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• W2006806528 abstract "Ribulose 1,5-bisphosphate carboxylase/oxygenase (RuBisCO) catalyzes the incorporation of atmospheric CO2 into ribulose 1,5-bisphosphate (RuBP). RuBisCOs are classified into four forms based on sequence similarity: forms I, II and III are bona fide RuBisCOs; form IV, also called the RuBisCO-like protein (RLP), lacks several of the substrate binding and catalytic residues and does not catalyze RuBP-dependent CO2 fixation in vitro. To contribute to understanding the function of RLPs, we determined the crystal structure of the RLP from Chlorobium tepidum. The overall structure of the RLP is similar to the structures of the three other forms of RuBisCO; however, the active site is distinct from those of bona fide RuBisCOs and suggests that the RLP is possibly capable of catalyzing enolization but not carboxylation. Bioinformatic analysis of the protein functional linkages suggests that this RLP coevolved with enzymes of the bacteriochlorophyll biosynthesis pathway and may be involved in processes related to photosynthesis. Ribulose 1,5-bisphosphate carboxylase/oxygenase (RuBisCO) catalyzes the incorporation of atmospheric CO2 into ribulose 1,5-bisphosphate (RuBP). RuBisCOs are classified into four forms based on sequence similarity: forms I, II and III are bona fide RuBisCOs; form IV, also called the RuBisCO-like protein (RLP), lacks several of the substrate binding and catalytic residues and does not catalyze RuBP-dependent CO2 fixation in vitro. To contribute to understanding the function of RLPs, we determined the crystal structure of the RLP from Chlorobium tepidum. The overall structure of the RLP is similar to the structures of the three other forms of RuBisCO; however, the active site is distinct from those of bona fide RuBisCOs and suggests that the RLP is possibly capable of catalyzing enolization but not carboxylation. Bioinformatic analysis of the protein functional linkages suggests that this RLP coevolved with enzymes of the bacteriochlorophyll biosynthesis pathway and may be involved in processes related to photosynthesis. Ribulose 1,5-bisphosphate carboxylase/oxygenase (RuBisCO, EC 4.1.1.39) is the most abundant enzyme found on earth (Ellis, 1979Ellis R.J. The most abundant protein in the world.Trends Biochem. Sci. 1979; 4: 241-244Abstract Full Text PDF Scopus (407) Google Scholar). It catalyzes the addition of CO2 to ribulose 1,5-bisphophate (RuBP) in the photosynthesis pathway. The resultant 6-carbon intermediate is then cleaved to generate two molecules of 3-phosphoglycerate (3-PGA). Carboxylation is actually the sum total of five steps: enolization, carboxylation, hydration, C-C cleavage, and protonation (Cleland et al., 1998Cleland W.W. Andrews T.J. Gutteridge S. Hartman F.C. Lorimer G.H. Mechanism of RuBisCO: the carbamate as general base.Chem. Rev. 1998; 98: 549-562Crossref PubMed Scopus (318) Google Scholar, Schneider et al., 1992Schneider G. Lindqvist Y. Branden C.I. RuBisCO: structure and mechanism.Annu. Rev. Biophys. Biomol. Struct. 1992; 21: 119-143Crossref PubMed Scopus (90) Google Scholar). In the first step, RuBP is enolized to the 2,3-enediol form. In the second step, one molecule of CO2 reacts with the C-2 carbon atom of the enediol to form a six carbon intermediate, 3-keto-2-carboxyarabinitol 1,5-bisphosphate (3-keto-CABP). 3-keto-CABP is then hydrated in the third step, and this derivative exists mainly in the gem diol form. A proton is abstracted from the gem diol and the bond between C-2 and C-3 is cleaved in the fourth step, resulting in the formation of one molecule of 3-PGA and one molecule of the C-2 carbanion of 3-PGA. Finally, the C-2 carbanion is quickly protonated into another molecule of 3-PGA in the fifth step. Of the four forms of RuBisCO (Tabita, 1999Tabita F.R. Microbial ribulose 1,5-bisphosphate carboxylase/oxygenase: A different perspective.Photosynth. Res. 1999; 60: 1-28Crossref Scopus (271) Google Scholar), form I is the most abundant class of RuBisCO. It is found in plants, algae, and bacteria, and is composed of eight large subunits and eight small subunits with 422 symmetry (L8S8) (Baker et al., 1977Baker T.S. Eisenberg D. Eiserling F. Ribulose bisphosphate carboxylase: a two-layered, square-shaped molecule of symmetry 422.Science. 1977; 196: 293-295Crossref PubMed Scopus (32) Google Scholar). Many form I RuBisCO structures from different organisms have been determined and show high similarity (Andersson, 1996Andersson I. Large structures at high resolution: the 1.6 A crystal structure of spinach ribulose-1,5-bisphosphate carboxylase/oxygenase complexed with 2-carboxyarabinitol bisphosphate.J. Mol. Biol. 1996; 259: 160-174Crossref PubMed Scopus (139) Google Scholar, Andersson and Taylor, 2003Andersson I. Taylor T.C. Structural framework for catalysis and regulation in ribulose-1,5-bisphosphate carboxylase/oxygenase.Arch. Biochem. Biophys. 2003; 414: 130-140Crossref PubMed Scopus (75) Google Scholar, Chapman et al., 1987Chapman M.S. Suh S.W. Cascio D. Smith W.W. Eisenberg D. Sliding-layer conformational change limited by the quaternary structure of plant RuBisCO.Nature. 1987; 329: 354-356Crossref PubMed Scopus (47) Google Scholar, Curmi et al., 1992Curmi P.M. Cascio D. Sweet R.M. Eisenberg D. Schreuder H. Crystal structure of the unactivated form of ribulose-1,5-bisphosphate carboxylase/oxygenase from tobacco refined at 2.0-Å resolution.J. Biol. Chem. 1992; 267: 16980-16989Abstract Full Text PDF PubMed Google Scholar, Hansen et al., 1999Hansen S. Vollan V.B. Hough E. Andersen K. The crystal structure of RuBisCO from Alcaligenes eutrophus reveals a novel central eight-stranded beta-barrel formed by beta-strands from four subunits.J. Mol. Biol. 1999; 288: 609-621Crossref PubMed Scopus (35) Google Scholar, Knight et al., 1990Knight S. Andersson I. Branden C.I. Crystallographic analysis of ribulose 1,5-bisphosphate carboxylase from spinach at 2.4 Å resolution: subunit interactions and active site.J. Mol. Biol. 1990; 215: 113-160Crossref PubMed Scopus (271) Google Scholar, Schreuder et al., 1993bSchreuder H.A. Knight S. Curmi P.M. Andersson I. Cascio D. Sweet R.M. Branden C.I. Eisenberg D. Crystal structure of activated tobacco RuBisCO complexed with the reaction-intermediate analogue 2-carboxy-arabinitol 1,5-bisphosphate.Protein Sci. 1993; 2: 1136-1146Crossref PubMed Scopus (47) Google Scholar, Shibata et al., 1996Shibata N. Inoue T. Fukuhara K. Nagara Y. Kitagawa R. Harada S. Kasai N. Uemura K. Kato K. Yokota A. Kai Y. Orderly disposition of heterogeneous small subunits in D-ribulose-1,5-bisphosphate carboxylase/oxygenase from spinach.J. Biol. Chem. 1996; 271: 26449-26452Crossref PubMed Scopus (22) Google Scholar, Spreitzer and Salvucci, 2002Spreitzer R.J. Salvucci M.E. RuBisCO: structure, regulatory interactions, and possibilities for a better enzyme.Annu. Rev. Plant Biol. 2002; 53: 449-475Crossref PubMed Scopus (620) Google Scholar, Sugawara et al., 1999Sugawara H. Yamamoto H. Shibata N. Inoue T. Okada S. Miyake C. Yokota A. Kai Y. Crystal structure of carboxylase reaction-oriented ribulose 1,5-bisphosphate carboxylase/oxygenase from a thermophilic red alga, Galdieria partita.J. Biol. Chem. 1999; 274: 15655-15661Crossref PubMed Scopus (52) Google Scholar, Taylor and Andersson, 1996Taylor T.C. Andersson I. Structural transitions during activation and ligand binding in hexadecameric RuBisCO inferred from the crystal structure of the activated unliganded spinach enzyme.Nat. Struct. Biol. 1996; 3: 95-101Crossref PubMed Scopus (79) Google Scholar, Taylor and Andersson, 1997aTaylor T.C. Andersson I. Structure of a product complex of spinach ribulose-1,5-bisphosphate carboxylase/oxygenase.Biochemistry. 1997; 36: 4041-4046Crossref PubMed Scopus (51) Google Scholar, Taylor and Andersson, 1997bTaylor T.C. Andersson I. The structure of the complex between RuBisCO and its natural substrate ribulose 1,5-bisphosphate.J. Mol. Biol. 1997; 265: 432-444Crossref PubMed Scopus (107) Google Scholar, Taylor et al., 1996Taylor T.C. Fothergill M.D. Andersson I. A common structural basis for the inhibition of ribulose 1,5-bisphosphate carboxylase by 4-carboxyarabinitol 1,5-bisphosphate and xylulose 1,5-bisphosphate.J. Biol. Chem. 1996; 271: 32894-32899Crossref PubMed Scopus (28) Google Scholar, Taylor et al., 2001Taylor T.C. Backlund A. Bjorhall K. Spreitzer R.J. Andersson I. First crystal structure of RuBisCO from a green alga, Chlamydomonas reinhardtii.J. Biol. Chem. 2001; 276: 48159-48164Crossref PubMed Scopus (76) Google Scholar, Zhang et al., 1994Zhang K.Y. Cascio D. Eisenberg D. Crystal structure of the unactivated ribulose 1,5-bisphosphate carboxylase/oxygenase complexed with a transition state analog, 2-carboxy-D-arabinitol 1,5-bisphosphate.Protein Sci. 1994; 3: 64-69Crossref PubMed Scopus (23) Google Scholar). Form II RuBisCO is found primarily in certain bacteria and is composed solely of large subunits that differ substantially in sequence from form I large subunits. Depending on the source, form II RuBisCO may be oligomerized to form dimers, tetramers, or even larger oligomers. The crystal structure of the form II RuBisCO from Rhodospirillum rubrum (L2) has been determined (Lundqvist and Schneider, 1989aLundqvist T. Schneider G. Crystal structure of the binary complex of ribulose-1,5-bisphosphate carboxylase and its product, 3-phospho-D-glycerate.J. Biol. Chem. 1989; 264: 3643-3646Abstract Full Text PDF PubMed Google Scholar, Lundqvist and Schneider, 1989bLundqvist T. Schneider G. Crystal structure of the complex of ribulose-1,5-bisphosphate carboxylase and a transition state analogue, 2-carboxy-D-arabinitol 1,5-bisphosphate.J. Biol. Chem. 1989; 264: 7078-7083Abstract Full Text PDF PubMed Google Scholar, Lundqvist and Schneider, 1991aLundqvist T. Schneider G. Crystal structure of activated ribulose-1,5-bisphosphate carboxylase complexed with its substrate, ribulose-1,5-bisphosphate.J. Biol. Chem. 1991; 266: 12604-12611Abstract Full Text PDF PubMed Google Scholar, Lundqvist and Schneider, 1991bLundqvist T. Schneider G. Crystal structure of the ternary complex of ribulose-1,5-bisphosphate carboxylase, Mg(II), and activator CO2 at 2.3-Å resolution.Biochemistry. 1991; 30: 904-908Crossref PubMed Scopus (54) Google Scholar, Schneider et al., 1990Schneider G. Lindqvist Y. Lundqvist T. Crystallographic refinement and structure of ribulose-1,5-bisphosphate carboxylase from Rhodospirillum rubrum at 1.7 Å resolution.J. Mol. Biol. 1990; 211: 989-1008Crossref PubMed Scopus (91) Google Scholar, Soderlind et al., 1992Soderlind E. Schneider G. Gutteridge S. Substitution of ASP193 to ASN at the active site of ribulose-1,5-bisphosphate carboxylase results in conformational changes.Eur. J. Biochem. 1992; 206: 729-735Crossref PubMed Scopus (12) Google Scholar) and reveals high similarity to the large subunit structure of form I RuBisCO. Form III RuBisCO is found only in archaea, and has been shown to form either dimers (L2) (Finn and Tabita, 2003Finn M.W. Tabita F.R. Synthesis of catalytically active form III ribulose 1,5-bisphosphate carboxylase/oxygenase in archaea.J. Bacteriol. 2003; 185: 3049-3059Crossref PubMed Scopus (65) Google Scholar, Watson et al., 1999Watson G.M. Yu J.P. Tabita F.R. Unusual ribulose 1,5-bisphosphate carboxylase/oxygenase of anoxic Archaea.J. Bacteriol. 1999; 181: 1569-1575Crossref PubMed Google Scholar) or decamers ([L2]5) (Maeda et al., 1999Maeda N. Kitano K. Fukui T. Ezaki S. Atomi H. Miki K. Imanaka T. Ribulose bisphosphate carboxylase/oxygenase from the hyperthermophilic archaeon Pyrococcus kodakaraensis KOD1 is composed solely of large subunits and forms a pentagonal structure.J. Mol. Biol. 1999; 293: 57-66Crossref PubMed Scopus (41) Google Scholar), depending on the organism. The crystal structure of the form III RuBisCO from Thermococcus kodakaraensis reveals that the protein is comprised of a pentamer of dimers (Kitano et al., 2001Kitano K. Maeda N. Fukui T. Atomi H. Imanaka T. Miki K. Crystal structure of a novel-type archaeal rubisco with pentagonal symmetry.Structure (Camb). 2001; 9: 473-481Abstract Full Text Full Text PDF PubMed Scopus (68) Google Scholar). Its dimeric interface is very similar to those observed in the large subunit of form I and form II RuBisCO. Form IV, also called the RuBisCO-like protein (RLP), was recently discovered to be a homolog of bona fide RuBisCO (Hanson and Tabita, 2001Hanson T.E. Tabita F.R. A ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO)-like protein from Chlorobium tepidum that is involved with sulfur metabolism and the response to oxidative stress.Proc. Natl. Acad. Sci. USA. 2001; 98: 4397-4402Crossref PubMed Scopus (145) Google Scholar). This report offers the structure and hints of the function of the RLP from Chlorobium tepidum. RLPs are found in physiologically and systematically diverse prokaryotes, including Bacillus subtilis (Kunst et al., 1997Kunst F. Ogasawara N. Moszer I. Albertini A.M. Alloni G. Azevedo V. Bertero M.G. Bessieres P. Bolotin A. Borchert S. et al.The complete genome sequence of the gram-positive bacterium Bacillus subtilis.Nature. 1997; 390: 249-256Crossref PubMed Scopus (2985) Google Scholar), C. tepidum (Eisen et al., 2002Eisen J.A. Nelson K.E. Paulsen I.T. Heidelberg J.F. Wu M. Dodson R.J. Deboy R. Gwinn M.L. Nelson W.C. Haft D.H. et al.The complete genome sequence of Chlorobium tepidum TLS, a photosynthetic, anaerobic, green-sulfur bacterium.Proc. Natl. Acad. Sci. USA. 2002; 99: 9509-9514Crossref PubMed Scopus (258) Google Scholar, Hanson and Tabita, 2001Hanson T.E. Tabita F.R. A ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO)-like protein from Chlorobium tepidum that is involved with sulfur metabolism and the response to oxidative stress.Proc. Natl. Acad. Sci. USA. 2001; 98: 4397-4402Crossref PubMed Scopus (145) Google Scholar), Rhodopseudomonas palustris (Larimer et al., 2004Larimer F.W. Chain P. Hauser L. Lamerdin J. Malfatti S. Do L. Land M.L. Pelletier D.A. Beatty J.T. Lang A.S. et al.Complete genome sequence of the metabolically versatile photosynthetic bacterium Rhodopseudomonas palustris.Nat. Biotechnol. 2004; 22: 55-61Crossref PubMed Scopus (509) Google Scholar), and the extremophilic archaeon Archaeoglobus fulgidus (Klenk et al., 1997Klenk H.P. Clayton R.A. Tomb J.F. White O. Nelson K.E. Ketchum K.A. Dodson R.J. Gwinn M. Hickey E.K. Peterson J.D. et al.The complete genome sequence of the hyperthermophilic, sulphate-reducing archaeon Archaeoglobus fulgidus.Nature. 1997; 390: 364-370Crossref PubMed Scopus (1165) Google Scholar), among others. Although these RLPs are related at the sequence level, it appears that different sources of RLP possess discrete functions (Ashida et al., 2003Ashida H. Saito Y. Kojima C. Kobayashi K. Ogasawara N. Yokota A. A functional link between RuBisCO-like protein of Bacillus and photosynthetic RuBisCO.Science. 2003; 302: 286-290Crossref PubMed Scopus (135) Google Scholar, Hanson and Tabita, 2003Hanson T.E. Tabita F.R. Insights into the stress response and sulfur metabolism revealed by proteome analysis of a Chlorobium tepidum mutant lacking the RuBisCO-like protein.Photosynth. Res. 2003; 78: 231-248Crossref PubMed Scopus (37) Google Scholar). B. subtilis RLP functions as a 2,3-diketomethythiopentyl-1-phosphate (2,3-DK-MTP-1-P) enolase in the methionine salvage pathway of this organism (Ashida et al., 2003Ashida H. Saito Y. Kojima C. Kobayashi K. Ogasawara N. Yokota A. A functional link between RuBisCO-like protein of Bacillus and photosynthetic RuBisCO.Science. 2003; 302: 286-290Crossref PubMed Scopus (135) Google Scholar, Murphy et al., 2002Murphy B.A. Grundy F.J. Henkin T.M. Prediction of gene function in methylthioadenosine recycling from regulatory signals.J. Bacteriol. 2002; 184: 2314-2318Crossref PubMed Scopus (41) Google Scholar, Sekowska and Danchin, 2002Sekowska A. Danchin A. The methionine salvage pathway in Bacillus subtilis.BMC Microbiol. 2002; 2: 8Crossref PubMed Scopus (78) Google Scholar). In the C. tepidum genome, however, there are no recognizable genes for a methionine salvage pathway. C. tepidum RLP is shown to be involved with sulfur oxidation, and inactivation of the rlp gene leads to an oxidative stress response (Hanson and Tabita, 2001Hanson T.E. Tabita F.R. A ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO)-like protein from Chlorobium tepidum that is involved with sulfur metabolism and the response to oxidative stress.Proc. Natl. Acad. Sci. USA. 2001; 98: 4397-4402Crossref PubMed Scopus (145) Google Scholar, Hanson and Tabita, 2003Hanson T.E. Tabita F.R. Insights into the stress response and sulfur metabolism revealed by proteome analysis of a Chlorobium tepidum mutant lacking the RuBisCO-like protein.Photosynth. Res. 2003; 78: 231-248Crossref PubMed Scopus (37) Google Scholar). Currently it is unclear which reaction is affected in sulfur metabolism, but RLP appears to be somehow involved with the oxidation of thiosulfate, but not sulfide. Interestingly, the R. palustris genome encodes two RLPs as well as both form I and form II RuBisCO (Larimer et al., 2004Larimer F.W. Chain P. Hauser L. Lamerdin J. Malfatti S. Do L. Land M.L. Pelletier D.A. Beatty J.T. Lang A.S. et al.Complete genome sequence of the metabolically versatile photosynthetic bacterium Rhodopseudomonas palustris.Nat. Biotechnol. 2004; 22: 55-61Crossref PubMed Scopus (509) Google Scholar). Sequence alignment analysis of RLPs from different organisms suggests that the two RLPs from R. palustris belong to different groups, perhaps indicating that these two RLPs may have different functions (Hanson and Tabita, 2003Hanson T.E. Tabita F.R. Insights into the stress response and sulfur metabolism revealed by proteome analysis of a Chlorobium tepidum mutant lacking the RuBisCO-like protein.Photosynth. Res. 2003; 78: 231-248Crossref PubMed Scopus (37) Google Scholar). As there are more than two hundred complete genome sequences available, bioinformatic approaches can assist us in understanding potential functions of uncharacterized proteins. Several genome-context-based methods have been developed to infer protein functions based on comparisons of tens and hundreds of genome sequences: the Phylogenetic Profile method infers protein functional linkages between two proteins based on their correlated evolution in multiple genomes (Pellegrini et al., 1999Pellegrini M. Marcotte E.M. Thompson M.J. Eisenberg D. Yeates T.O. Assigning protein functions by comparative genome analysis: protein phylogenetic profiles.Proc. Natl. Acad. Sci. USA. 1999; 96: 4285-4288Crossref PubMed Scopus (1395) Google Scholar); the Rosetta Stone method infers the linkages based on the fusion of two protein-encoded genes in another genome (Enright et al., 1999Enright A.J. Iliopoulos I. Kyrpides N.C. Ouzounis C.A. Protein interaction maps for complete genomes based on gene fusion events.Nature. 1999; 402: 86-90Crossref PubMed Scopus (844) Google Scholar, Marcotte et al., 1999Marcotte E.M. Pellegrini M. Ng H.L. Rice D.W. Yeates T.O. Eisenberg D. Detecting protein function and protein-protein interactions from genome sequences.Science. 1999; 285: 751-753Crossref PubMed Scopus (1311) Google Scholar); the Gene Neighbor method assigns protein functional linkages based on the close proximity of two genes on the chromosomes in many genomes (Dandekar et al., 1998Dandekar T. Snel B. Huynen M. Bork P. Conservation of gene order: A fingerprint of proteins that physically interact.Trends Biochem. Sci. 1998; 23: 324-328Abstract Full Text Full Text PDF PubMed Scopus (784) Google Scholar, Overbeek et al., 1999Overbeek R. Fonstein M. D’Souza M. Pusch G.D. Maltsev N. The use of gene clusters to infer functional coupling.Proc. Natl. Acad. Sci. USA. 1999; 96: 2896-2901Crossref PubMed Scopus (956) Google Scholar); and the Gene Cluster method infers the linkages between two genes based on the operon structure (Bowers et al., 2004Bowers P.M. Pellegrini M. Thompson M.J. Fierro J. Yeates T.O. Eisenberg D. Prolinks: a database of protein functional linkages derived from coevolution.Genome Biol. 2004; 5: R35Crossref PubMed Google Scholar, Pellegrini et al., 2001Pellegrini M. Thompson M. Fierro J. Bowers P. Computational method to assign microbial genes to pathways.J. Cell. Biochem. Suppl. 2001; : 106-109Crossref PubMed Scopus (18) Google Scholar). In this study the structure of the RLP from C. tepidum was determined using X-ray crystallography and the active site was analyzed and compared to other forms of RuBisCO. The RLPs from C. tepidum, R. palustris, and B. subtilis were identified by sequence similarity to RubisCO and their functional linkages were calculated by comparing them with the genome sequences of 168 organisms in the Prolinks database (Bowers et al., 2004Bowers P.M. Pellegrini M. Thompson M.J. Fierro J. Yeates T.O. Eisenberg D. Prolinks: a database of protein functional linkages derived from coevolution.Genome Biol. 2004; 5: R35Crossref PubMed Google Scholar). The monomer structure of the RLP from C. tepidum is similar to those of other RuBisCOs and may be divided into two domains (Figures 1A and 1C ). The smaller N-terminal domain (residues 1–145) consists of a four-stranded β sheet with helices on one side of the sheet. The larger C-terminal domain (residues 146–435) consists of an eight-stranded α/β barrel with two additional small α helices forming a cap at the C terminus. The monomer of the RLP is composed of 435 residues, and the model contains most of the residues except N-terminal residues 1–3, C-terminal residues 429–435 and two disordered regions on the surface (residues 47–58 for chains A and B and residues 173–174 for chain B only) (Table 1). A RuBisCO active site residue, Q49, is within one of the disordered regions.Table 1X-Ray Data Collection and Refinement Statistics of the RLP StructureData CollectionNativeWavelength (Å)1.127Temperature (K)100Space groupP21Cell parameters a (Å)67.35 b (Å)78.45 c (Å)90.37 β (°)99.95Resolution (Å)aStatistics for the outer resolution shell are given in parentheses.87.7–2.0 (2.07–2.00)Reflections Total186,455 Unique60,951CompletenessaStatistics for the outer resolution shell are given in parentheses. (%)97.5 (84.7)<I/σ>aStatistics for the outer resolution shell are given in parentheses.7.7 (2.0)RsymaStatistics for the outer resolution shell are given in parentheses.,bRsym = ∑(I − <I>)2/∑I2 (%)12.9 (39.7)Model RefinementR (%)/RfreeaStatistics for the outer resolution shell are given in parentheses. (%)20.1/24.5 (25/31)Number of atoms Protein6419 Solvent317Rms bond length (Å)0.013Rms bond angles (°)1.626Ramachandran plot Most favored641 residues, 92.2% Additional allowed48 residues, 6.9% Generously allowed3 residues, 0.4% Disallowed3 residues, 0.4%a Statistics for the outer resolution shell are given in parentheses.b Rsym = ∑(I − <I>)2/∑I2 Open table in a new tab The RLP from C. tepidum forms homodimers (Figure 1B). In the asymmetric unit, two monomers form a closely packed dimer with two-fold symmetry. It is similar to the dimeric functional units of other forms of RuBisCO. When the dimer structures of the RLP and the RuBisCO from R. rubrum ( 5RUB , form II) are superimposed, the root mean square deviation (rmsd) of Cα atoms is 1.8 Å with 570 residues aligned, showing that they share a similar structure even though their amino acid sequence identity is low (30%). Like the other three forms of RuBisCO (Kitano et al., 2001Kitano K. Maeda N. Fukui T. Atomi H. Imanaka T. Miki K. Crystal structure of a novel-type archaeal rubisco with pentagonal symmetry.Structure (Camb). 2001; 9: 473-481Abstract Full Text Full Text PDF PubMed Scopus (68) Google Scholar, Schreuder et al., 1993aSchreuder H.A. Knight S. Curmi P.M. Andersson I. Cascio D. Branden C.I. Eisenberg D. Formation of the active site of ribulose-1,5-bisphosphate carboxylase/oxygenase by a disorder-order transition from the unactivated to the activated form.Proc. Natl. Acad. Sci. USA. 1993; 90: 9968-9972Crossref PubMed Scopus (54) Google Scholar), the active site of the RLP is formed between two subunits, the C-terminal α/β barrel domain from one subunit and the N-terminal β sheet domain from another subunit. However, 10 of the 19 mechanistically significant residues of the RuBisCO active site differ in the RLP of C. tepidum (Figure 2). These replacements in the amino acid sequence alter the shape and chemical properties of the active site, making it evident that this RLP may not bind RuBP, but may perhaps bind a structurally related molecule. The differences between the active sites of the RLP and other RuBisCOs may be illustrated by visualizing the ability of the RLP to interact with the 6-carbon transition state analog, 2-carboxyarabinitol 1,5-bisphosphate (CABP), of RuBisCOs. From studies with form I RuBisCO, the residues involved in CABP binding can be divided into four groups: those involved in forming hydrogen bonds with (1) P1 phosphate, (2) P2 phosphate, and (3) the carboxyarabinitol backbone; and those involved in (4) coordinating the metal ion (Knight et al., 1990Knight S. Andersson I. Branden C.I. Crystallographic analysis of ribulose 1,5-bisphosphate carboxylase from spinach at 2.4 Å resolution: subunit interactions and active site.J. Mol. Biol. 1990; 215: 113-160Crossref PubMed Scopus (271) Google Scholar). The RLP active site appears to be compatible with binding the P1 phosphate group. Some of the active site residues involved in forming hydrogen bonds are structurally conserved in the RLP compared to form I RuBisCO. The backbones of residues G382 and R383 can still make hydrogen bonds with the P1 phosphate group, as do the residues G403 and G404 in 8RUC (the structure of activated spinach RuBisCO [form I]) (Figure 3). The backbone of residue R327 in loop 6 superimposes well with that of K334 in 8RUC , and its side chain is quite close, so that R327 can possibly make hydrogen bonds with atoms O3P and O7 of CABP. Residue G381 in 8RUC is changed to S359 in the RLP, but S359 is capable of forming a hydrogen bond with atom O3P of CABP. Residue Q49 of the RLP is structurally equivalent to T65 of 8RUC and, in principle, is capable of donating a hydrogen bond to the P1 phosphate, although it is disordered in the RLP structure. The largest change in the active site is at the P2 phosphate binding site. When the active sites of spinach RuBisCO ( 8RUC , form I) and C. tepidum RLP are superimposed, the P2 phosphate group of CABP does not fit into the active site of the RLP. In 8RUC , residue R295 donates two hydrogen bonds to the P2 phosphate group of CABP (Andersson, 1996Andersson I. Large structures at high resolution: the 1.6 A crystal structure of spinach ribulose-1,5-bisphosphate carboxylase/oxygenase complexed with 2-carboxyarabinitol bisphosphate.J. Mol. Biol. 1996; 259: 160-174Crossref PubMed Scopus (139) Google Scholar), but in the RLP, the arginine is nonconservatively substituted by a phenylalanine (F288). Thus, residue F288’s side chain would block the P2 phosphate group of RuBP from binding to the RLP (Figure 3). Similarly, in 8RUC , residue H327 donates a hydrogen bond to this same P2 phosphate group, but in the RLP the histidine is replaced by an isoleucine (I320). These two amino acid substitutions in the RLP contribute to the increase of the hydrophobicity of the substrate binding pocket in the RLP compared to forms I, II, and III RuBisCO. The RLP active site appears compatible with binding the CABP backbone. The residues involved in making hydrogen bonds with the carboxyarabinitol moiety are partially conserved (Figure 3). Residue K172 in C. tepidum RLP, the equivalent to residue K175 in 8RUC , can still form a hydrogen bond with O2. Residue T173 in 8RUC , which contributes another hydrogen bond to O2, is replaced with V170 in the RLP. However, this residue is not conserved in forms II and III RuBisCO either, indicating that T173 probably does not play a key role in binding the substrate. Residue H294, which forms a hydrogen bond with O3, is conserved in the RLP (residue H287). Residue K177 forms a hydrogen bond with O6 in 8RUC , but is replaced by N174, which is partially disordered in the RLP structure. Residue N123 in 8RUC also contributes one hydrogen bond to O6. It is replaced by E119 in the RLP, but this residue can still possibly make a hydrogen bond with O6 of CABP. Residue S379’s side chain in 8RUC contributes a hydrogen bond to O4, but this residue is changed to G357 in the RLP. As with other RuBisCO proteins, the RLP active site is compatible with binding a metal ion. The residues involved in metal ion binding are structurally conserved in the RLP, including residues K198, D200, and E201. During RuBisCO catalysis, carbamylation at a particular lysine residue, K201 in 8RUC , must occur in order for the enzyme to be activated prior to carboxylation or oxygenation. The ϵ-amino group of the lysine reacts with a CO2 molecule to form a carbamate, stabilized by the binding of Mg2+ or other divalent cations. The carbamate removes the C-3 proton and transfers it to residue K175 (Cleland et al., 1998Cleland W.W. Andrews T.J. Gutteridge S. Hartman F.C. Lorimer G.H. Mechanism of RuBisCO: the carbamate as general base.Chem. Rev. 1998; 98: 549-562Crossref PubMed Scopus (318) Google Scholar, Spreitzer and Salvucci, 2002Spreitzer R.J. Salvucci M.E. RuBisCO: structure, regulatory interactions, and possibilities for a better enzyme.Annu. Rev. Plant Biol. 2002; 53: 449-475Crossref PubMed Scopus (620) Google Scholar). Residue K201 in the activated spinach RuBisCO is carbamylated (Andersson, 1996Andersson I. Large structures at high resolution: the 1.6 A crystal structure of spinach ribulose-1,5-bisphosphate carboxylase/oxygenase complexed with 2-carboxyarabinitol bisphosphate.J. Mol. Biol. 1996; 259: 160-174Crossref PubMed Scopus (139) Google Scholar). In our RLP crystal, the equivalent lysine residue, K198, was not c" @default.
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• W2006806528 title "Crystal Structure of a RuBisCO-like Protein from the Green Sulfur Bacterium Chlorobium tepidum" @default.
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• W2006806528 doi "https://doi.org/10.1016/j.str.2005.02.017" @default.
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