|
|
||||||||
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
1 Biosciences Division, Argonne National Laboratory, Argonne, Illinois 60439, USA
2 Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Rua da Quinta Grande 6, 2780-156 Oeiras, Portugal
3 Departamento de Química da Faculdade de Ciências e Tecnologia da Universidade Nova de Lisboa, Quinta da Torre, 2825-114 Caparica, Portugal
Reprint requests to: Marianne Schiffer, Biosciences Division, Argonne National Laboratory, Argonne, IL 60439, USA; e-mail: mschiffer{at}anl.gov; fax: (630) 252-3387.
(RECEIVED January 12, 2004; FINAL REVISION February 27, 2004; ACCEPTED March 1, 2004)
| Abstract |
|---|
|
|
|---|
Keywords: multiheme cytochrome c; cytochrome c7; Geobacter metallireducens; Geobacter sulfurreducens; heme coordination in c-type cytochromes; protein structure
Abbreviations: Eapp, apparent midpoint reduction potential MAD, multiple wavelength anamolous dispersion PDB, Protein Data Bank
4 These authors contributed equally to this work. ![]()
Article published online ahead of print. Article and publication are at http://www.proteinscience.org/cgi/doi/10.1110/ps.04626204.
| Introduction |
|---|
|
|
|---|
Among the multiheme cytochromes from the class III cytochrome family, the cytochromes c3 from the sulfur- and sulfate-reducing bacteria are best studied (for review, see Mathews 1985; Coutinho and Xavier 1994; Aragao et al. 2003). They consist of about 120 amino acid residues and four covalently linked heme groups. The hemes are numbered sequentially according to the cysteine residues to which they are attached in the amino acid sequence. Heme IV is suggested to interact with hydrogenases (Aubert et al. 1997; Brugna et al. 1998). Although the sequence identity among the four-heme proteins is relatively low, ~25%, the positions and orientations of the hemes in the three-dimensional structures are maintained (Aragao et al. 2003). The three-heme cytochromes c7 from Fe(III)-reducing bacteria (Seeliger et al. 1998; Afkar and Fukumori 1999; Lloyd et al. 2003) are structurally homologous to the four-heme cytochromes c3, but are missing heme II of the cytochrome c3 molecules and the amino acid chain segment that keeps that heme in place. For comparison with the more extensively studied four-heme cytochromes, the cytochrome c3 nomenclature for labeling the hemes in the cytochrome c7 proteins is maintained.
We have previously expressed in Escherichia coli and determined the structure of cytochrome c7 from Geobacter sulfurreducens, designated PpcA, a protein with 71 residues that contains three covalently bound hemes (Londer et al. 2002; Lloyd et al. 2003; Pokkuluri et al. 2004). It is one of the smallest cytochrome c-type molecules with the highest ratio of hemes to protein residues. Searching the G. sulfurreducens genome with the PpcA sequence we identified three ORFs coding for proteins that are polymers formed with repeats of homologous c7-type domains. Two of the proteins (coded by ORF00991and ORF03300 have four repeats (total of 12 hemes) and one (coded by ORF03649 has nine repeats (total of 27 hemes) of the cytochrome c7-type domain (Pokkuluri et al. 2004). We also found homologous polymers in the G. metallireducens genome (four unit polymers are encoded by Gmet_6, Gmet_8 and the nine unit polymer is encoded by Gmet_2 in the G. metallireducens genome [http://www.ncbi.nlm.nih.gov, accession number NZ_AAAS00000000]) with 77%, 75%, and 72% identity, respectively, with the ones identified in the G. sulfurreducens genome. We predicted based on the crystal packing observed in the PpcA crystals that the domains in the above polymers will be linearly arranged (Pokkuluri et al. 2004). The functions of the polymers are presently unknown. The repeats within each of the three poly-cytochrome c7-type proteins are highly homologous. The repeat lengths are longer than that of the cytochrome c7 PpcA molecule (71 residues); they vary from 73 to 82 residues.
These proteins appear to represent a new type of cytochrome. Interestingly, in each repeat of the multi-cytochrome c7 sequences, the sixth His ligand to heme IV is absent, the homologous residue in the sequence is mostly Lys or Gln. We proposed earlier that either the Lys or Gln residues or one of the two conserved Met residues in the vicinity could be the second axial ligand to heme IV in those domains (Pokkuluri et al. 2004). Because the chain segments between the heme I and heme III binding sites are longer in the poly-cytochrome c7-type domains than in the cytochrome c7 molecule PpcA, the structure of this segment, and therefore the residue that forms the sixth ligand of heme IV, could not be predicted with confidence.
To characterize these cytochrome c7-type domains, we have expressed in E. coli the four individual domains of the mature protein coded by ORF003300 (Fig. 1
) of the G. sulfurreducens genome, and have determined the three-dimensional structure by X-ray diffraction of single crystals at 1.7 Å resolution of the third domain, domain C. In this manuscript, we describe the structural features of this protein in comparison with the structure of cytochrome c7 (PpcA) from G. sulfurreducens. The alignment of the amino acid sequence of domain C with that of PpcA is shown in Figure 2
.
|
|
| Results and Discussion |
|---|
|
|
|---|
We cloned separately each of the four cytochrome c7-type domains (A, B, C, and D) of the four-unit polymer (ORF03300 into the periplasmic expression vector pVA203. Domain A was cloned both as a fusion to the OmpA leader sequence and with its native leader sequence. All five constructs produced c-type cytochromes as judged by the pink color of the harvested cells. The overall yields of domains increased in the following order: A with native leader sequence << A with OmpA leader sequence < B < C << D. The yield of domain A was very low, and its isolation was not attempted. Domains B, C, and D were purified by cation-exchange chromatography and gel filtration as described previously (Londer et al. 2002). The yields of pure proteins per liter of cell culture were: domain B, 0.2 mg; domain C, 0.25 mg; domain D, 1.1 mg.
Structure determination
Crystals were obtained from domains C and D; crystals of domain C diffracted well and allowed structure determination at a resolution of 1.7 Å. The structure was solved by multiple wavelength anomalous dispersion (MAD) method with program CNS (Brünger et al. 1998) using data collected at the Fe K-absoption edge at the SBC beam line 19BM (APS). The structure was refined to 1.7 Å resolution with data collected at beam line 19ID (APS); the R-factor and R-free are 19.5% and 21.8%, respectively (see Table 1
).
|
-bend of domain C; four hydrophobic amino acids, Leu, Phe, Ala, and Tyr are inserted after the conserved lysine, Lys33 in PpcA; there is also an insertion of two residues (Asn and Gly) after the His residue of the heme III binding site.
|
|
-sheet segment near its N terminus, and five helical regions, one less than PpcA. The helical segments include the three heme-binding sites, the segment that contain the sixth ligands to hemes I, III, and the segment that contains the sixth ligand to heme IV. Although the latter segments in the two structures are in homologous positions in the amino acid sequences (Fig. 2
Domain C has a more conventional structure than PpcA. The number of hydrophobic residues larger than Ala in the core of domain C and the number of side-chain-to-main-chain hydrogen bonds (see Table 2
) are more similar to what is observed for globular proteins in general; they are very low in PpcA. Domain C has 12 Lys and one Arg residue, compared with 17 Lys and no Arg residues in PpcA.
|
|
The iron to iron distances of the hemes III and IV, hemes III and I, and hemes IV and I, respectively, are 11.4, 12.0, and 17.8 Å in domain C compared to 11.2, 12.6, and 20.8 Å in PpcA. These FeFe distances are probably determined by the differences in number of residues between the heme binding sites. Surprisingly, the iron to iron distances found in this c7-type domain are closer to the ones observed in cytochromes c3 (average FeFe distances between hemes III and IV, hemes III and I, and hemes I and IV for six proteins are 11.1, 12.2, and 17.7 Å (Higuchi et al. 1984; Matias et al. 1993, 1996; Czjzek et al. 1994; Morais et al. 1995; Einsle et al. 2001).
Crystal packing
As we previously observed in the PpcA crystal packing, the domain C molecules also form a long chain in the crystal. In domain C crystal, molecules are arranged in infinite chains parallel to the crystallographic c axis with the neighboring molecules related by a 41 axis (90° rotation and 1/4 unit cell translation) instead of one unit-cell translations along a and b axes as in the PpcA crystal (Pokkuluri et al 2004). In both crystals, the molecules in these chains are arranged such a way that heme I from one molecule is close to heme IV of the neighboring molecule. The iron to iron distance between these hemes in neighboring molecules in domain C is 13.8 Å compared to 12.9 Å in PpcA, but due to the difference in the relative angles of the prophyrin rings the heme edges are closer together in domain C crystals with the CMB atoms of heme I and heme IV 3.9 Å apart compared to 5.6 Å between the same atoms in PpcA crystals. Although the molecules also form infinite chains in the crystal of domain C, the N-and C-terminii cannot be connected, as they point in the opposite directions, and therefore, the crystal packing in domain C cannot form a model for the polymers, whereas the crystal packing in PpcA clearly suggested a model for them.
Visible redox titrations
The redox behavior of domain C and PpcA was investigated by redox titrations followed by visible spectroscopy. Results are given in Figure 6
. The analysis of the redox titrations of the two proteins showed that the curve corresponding to domain C is clearly shifted to more positive reduction potential values relative to that of PpcA. This shift is reflected in the apparent midpoint reduction potential, Eapp, of each protein (i.e., the point at which the oxidized and reduced fractions are equal). The value of Eapp for PpcA is 155 mV; it is increased by 50 mV to 105 mV for domain C. The observed positive direction of the shift in the redox curves was expected (Mus-Veteau et al. 1992; Dolla et al. 1994) on the basis of different heme IV axial coordination for PpcA (HisHis) and domain C (HisMet).
|
| Materials and methods |
|---|
|
|
|---|
Expression and purification of the domains were performed with slight modification of the procedure previously described (Londer et al. 2002); induction was carried out with 10 µM IPTG and a final gelfiltration step was added to the purification protocol.
Crystallization of domain C
The protein was crystallized by hanging drops from 2.4 M sodium malonate (pH 7) (Hampton Research, Index screen-27). Tetragonal crystals, space group P41212 or P43212, with a unit cell of a = b = 43.8 Å, c = 123.8 Å, diffracted to a resolution of about 1.7 Å at the Structural Biology Centers 19ID beam line at the Advanced Photon Source (APS).
Structure determination of domain C
Structure of domain C was determined by MAD method using four wavelength data sets (see Table 1
) collected at the Fe K absorption edge at the 19BM (APS). Crystals were flash-cooled by briefly transferring them from mother liquor to a cryoprotectant solution (Index screen-27 containing 25% ethylene glycol). Data were processed with HKL2000 (Otwinowski and Minor 1997). Data collected at low-energy remote wavelength was used as the reference data set for structure determination using MAD method. Structure was solved with the program CNS (Brünger et al. 1998). After density modification the electron density map generated in space group P41212 was of excellent quality (FOM = 0.95) and allowed model building. The protein model was built manually into the electron density map using the program CHAIN (Sack 1988) and refined against high resolution data collected at 19ID (APS). Refinement of the model was carried out with CNS (Brünger et al. 1998). There are no residues in the disallowed regions of the Ramachandran plot, and 87% residues are in most favored regions. The data collection and refinement parameters are summarized in Table 1
. The structure and structure factors were deposited in the Protein Data Bank with accession code, 1rwj. Figure 3
was generated by the program SETOR (Evans 1993); Figures 4
and 5
were generated by the program CHAIN (Sack 1988). Accessible surface area was calculated by the program SURFACE (Lee and Richards 1971).
Sequence database search and analysis
Protein sequences homologous to the cytochrome c7 were identified by searching the G. sulfurreducens and G. metallireducens genomes (www.ncbi.nlm.nih.gov, accession numbers NC_002939
[GenBank]
and NZ_AAAS00000000) with the sequence of the cytochrome c7 (PpcA, ORF01023 using BLAST software (Altschul et al. 1997). The SignalP software (http://www.cbs.dtu.dk/services/SignalP; Nielsen et al. 1997) was used for prediction of leader sequence cleavage sites. Genetic Computer Group Software package (Genetics Computer Group) was used for alignments.
Redox titrations followed by visible spectroscopy
Anaerobic redox titrations of domain C and PpcA, followed by visible spectroscopy were performed as described by Louro et al. (2001), with approximately 18 µM protein solutions in 100 mM Tris-maleate buffer at pH 7.9 and 298 ± 1 K. To check for hysteresis, each redox titration was performed in both oxidative and reductive directions, using sodium dithionite as the reductant, and potassium ferricyanide as the oxidant. To ensure a good equilibrium between the redox centers and the working electrode (Dutton 1978), a mixture of the following redox mediators were added to domain C and PpcA solutions, all at approximately 4 µM final concentration: Methylene Blue, gallocyanine, Indigo Tetrasulphonate, Indigo Trisulphonate, Indigo Disulphonate, anthraquinone-2,7-disulphonate, 2-hydroxy-1,4-naphthoquinone, anthraquinone-2-sulphonate, safranine O, diquat, benzylviologen, Neutral Red, methylviologen. For domain C the following additional mediators were also used, all at approximately 4 µM final concentration: p-benzoquinone, 1,2-naphtoquinone-4-sulfonic acid, 1,2-naphtoquinone, trimethylhydroquinone, phenasine methosulphate, and phenasine ethosulphate. The reduced fraction of each protein was determined using the
band peak, 552 nm for domain C and 551 nm for PpcA, according to the method described by Louro et al. (2001).
| 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 |
|---|
|
|
|---|
Altschul, S.F., Madden, T.L., Schäffer, A.A., Zhang, J., Zhang, Z., Miller, W., and Lipman, D.J. 1997. Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res. 25: 33893402.
Aragao, D., Frazao, C., Sieker, L., Sheldrick, G.M., LeGall, J., and Carrondo, M.A. 2003. Structure of dimeric cytochrome c3 from Desulfovibrio gigas at 1.2 Å resolution. Acta Crystallogr. D 59: 644653.[Medline]
Aubert, C., Leroy, G., Bruschi, M., Wall, J.D., and Dolla, A. 1997. A single mutation in the heme 4 environment of Desulfovibrio desulfuricans Norway cytochrome c3 (Mr 26,000) greatly affects the molecule reactivity. J. Biol. Chem. 272: 1512815134.
Bothmann, H. and Pluckthun, A. 1998. Selection for a periplasmic factor improving phage display and functional periplasmic expression. Nat. Biotechnol. 16: 376380.[CrossRef][Medline]
Brugna, M., Giudici-Orticoni, M.T., Spinelli, S., Brown, K., Tegoni, M., and Bruschi, M. 1998. Kinetics and interaction studies between cytochrome c3 and Fe-only hydrogenase from Desulfovibrio vulgaris Hildenborough. Proteins 33: 590600.[CrossRef][Medline]
Brünger, A.T., Adams, P.D., Clore, G.M., Delano, W.L., Gros, P., Grosse-Kunstleve, R.W., Jiang, J.-S., Kuszewski, J., Nigles, M., Pannu, N.S, et al. 1998. Crystallography and NMR system: A new software suite for macro-molecular structure determination. Acta Crystallogr. D 54: 905921.[CrossRef][Medline]
Coutinho, I.B. and Xavier, A.V. 1994. Tetraheme cytochromes. Methods Enzymol. 243: 119140.[Medline]
Czjzek, M., Payan, F., Guerlesquin, F., Bruschi, M., and Haser, R. 1994. Crystal structure of cytochrome c3 from Desulfovibrio desulfuricans Norway at 17 Å resolution. J. Mol. Biol. 243: 653667.[CrossRef][Medline]
Degtyarenko, K.N., North, A.C.T., and Findlay, J.B.C. 1997. PROMISE: A new database of information on prosthetic centres and metal ions in protein active sites. Protein Eng. 10:183186.
Deisenhofer, J., Epp, O., Sinning, I., and Michel, H. 1995. Crystallographic refinement at 2.3 Å resolution and refined model of the photosynthetic reaction centre from Rhodopseudomonas viridis. J. Mol. Biol. 246: 429457.[CrossRef][Medline]
Dolla, A., Blanchard, L., Guerlesquin, F., and Bruschi M. 1994. The protein moiety modulates the redox potential in cytochromes c. Biochimie 76: 471479.[CrossRef]
Dutton, P.L. 1978. Redox potentiometry: Determination of mid-point potentials of oxidation-reduction components of biological electron-transfer systems. Methods Enzymol. 54: 411435.[Medline]
Einsle, O., Stach, P., Messerschmidt A., Simon, J., Kröger, A., Huber, R., and Kroneck, P.M.H. 2000. Cytochrome c nitrite reductase from Wolinella succinogenes. J. Biol. Chem. 275: 3960839616.
Einsle, O., Foerster, S., Mann, K., Fritz, G., Messerschmidt, A., and Kroneck, P.M.H. 2001. Spectroscopic investigation and determination of reactivity and structure of the tetraheme cytochrome c3 from Desulfovibrio desulfuricans Essex 6. Eur. J. Biochem. 268: 30283035.[Medline]
Evans, S.V. 1993. Hardware lighted three-dimensional solid model representations of macromolecules. J. Mol. Graphics 11:134138.[CrossRef][Medline]
Fülöp, V., Ridout, C.J., Greenwood, C., and Hajdu, J. 1995. Crystal structure of the dihaem cytochrome c peroxidase from Pseudomonas aeruginosa. Structure 3: 12251233.[Medline]
Higuchi, Y., Kusunoki, M., Matsuura, Y., Yasuoka, N., and Kakudo, M. 1984. Refined structure of cytochrome c3 at 1.8 Å resolution. J. Mol. Biol. 172: 109139.[CrossRef][Medline]
Jabs, A., Weiss, M.S., and Hilgenfeld, R. 1999. Non-proline cis peptide bonds in proteins. J. Mol. Biol. 286: 291304.[CrossRef][Medline]
Lee, B. and Richards, F.M. 1971. The interpretation of protein structures: Total volume, group volume distributions and packing density. J. Mol. Biol. 55: 379400.[CrossRef][Medline]
Leys, D., Meyer, T.E., Tsapin, A.S., Nealson, K.H., Cusanovich, M.A., and Van Beeumen, J.J. 2002. Crystal structures at atomic resolution reveal the novel concept of "Electron-harvesting" as a role for the small tetraheme cytochrome c. J. Biol. Chem. 277: 3570335711.
Lloyd, J.R., Leang, C., Hodges Myerson, A.L., Coppi, M.V., Cuifo, S., Methe, B., Sandler, S.J., and Lovley, D.R. 2003. Biochemical and genetic characterization of PpcA, a periplasmic c-type cytochrome in Geobacter sulfurreducens. Biochem. J. 369: 153161.[CrossRef][Medline]
Londer, Y.Y., Pokkuluri, P.R., Tiede, D.M., and Schiffer, M. 2002. Production and preliminary characterization of a recombinant triheme cytochrome c7 from Geobacter sulfurreducens in Escherichia coli. Biochim. Biophys. Acta 1554: 202211.[Medline]
Louro, R.O., Catarino, T., LeGall, J., Turner, D.L., and Xavier, A.V. 2001. Cooperativity between electrons and protons in a monomeric cytochrome c3: The importance of mechanochemical coupling for energy transduction. Chembiochem. 2: 831837.[CrossRef][Medline]
Lovell, S.C., Word, J.M., Richardson, J.S., and Richardson, D.C. 2000. The penultimate rotamer library. Proteins 40: 389408.[CrossRef][Medline]
Mathews, F.S. 1985. The structure, function and evolution of cytochromes. Prog. Biophys. Mol. Biol. 45: 156.[CrossRef][Medline]
Matias, P.M., Frazão, C., Morais, J., Coll, M., and Carrondo, M.A. 1993. Structure analysis of cytochrome c3 from Desulfovibrio vulgaris Hildenborough at 19 Å resolution. J. Mol. Biol. 234: 680699.[CrossRef][Medline]
Matias, P.M., Morais, J., Coelho, R., Carrondo, M.A., Wilson, K., Dauter, Z., and Sieker, L. 1996. Cytochrome c3 from Desulfovibrio gigas: Crystal structure at 1.8 Å resolution and evidence for a specific calcium-binding site. Protein Sci. 5: 13421354.[Abstract]
Mavrangelos, C., Thiel, M., Adamson, P.J., Millard, D.J., Nobbs, S., Zola, H., and Nicholson, I.C. 2001. Increased yield and activity of soluble single-chain antibody fragments by combining high-level expression and the Skp periplasmic chaperonin. Protein Expr. Purif. 23: 289295.[CrossRef][Medline]
Morais, J., Palma, P.N., Frazão, C., Caldeira, J., LeGall, J., Moura, I., Moura, J.J.G., and Carrondo, M.A. 1995. Structure of the tetraheme cytochrome from Desulfovibrio desulfuricans ATCC 27774: X-ray diffraction and electron paramagnetic resonance studies. Biochemistry 34: 1283012841.[CrossRef][Medline]
Mus-Veteau, I., Dolla, A., Guerlesquin, F., Payan, F., Czjzek, M., Haser, R., Bianco, P., Haladjian, J., Rapp-Giles, B.J., and Wall, J.D. 1992. Site-directed mutagenesis of tetraheme cytochrome c3. Modification of oxidore-duction potentials after heme axial ligand replacement. J. Biol. Chem. 267: 1685116858.
Nielsen, H., Engelbrecht, J., Brunak, S., and von Heijne, G. 1997. Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites. Protein Eng. 10: 16.
Otwinowski, Z. and Minor, W. 1997. Processing of x-ray diffraction data collected in oscillation mode. Methods Enzymol. 276: 307326.
Pokkuluri, P.R., Londer, Y.Y., Duke, N.E.C., Long, W.C., and Schiffer, M. 2004. Family of cytochrome c7-type proteins from Geobacter sulfurreducens: The structure of one cytochrome c7 at 1.45 Å resolution. Biochemistry 43: 849859.[Medline]
Sack, J.S. 1988. CHAINA crystallographic modeling program. J. Mol. Graphics 6: 224225.
Santos, H., Moura, J.J.G., Moura, I., LeGall, J., and Xavier, A.V. 1984. NMR studies of electron transfer mechanisms in a protein with interacting redox centres: Desulfovibrio gigas cytochrome c3. Eur. J. Biochem. 141: 283296.[Medline]
Schäfer, U., Beck, K., and Müller, M. 1999. Skp, a molecular chaperone of Gram-negative bacteria, is required for the formation of soluble periplasmic intermediates of outer membrane proteins. J. Biol. Chem. 274: 2456724574.
Seeliger, S., Cord-Ruwisch, R., and Schink, B. 1998. A periplasmic and extra-cellular c-type cytochrome of Geobacter sulfurreducens acts as a ferric iron reductase and as an electron carrier to other acceptors or to partner bacteria. J. Bacteriol. 180: 36863691.
Shimizu, H., Schuller, D.J., Lanzilotta, W.N., Sundaramoorthy, M., Arciero, D.M., Hooper, A.B., and Poulos, T.L. 2001. Crystal structure of Nitrosomonas europa cytochrome c peroxidase and the structural basis for ligand switching in bacterial diheme peroxidases. Biochemistry 40: 1348313490.[CrossRef][Medline]
Wang, D.L., Stankovich, M.T., Eng, L.H., and Neujahr, H.Y. 1991. Redox properties of cytochrome c3 from Desulfovibrio desulfuricans NCIMB 8372. Effects of electrode materials and sodium chloride. J. Electroanal. Chem. 318: 291307.[CrossRef]
![]()
CiteULike
Connotea
Del.icio.us
Digg
Reddit
Technorati What's this?
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| HOME | HELP | FEEDBACK | SUBSCRIPTIONS | ARCHIVE | SEARCH | TABLE OF CONTENTS |