart, F.R., Huberman, E., and Grifantini, M. 1998. Isosteric analogues of nicotinamide adenine dinucleotide derived from furanfurin, thiophenfurin, and selenophenfurin as mammalian inosine monophosphate dehydrogenase (type I and II) inhibitors. J. Med. Chem. 41: 1702–1707.[CrossRef][Medline]
Gleason, W.B., Fu, Z., Birktoft, J., and Banaszak, L. 1994. Refined crystal structure of mitochondrial malate dehydrogenase from porcine heart and the consensus structure for dicarboxylic acid oxidoreductases. Biochemistry 33: 2078–2088.[CrossRef][Medline]
Gourley, D.G., Schuttelkopf, A.W., Leonard, G.A., Luba, J., Hardy, L.W., Beverley, S.M., and Hunter, W.N. 2001. Pteridine reductase mechanism correlates pterin metabolism with drug resistance in trypanosomatid parasites. Nat. Struct. Biol. 8: 521–525.[CrossRef][Medline]
Hall, M.D. and Banaszak, L.J. 1993. Crystal structure of a ternary complex of Escherichia coli malate dehydrogenase citrate and NAD at 1.9 Å resolution. J. Mol. Biol. 232: 213–222.[CrossRef][Medline]
Hegeman, A.D., Gross, J.W., and Frey, P.A. 2001. Probing catalysis by Escherichia coli dTDP-glucose-4,6-dehydratase: Identification and preliminary characterization of functional amino acid residues at the active site. Biochemistry 40: 6598–6610.[CrossRef][Medline]
Horer, S., Stoop, J., Mooibroek, H., Baumann, U., and Sassoon, J. 2001. The crystallographic structure of the mannitol 2-dehydrogenase NADP+ binary complex from Agaricus bisporus. J. Biol. Chem. 276: 27555–27561.
Janin, J. 1999. Wet and dry interfaces: The role of solvent in protein–protein and protein–DNA recognition. Struct. Fold. Des. 7: R277–279.[Medline]
Jeffrey, G.A. 1997. An introduction to hydrogen bonding. Oxford University Press, New York.
Jones, T.A., Zou, J.Y., Cowan, S.W., and Kjeldgaard. 1991. Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr. A 47: 110–119.
Karplus, P.A. and Schulz, G.E. 1987. Refined structure of glutathione reductase at 1.54 Å resolution. J. Mol. Biol. 195: 701–729.[CrossRef][Medline]
———. 1989. Substrate binding and catalysis by glutathione reductase as derived from refined enzyme: Substrate crystal structures at 2 Å resolution. J. Mol. Biol. 210: 163–180.[CrossRef][Medline]
Kelly, C.A., Nishiyama, M., Ohnishi, Y., Beppu, T., and Birktoft, J.J. 1993. Determinants of protein thermostability observed in the 1.9-Å crystal structure of malate dehydrogenase from the thermophilic bacterium Thermus flavus. Biochemistry 32: 3913–3922.
Konno, Y., Natsumeda, Y., Nagai, M., Yamaji, Y., Ohno, S., Suzuki, K., and Weber, G. 1991. Expression of human IMP dehydrogenase types I and II in Escherichia coli and distribution in human normal lymphocytes and leukemic cell lines. J. Biol. Chem. 266: 506–509.
Korkhin, Y., Kalb, A.J., Peretz, M., Bogin, O., Burstein, Y., and Frolow, F. 1998. NADP-dependent bacterial alcohol dehydrogenases: Crystal structure, cofactor-binding and cofactor specificity of the ADHs of Clostridium beijerinckii and Thermoanaerobacter brockii. J. Mol. Biol. 278: 967–981.
Kraulis, P.J. 1991. MOLSCRIPT: A program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallogr. 24: 946–950.[CrossRef]
Lamzin, V.S., Dauter, Z., Popov, V.O., Harutyunyan, E.H., and Wilson, K.S. 1994. High resolution structures of holo and apo formate dehydrogenase. J. Mol. Biol. 236: 759–785.[CrossRef][Medline]
Lee, B.I., Chang, C., Cho, S.J., Eom, S.H., Kim, K.K., Yu, Y.G., and Suh, S.W. 2001. Crystal structure of the MJ0490 gene product of the hyperthermophilic archaebacterium Methanococcus jannaschii, a novel member of the lactate/malate family of dehydrogenases. J. Mol. Biol. 307: 1351–1362.[CrossRef][Medline]
Lesk, A.M. 1995. NAD-binding domains of dehydrogenases. Curr. Opin. Struct. Biol. 5: 775–783.[CrossRef][Medline]
Li, J., Vrielink, A., Brick, P., and Blow, D.M. 1993. Crystal structure of cholesterol oxidase complexed with a steroid substrate: Implications for flavin adenine dinucleotide dependent alcohol oxidases. Biochemistry 32: 11507–11515.[CrossRef][Medline]
Li, R., Sirawaraporn, R., Chitnumsub, P., Sirawaraporn, W., Wooden, J., Athappilly, F., Turley, S., and Hol, W.G. 2000. Three-dimensional structure of M. tuberculosis dihydrofolate reductase reveals opportunities for the design of novel tuberculosis drugs. J. Mol. Biol. 295: 307–323.[CrossRef][Medline]
Liao, D.I., Thompson, J.E., Fahnestock, S., Valent, B., and Jordan, D.B. 2001. A structural account of substrate and inhibitor specificity differences between two naphthol reductases. Biochemistry 40: 8696–8704.[CrossRef][Medline]
Likic, V.A., Juranic, N., Macura, S., and Prendergast, F.G. 2000. A "structural" water molecule in the family of fatty acid binding proteins. Protein Sci. 9: 497–504.[Abstract]
Luscombe, N.M., Laskowski, R.A., and Thornton, J.M. 2001. Amino acid-base interactions: A three-dimensional analysis of protein–DNA interactions at an atomic level. Nucleic Acids Res. 29: 2860–2874.
Marrone, T.J., Briggs, J.M., and McCammon, J.A. 1997. Structure-based drug design: Computational advances. Annu. Rev. Pharmacol. Toxicol. 37: 71–90.[CrossRef][Medline]
Martz, E. 2001. "Protein explorer software," http://proteinexplorer.org. For a list of further references, see http://molvis.sdsc.edu/protexpl/pe_lit.htm.
Mattevi, A., Tedeschi, G., Bacchella, L., Coda, A., Negri, A., and Ronchi, S. 1999. Structure of L-aspartate oxidase: Implications for the succinate dehydrogenase/fumarate reductase oxidoreductase family. Struct. Fold. Des. 7: 745–756.[Medline]
Matthews, D.A., Bolin, J.T., Burridge, J.M., Filman, D.J., Volz, K.W., Kaufman, B.T., Beddell, C.R., Champness, J.N., Stammers, D.K., and Kraut, J. 1985. Refined crystal structures of Escherichia coli and chicken liver dihydrofolate reductase containing bound trimethoprim. J. Biol. Chem. 260: 381–391.
Meijers, R., Morris, R.J., Adolph, H.W., Merli, A., Lamzin, V.S., and Cedergren-Zeppezauer, E.S. 2001. On the enzymatic activation of NADH. J. Biol. Chem. 276: 9316–9321.
Merritt, E.A. and Bacon, D.J. 1997. Raster3D photorealistic molecular graphics. Methods Enzymol. 277: 505–524.[Medline]
Mittl, P.R. and Schulz, G.E. 1994. Structure of glutathione reductase from Escherichia coli at 1.86 Å resolution: Comparison with the enzyme from human erythrocytes. Protein Sci. 3: 799–809.[Abstract]
Mulichak, A.M., Theisen, M.J., Essigmann, B., Benning, C., and Garavito, R.M. 1999. Crystal structure of SQD1, an enzyme involved in the biosynthesis of the plant sulfolipid headgroup donor UDP-sulfoquinovose. Proc. Natl. Acad. Sci. 96: 13097–13102.
Murzin, A.G., Brenner, S.E., Hubbard, T., and Chothia, C. 1995. SCOP: A structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol. 247: 536–540.[CrossRef][Medline]
Nagai, M., Natsumeda, Y., Konno, Y., Hoffman, R., Irino, S., and Weber, G. 1991. Selective up-regulation of type II inosine 5`-monophosphate dehydrogenase messenger RNA expression in human leukemias. Cancer Res. 51: 3886–3890.
Nishiya, Y. and Imanaka, T. 1996. Analysis of interaction between the Arthrobacter sarcosine oxidase and the coenzyme flavin adenine dinucleotide by site-directed mutagenesis. Appl. Environ. Microbiol. 62: 2405–2410.[Abstract]
Otagiri, M., Kurisu, G., Ui, S., Takusagawa, Y., Ohkuma, M., Kudo, T., and Kusunoki, M. 2001. Crystal structure of meso-2,3-butanediol dehydrogenase in a complex with NAD+ and inhibitor mercaptoethanol at 1.7 Å resolution for understanding of chiral substrate recognition mechanisms. J. Biochem. (Tokyo) 129: 205–208.
Pantano, S., Alber, F., Lamba, D., and Carloni, P. 2002. NADH interactions with WT- and S94A-acyl carrier protein reductase from Mycobacterium tuberculosis: An ab initio study. Proteins 47: 62–68.[CrossRef][Medline]
Pereira, P.J., Macedo-Ribeiro, S., Parraga, A., Perez-Luque, R., Cunningham, O., Darcy, K., Mantle, T.J., and Coll, M. 2001. Structure of human biliverdin IXß reductase, an early fetal bilirubin IXß producing enzyme. Nat. Struct. Biol. 8: 215–220.[CrossRef][Medline]
Poornima, C.S. and Dean, P.M. 1995. Hydration in drug design. 3. Conserved water molecules at the ligand-binding sites of homologous proteins. J. Comput. Aided Mol. Des. 9: 521–531.[CrossRef][Medline]
Powell, A.J., Read, J.A., Banfield, M.J., Gunn-Moore, F., Yan, S.D., Lustbader, J., Stern, A.R., Stern, D.M., and Brady, R.L. 2000. Recognition of structurally diverse substrates by type II 3-hydroxyacyl-CoA dehydrogenase (HADH II)/amyloid-beta binding alcohol dehydrogenase (ABAD). J. Mol. Biol. 303: 311–327.[CrossRef][Medline]
Prasad, G.S., Sridhar, V., Yamaguchi, M., Hatefi, Y., and Stout, C.D. 1999. Crystal structure of transhydrogenase domain III at 1.2 Å resolution. Nat. Struct. Biol. 6: 1126–1131.[CrossRef][Medline]
Rafferty, J.B., Simon, J.W., Baldock, C., Artymiuk, P.J., Baker, P.J., Stuitje, A.R., Slabas, A.R., and Rice, D.W. 1995. Common themes in redox chemistry emerge from the X-ray structure of oilseed rape (Brassica napus) enoyl acyl carrier protein reductase. Structure 3: 927–938.[Medline]
Raymer, M.L., Sanschagrin, P.C., Punch, W.F., Venkataraman, S., Goodman, E.D., and Kuhn, L.A. 1997. Predicting conserved water-mediated and polar ligand interactions in proteins using a K-nearest-neighbors genetic algorithm. J. Mol. Biol. 265: 445–464.[CrossRef][Medline]
Rescigno, M. and Perham, R.N. 1994. Structure of the NADPH-binding motif of glutathione reductase: Efficiency determined by evolution. Biochemistry 33: 5721–5727.[CrossRef][Medline]
Rosano, C., Bisso, A., Izzo, G., Tonetti, M., Sturla, L., De Flora, A., and Bolognesi, M. 2000. Probing the catalytic mechanism of GDP-4-keto-6-deoxy-d-mannose Epimerase/Reductase by kinetic and crystallographic characterization of site-specific mutants. J. Mol. Biol. 303: 77–91.[CrossRef][Medline]
Rossmann, M.G., Moras, D., and Olsen, K.W. 1974. Chemical and biological evolution of a nucleotide-binding protein. Nature 250: 194–199.[CrossRef][Medline]
Roujeinikova, A., Levy, C.W., Rowsell, S., Sedelnikova, S., Baker, P.J., Minshull, C.A., Mistry, A., Colls, J.G., Camble, R., Stuitje, A.R., Slabas, A.R., Rafferty, J.R., Pauptit, R.A., Viner, R., and Rice, D.W. 1999. Crystallographic analysis of triclosan bound to enoyl reductase. J. Mol. Biol. 294: 527–535.[CrossRef][Medline]
Saridakis, V., Christendat, D., Kimber, M.S., Dharamsi, A., Edwards, A.M., and Pai, E.F. 2001. Insights into ligand binding and catalysis of a central step in NAD+ synthesis: Structures of Methanobacterium thermoautotrophicum NMN adenylyltransferase complexes. J. Biol. Chem. 276: 7225–7232.
Sawaya, M.R. and Kraut, J. 1997. Loop and subdomain movements in the mechanism of Escherichia coli dihydrofolate reductase: Crystallographic evidence. Biochemistry 36: 586–603.[CrossRef][Medline]
Scheiner, S., Kar, T., and Gu, Y. 2001. Strength of the CH..O hydrogen bond of amino acid residues. J. Biol. Chem. 276: 9832–9837.
Schreuder, H.A., Prick, P.A., Wierenga, R.K., Vriend, G., Wilson, K.S., Hol, W.G., and Drenth, J. 1989. Crystal structure of the p-hydroxybenzoate hydroxylase-substrate complex refined at 1.9 A resolution. Analysis of the enzyme–substrate and enzyme–product complexes. J. Mol. Biol. 208: 679–696.[CrossRef][Medline]
Schultze, P. and Feigon, J. 1997. Chirality errors in nucleic acid structures. Nature 387: 668.[CrossRef][Medline]
Skarzynski, T., Moody, P.C., and Wonacott, A.J. 1987. Structure of holo-glyceraldehyde-3-phosphate dehydrogenase from Bacillus stearothermophilus at 1.8 Å resolution. J. Mol. Biol. 193: 171–187.[CrossRef][Medline]
Smith, P.E. and Tanner, J.J. 1999. Molecular dynamics simulations of NAD+ in solution. J. Am. Chem. Soc. 121: 8637–8644.[CrossRef]
———. 2000. Conformations of nicotinamide adenine dinucleotide (NAD+) in various environments. J. Mol. Recognit. 13: 27–34.[CrossRef][Medline]
Sreenivasan, U. and Axelsen, P.H. 1992. Buried water in homologous serine proteases. Biochemistry 31: 12785–12791.[CrossRef][Medline]
Stewart, M.J., Parikh, S., Xiao, G., Tonge, P.J., and Kisker, C. 1999. Structural basis and mechanism of enoyl reductase inhibition by triclosan. J. Mol. Biol. 290: 859–865.[CrossRef][Medline]
Strickland, C.L. and Karplus, P.A. 1995. Overexpression of Crithidia fasciculata trypanothione reductase and crystallization using a novel geometry. Acta Crystallogr. D Biol. Crystallogr. 51: 337–341.
