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University of Toledo, Department of Chemistry, Toledo, Ohio 43606, USA
Reprint requests to: Ronald E. Viola, University of Toledo, Department of Chemistry, 2801 W. Bancroft Street, Toledo, OH 43606, USA; e-mail: ron.viola{at}utoledo.edu; fax: (419) 530-1583.
(RECEIVED August 28, 2002; FINAL REVISION October 10, 2002; ACCEPTED October 17, 2002)
Article and publication are at http://www.proteinscience.org/cgi/doi/10.1110/ps.0230803.
| Abstract |
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Keywords: Enzyme mechanism; enzyme structure; X-ray crystallography; L-aspartate-ß-semialdehyde dehydrogenase; S-methyl-L-cysteine sulfoxide; Vibrio cholerae
Abbreviations: ASADH, L-aspartate-ß-semialdehyde dehydrogenase ßAP, ß-aspartyl phosphate ASA, L-aspartate-ß-semialdehyde SMCS, S-methyl-L-cysteine sulfoxide NADP, ß-nicotinamide adenine dinucleotide phosphate DTT, dithiothreitol vc ASADH, Vibrio cholerae ASADH ORF, open reading frame
| Introduction |
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Studies on Salmonella typhimurium (Galan et al. 1990) and Legionella pneumophila (Harb and Kwaik 1998) demonstrated that perturbations of the asd gene encoding for ASADH can be lethal to a micro-organism. An experimental S. typhimurium vaccine, using a balanced-lethal host-vector system based upon a deletion mutation of the asd gene, has given encouraging results in mice (Kang et al. 2002). There is continued interest in the development of effective microbial ASADH inhibitors (Cox et al. 2001, 2002), and the first purification of a plant ASADH has now been reported (Paris et al. 2002). The structure of Escherichia coli ASADH has been solved, both as the apoenzyme (Hadfield et al. 1999) and as an inhibitorcoenzyme complex (Hadfield et al. 2001). As a continuation of this work, we have expressed and purified ASADH from a number of infectious micro-organisms and have begun their characterization (Moore et al. 2002).
In this article, we focus on ASADH from Vibrio cholerae, the causative agent of cholera, a severe diarrhoeal disease known for its explosive outbreaks, rapid onset, and high morbidity (Wachsmuth et al. 1994; Faruque et al. 1998). Contaminated waters in various regions of the world have allowed pathogenic strains of V. cholerae to thrive, resulting in sporadic outbreaks and seven pandemics in the last two centuries (Wachsmuth et al. 1994). The prevailing model of bacterial cells containing only one chromosome, based primarily on studies of E. coli, is rapidly changing with the discovery of numerous micro-organisms containing multiple chromosomes. One such organism is V. cholerae El Tor, maintaining both a large and a small chromosome (
3 million and 1 million bp, respectively). Both chromosomes have been sequenced by whole-genome random sequencing (Heidelberg et al. 2000). Chromosome 1 contains most genes involved in DNA replication, pathogenicity, biosynthetic pathways, and cell-wall biosynthesis. However, some genes thought to be essential to normal cellular function (e.g., certain genes encoding ribosomal proteins) are found only on chromosome 2. A significant number of ORFs are duplicated on both chromosomes suggesting a high level of crossover between the two chromosomes. Interestingly, there are two asd genes in chromosome 1 and none in chromosome 2. We have purified both enzymes encoded by theses genes, and each displays significant ASADH activity (Moore et al. 2002). We now report the structure of a V. cholerae ASADH (vcASADH) in two states, the apoenzyme and an NADPinhibitor complex, and an analysis and comparison of the E. coli and V. cholerae enzyme structures.
| Results and Discussion |
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NADP binding
The binding and orientation of NADP to ASADH is characterized by a number of interactions. There is hydrogen bonding of the Gln350 amide nitrogen to the amide carbonyl of NADP, stabilized by Ser164, which hydrogen bonds to both Gln350 via its side-chain hydroxyl and the NADP amide group via its main-chain carbonyl group. The hydrogen bonding between the Asn133 amide nitrogen and Glu240 is present in both the NADP-bound and unbound state, therefore not forming as a consequence of NADP binding as previously proposed. The side-chain hydroxyls of Ser37 and Thr36 form new hydrogen bonds with the 2'-phosphate of NADP, while the Ser35 hydroxyl forms a water-mediated hydrogen bond with phosphate. The main-chain amide nitrogens of Val12 and Met11 bind to pyrophosphate moiety of NADP, as does the main-chain nitrogen of Ala168 via a water molecule. The side-chain carbonyl group of Gln72 interacts with the 3' hydroxyl of the adenine ribose. Another notable difference between the binding of NADP in E. coli and V. cholerae is that in the vcASADH Lys243 is at least 7 Å away from either ribose hydroxyl group and does not form hydrogen bonds with them. It is more likely that this lysine plays a direct role in stabilizing the phosphate of ßAP.
Examination of the E. coli ASADH structure resulted in the identification of an internal loop from Asp230 to Glu240, located near the active site, which is disordered in the apoenzyme. The driving force for ordering this loop was proposed to be the formation of new hydrogen bonds during NADP binding. While the loop does cross the active site, it is already ordered in the V. cholerae apoenzyme, and retains essentially the same conformation in the ternary complex. The active site appears to be preformed to accommodate the substrate, and it is only when NADP binds that the cleft closes around it. Previously identified hydrogen bonds between Ser98 and Arg240 (E. coli numbering) that formed upon complex formation are not seen in the new structures. In fact, the corresponding arginine is replaced by Lys239 in vcASADH. When NADP is enveloped by vcASADH there is a conformational change, primarily in the repositioning of a surface loop (Leu189Ser195) with respect to NADP. This is best observed as the main-chain Pro192 carbonyl of one subunit moves roughly 3 Å closer to the NADP adenine ring in the opposing subunit, forming a new hydrogen bond with the amino group (Fig. 5A
). On the opposite side of the cleft, Arg9 is repositioned to form a new hydrogen bond with the 2'-phosphate of NADP while also forming a
-charge interaction with the adenine ring of NADP. The distance between C
of Arg9 and the main-chain carbonyl of Pro192 is particularly diagnostic of this domain closure. In both the E. coli and V. cholerae apoenzymes that distance is approximately 13.5 Å. In the E. coli ternary complex this proline carbonyl to arginine C
distance shortens to 10.7 Å in both subunits, each containing NADP, but only one of which is SMCS modified. Interestingly, the V. cholerae ternary complex, having NADP and SMCS bound in both active sites, displays an open conformation in one subunit and a closed conformation in the other. In the closed subunit, the Pro192 carbonyl to Arg9 C
distance is 10.3 Å, indicative of domain closure, while this distance is 13.1 Å in the open subunit, causing asymmetry between the two monomers. This can be observed by the differing positions of the critical loops (Leu189Ser195, Ser37Asn45) in the closed versus open conformations (Fig. 3
).
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of His274 (Fig. 4
Catalysis
The proposed role of His274 as the acid/base catalyst that facilitates deprotonation of Cys134 is well supported by this structure. The N
atom is 3.1 Å from the sulfur atom of Cys134 in both subunits, perfectly placed for proton abstraction (Fig. 4
). Attack of the thiolate at the carbonyl of ßAP (or S
of SMCS) yields a tetrahedral intermediate, stabilized by hydrogen bonding to active site water molecules. Collapse of the initial tetrahedral intermediate and the concomitant expulsion of phosphate, stabilized by Arg102 and Lys243, gives a relatively stable thioester intermediate. Hydride transfer from bound NADPH leads to the formation of a second tetrahedral intermediate, the collapse of which produces ASA and the free thiol of Cys134. Gln161 is not likely to play a role in positioning His274 (Ouyang and Viola 1995) because it is too far away in both V. cholerae structures. In the current model, Gln161 has no interaction with the substrate amino group, mainly due to differences in the way that the inhibitor amino group was fit into the electron density for this enzyme relative to E. coli ASADH (Hadfield et al. 2001). Mutations of Gln161 to Asn and His, conducted with E. coli ASADH before structural data were available (Ouyang and Viola 1995), show a 13-fold and threefold reduction in kcat for the Asn and His mutants, respectively. The Km values for both variants were unaffected. We postulate that Gln161 plays a more supplemental role in catalysis by forming a hydrogen bond between its amide nitrogen and the strategically located Glu240 carboxyl group that hydrogen bonds to the SMCS amino group.
Communication between the active sites
The current mechanism proposed for ASADH favors a model of alternating site reactivity orchestrated by communication between the active sites. It has been proposed (Biellmann et al. 1980), based upon affinity labeling studies with covalent inactivators, that the mechanism for ASADH was an "alternating" or "half-of-sites" reactivity in which the binding order is NADPH followed by the substrate ßAP and the order of release is ASA before NADP. Kinetic experiments further demonstrated that E. coli ASADH has a preferred, but not obligatory, binding order with NADP binding before the substrate ASA (Karsten and Viola 1991b).
There are a number of electrostatic interactions between the subunits that serve to maintain the conformational integrity of the dimer. The Glu241 adjacent to active site Glu240 is engaged in a bidentate interaction with Arg330 of the opposite subunit. In a similar manner, Asp261 is engaged with Arg332 of the opposing subunit. From this ensemble of interactions, we have identified a plausible route by which one active site could relay information to the other. There are
-stacking interactions between Tyr160 of opposite subunits in the center of the dimer. Both Tyr160 aromatic rings are slightly offset relative to each other, each flanked by Phe345 of the same subunit in a perpendicular
-stacking interaction (Fig. 5B
). The hydroxyl group of Tyr160 from one subunit is hydrogen bonded to the main-chain Thr159 carbonyl of the opposing subunit, which in turn, is hydrogen bonded through its side-chain hydroxyl group to the amide carbonyl oxygen of active site residue Gln161. This results in a symmetrical 4-amino acid bridge linking the active site glutamines in adjacent subunits (Fig. 5B
). Catalytic and binding events between the active sites are likely synchronized by perturbations along this route. Thus, interaction between the subunits is maintained not only by the previously observed (Hadfield et al. 2001) hydrophobic core at the center of the enzyme, but also by a conduit of hydrogen bonding interactions spanning the entire length of the dimer interface as well as significant electrostatic interactions between the subunits.
| Materials and methods |
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Crystallization of the ternary complex
The ASADH inhibitor S-methyl-L-cysteinesulfoxide (SMCS) was purchased from Karlan Research Products, and was found to be at least 99% pure by 1H and 13C NMR analysis. DTNB titration of the SMCS showed no (<0.1%) free thiol in the sample. Crystals of the enzyme in the presence of 5 mM NADP and 5 mM SMCS were grown at 20°C from 1:1 mixtures of enzyme solution (12 mg/mL) and precipitant (22% PEG 3350, 0.2 M sodium acetate and 0.1 M sodium citrate, pH 5.6). Tetragonal crystals belonging to the P41212 space group with unit cell dimensions a = b = 107.1 Å and c = 153.1 Å and one dimer in the asymmetric unit formed after 10 d. Prior to freezing, crystals were soaked without DTT for 1 h in 22% PEG 3350, 0.2 M sodium acetate, 5 mM SMCS, 5 mM NADP, 20% glycerol and 0.1 M sodium citrate, pH 5.6.
Data collection and processing
A data set was collected from a single frozen crystal of apoenzyme on a Quantum-IV imaging plate (detector distance 200 mm; 0.75° oscillation per image) at Argonne National Laboratory (APS) BioCARS beamline (14-D). For the ternary ASADH/NADP/SMCS complex, a complete data set up to 1.8 Å was collected at SSRL Stanford synchrotron beamline 5A (detector distance 150 mm; 1° oscillation per image). The images were processed and scaled using the program HKL2000 (Otwinowski and Minor 1997). The data collection statistics for each of these data sets are summarized in Table 1
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The final refinement statistics for the structures are listed in Table 2
. The refined coordinates have been deposited with the PDB and assigned the entry code 1MC4 for apoenzyme and 1MB4 for the NADP/SMCS complex.
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1 pmole/µL and infused into the nanospray source at a rate of 1 µL/min. Optimal ESI conditions were: capillary voltage 3000 V, source temperature 110°C and a cone voltage of 60 V. All ions were scanned over m/z 500 to 3000 with a l -sec integration time, and data was acquired in continuum mode until acceptable averaged data was obtained (1015 min). ESI data was deconvoluted using MaxEnt I software that was provided by Micromass.
| Acknowledgments |
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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 |
|---|
|
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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. D54: 905921.[CrossRef][Medline]
Cohen, G.N. 1983. The common pathway to lysine, methionine, and threonine. In Amino acids: Biosynthesis and genetic regulation (eds. K.M. Herrmann and R.L. Somerville), pp. 147171. Addison-Wesley, Reading, MA.
Cox, R.J., Hadfield, A.T., and Mayo-Martin, M.B. 2001. Difluoromethylene analogues of aspartyl phosphate: The first synthetic inhibitors of aspartate semi-aldehyde dehydrogenase. Chem. Commun. 18: 17101711.[CrossRef]
Cox, R.J., Gibson, J.S., and Martin, M.B. 2002. Aspartyl phosphonates and phosphoramidates: The first synthetic inhibitors of bacterial aspartate-semialdehyde dehydrogenase. Chem. BioChem. 3: 874886.
Faruque, S.M., Albert, M.J., and Mekalanos, J.J. 1998. Epidemiology, genetics, and ecology of toxigenic Vibrio cholerae. Microbiol. Mol. Biol. Rev. 62: 13011314.
Galan, J.E., Nakayama, K., and Curtiss, R. 1990. Cloning and characterization of the asd gene of Salmonella typhimurium: Use in stable maintenance of recombinant plasmids in Salmonella vaccine strains. Gene 94: 2935.[CrossRef][Medline]
Hadfield, A.T., Kryger, G., Ouyang, J., Petsko, G.A., Ringe, D., and Viola, R.E. 1999. Structure of aspartate-ß-semialdehyde dehydrogenase from Escherichia coli, a key enzyme in the aspartate family of amino acid biosynthesis. J. Mol. Biol. 289: 9911002.[CrossRef][Medline]
Hadfield, A.T., Shammas, C., Kryger, G., Ringe, D., Petsko, G.A., Ouyang, J., and Viola, R.E. 2001. Active site analysis of the potential antimicrobial target aspartate semialdehyde dehydrogenase. Biochemistry 40: 14475 14483.[CrossRef][Medline]
Harb, O.S. and Kwaik, Y.A. 1998. Identification of the aspartate-ß-semialdehyde dehydrogenase gene of Legionella pneumolphila and characterization of a null mutant. Infect. Immun. 66: 18981903.
Heidelberg, J.F., Eisen, J.A., Nelson, W.C., Clayton, R.A., Gwinn, M.L., Dodson, R.J., Haft, D.H., Peterson, J.D., Umayam, L., and Gill S.R. 2000. DNA sequence of both chromosomes of the cholera pathogen Vibrio cholerae. Nature 406: 477483.
Kang, H.Y., Srinivasan, J., and Curtiss, R. 2002. Immune responses to recombinant pneumococcal PspA antigen delivered by live attenuated Salmonella enterica Serovar typhimurium vaccine. Infect. Immun. 70: 17391749.
Karsten, W.E. and Viola, R.E. 1991a. Chemical and kinetic mechanism of aspartate-ß-semialdehyde dehydrogenase from Escherichia coli. Biochim. Biophys. Acta 1077: 209219.[CrossRef][Medline]
. 1991b. Kinetic studies of L-aspartase from Escherichia coli: pH dependent activity changes. Arch. Biochem. Biophys. 287: 6067.[CrossRef][Medline]
Lowther, W.T., Brot, N., Weissbach, H., Honek, J.F., and Matthews, B.W. 2000. Thiol-disulfide exchange is involved in the catalytic mechanism of peptide methionine sulfoxide reductase. Proc. Natl. Acad. Sci. 97: 64636468.
McRee, D.E. 1999. XtalView/XfitA versatile program for manipulating atomic coordinates and electron density. J. Struct. Biol. 125: 156165.[CrossRef][Medline]
Moore, R.A., Bocik, W.E., and Viola, R.E. 2002. Expression and purification of L-aspartate-ß-semialdehyde dehydrogenase from infectious microorganisms. Protein Expr. Purif. 25: 189194.[CrossRef][Medline]
Otwinowski, Z. and Minor, W. 1997. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276: 307326.
Ouyang, J. and Viola, R.E. 1995. Use of structural comparisons to select mutagenic targets in aspartate-ß-semialdehyde dehydrogenase. Biochemistry 34: 63946399.[CrossRef][Medline]
Paris, S., Wessel, P.M., and Dumas, R. 2002. Overproduction, purification, and characterization of recombinant aspartate semialdehyde dehydrogenase from Arabidopsis thaliana. Protein Expr. Purif. 24: 99104.[CrossRef][Medline]
Patte, J.C. 1983. Diaminopimelate and lysine. In Amino acids: Biosynthesis and genetic regulation (eds. K.M. Herrmann and R.L. Somerville), pp. 213228. Addison-Wesley, Reading, MA.
Viola, R.E. 2001. The central enzymes of the aspartate family of amino acid biosynthesis. Acc. Chem. Res. 34: 339349.[CrossRef][Medline]
Wachsmuth, K., Olsvik, O., Evins, G.M., and Popovic, T. 1994. In Vibrio cholerae and cholera: Molecular to global perspective (eds. I.K. Wachsmuth, P.A. Blake, and O. Olsvik), pp. 357370. ASM Press, Washington, D.C.
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