ID RBL_PYRHO Reviewed; 430 AA. AC O58677; DT 26-SEP-2003, integrated into UniProtKB/Swiss-Prot. DT 01-AUG-1998, sequence version 1. DT 27-MAR-2024, entry version 145. DE RecName: Full=Ribulose bisphosphate carboxylase {ECO:0000255|HAMAP-Rule:MF_01133}; DE Short=RuBisCO {ECO:0000255|HAMAP-Rule:MF_01133}; DE EC=4.1.1.39 {ECO:0000255|HAMAP-Rule:MF_01133}; GN Name=rbcL {ECO:0000255|HAMAP-Rule:MF_01133}; OrderedLocusNames=PH0939; OS Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC OS 100139 / OT-3). OC Archaea; Euryarchaeota; Thermococci; Thermococcales; Thermococcaceae; OC Pyrococcus. OX NCBI_TaxID=70601; RN [1] RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. RC STRAIN=ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3; RX PubMed=9679194; DOI=10.1093/dnares/5.2.55; RA Kawarabayasi Y., Sawada M., Horikawa H., Haikawa Y., Hino Y., Yamamoto S., RA Sekine M., Baba S., Kosugi H., Hosoyama A., Nagai Y., Sakai M., Ogura K., RA Otsuka R., Nakazawa H., Takamiya M., Ohfuku Y., Funahashi T., Tanaka T., RA Kudoh Y., Yamazaki J., Kushida N., Oguchi A., Aoki K., Yoshizawa T., RA Nakamura Y., Robb F.T., Horikoshi K., Masuchi Y., Shizuya H., Kikuchi H.; RT "Complete sequence and gene organization of the genome of a hyper- RT thermophilic archaebacterium, Pyrococcus horikoshii OT3."; RL DNA Res. 5:55-76(1998). RN [2] RP X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS). RG RIKEN structural genomics initiative (RSGI); RT "Crystal structure of octameric ribulose-1,5-bisphosphate RT carboxylase/oxygenase (Rubisco) from Pyrococcus horikoshii OT3 (form-1 RT crystal)."; RL Submitted (JUN-2005) to the PDB data bank. CC -!- FUNCTION: Catalyzes the addition of molecular CO(2) and H(2)O to CC ribulose 1,5-bisphosphate (RuBP), generating two molecules of 3- CC phosphoglycerate (3-PGA). Functions in an archaeal AMP degradation CC pathway, together with AMP phosphorylase and R15P isomerase. CC {ECO:0000255|HAMAP-Rule:MF_01133}. CC -!- CATALYTIC ACTIVITY: CC Reaction=2 (2R)-3-phosphoglycerate + 2 H(+) = CO2 + D-ribulose 1,5- CC bisphosphate + H2O; Xref=Rhea:RHEA:23124, ChEBI:CHEBI:15377, CC ChEBI:CHEBI:15378, ChEBI:CHEBI:16526, ChEBI:CHEBI:57870, CC ChEBI:CHEBI:58272; EC=4.1.1.39; Evidence={ECO:0000255|HAMAP- CC Rule:MF_01133}; CC -!- CATALYTIC ACTIVITY: CC Reaction=D-ribulose 1,5-bisphosphate + O2 = (2R)-3-phosphoglycerate + CC 2-phosphoglycolate + 2 H(+); Xref=Rhea:RHEA:36631, ChEBI:CHEBI:15378, CC ChEBI:CHEBI:15379, ChEBI:CHEBI:57870, ChEBI:CHEBI:58033, CC ChEBI:CHEBI:58272; Evidence={ECO:0000255|HAMAP-Rule:MF_01133}; CC -!- COFACTOR: CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420; Evidence={ECO:0000255|HAMAP- CC Rule:MF_01133}; CC Note=Binds 1 Mg(2+) ion per subunit. {ECO:0000255|HAMAP-Rule:MF_01133}; CC -!- SUBUNIT: Homodimer or homodecamer. In contrast to form I RuBisCO, the CC form III RuBisCO is composed solely of large subunits. CC {ECO:0000255|HAMAP-Rule:MF_01133}. CC -!- MISCELLANEOUS: Because the Archaea possessing a type III RuBisCO are CC all anaerobic, it is most likely that only the carboxylase activity of CC RuBisCO, and not the competitive oxygenase activity (by which RuBP CC reacts with O(2) to form one molecule of 3-phosphoglycerate and one CC molecule of 2-phosphoglycolate), is biologically relevant in these CC strains. {ECO:0000255|HAMAP-Rule:MF_01133}. CC -!- SIMILARITY: Belongs to the RuBisCO large chain family. Type III CC subfamily. {ECO:0000255|HAMAP-Rule:MF_01133}. CC --------------------------------------------------------------------------- CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms CC Distributed under the Creative Commons Attribution (CC BY 4.0) License CC --------------------------------------------------------------------------- DR EMBL; BA000001; BAA30036.1; -; Genomic_DNA. DR PIR; F71084; F71084. DR PDB; 2CWX; X-ray; 2.00 A; A/E=1-430. DR PDB; 2CXE; X-ray; 3.00 A; A/B/C/D=1-430. DR PDB; 2D69; X-ray; 1.90 A; A/B/D/E=1-430. DR PDBsum; 2CWX; -. DR PDBsum; 2CXE; -. DR PDBsum; 2D69; -. DR AlphaFoldDB; O58677; -. DR SMR; O58677; -. DR STRING; 70601.gene:9377894; -. DR EnsemblBacteria; BAA30036; BAA30036; BAA30036. DR KEGG; pho:PH0939; -. DR eggNOG; arCOG04443; Archaea. DR OrthoDB; 52787at2157; -. DR BRENDA; 4.1.1.39; 5244. DR EvolutionaryTrace; O58677; -. DR Proteomes; UP000000752; Chromosome. DR GO; GO:0000287; F:magnesium ion binding; IEA:UniProtKB-UniRule. DR GO; GO:0016491; F:oxidoreductase activity; IEA:UniProtKB-KW. DR GO; GO:0016984; F:ribulose-bisphosphate carboxylase activity; IEA:UniProtKB-UniRule. DR GO; GO:0006196; P:AMP catabolic process; IEA:UniProtKB-UniRule. DR GO; GO:0015977; P:carbon fixation; IEA:UniProtKB-KW. DR CDD; cd08213; RuBisCO_large_III; 1. DR Gene3D; 3.20.20.110; Ribulose bisphosphate carboxylase, large subunit, C-terminal domain; 1. DR Gene3D; 3.30.70.150; RuBisCO large subunit, N-terminal domain; 1. DR HAMAP; MF_01133; RuBisCO_L_type3; 1. DR InterPro; IPR033966; RuBisCO. DR InterPro; IPR017712; RuBisCO_III. DR InterPro; IPR000685; RuBisCO_lsu_C. DR InterPro; IPR036376; RuBisCO_lsu_C_sf. DR InterPro; IPR017443; RuBisCO_lsu_fd_N. DR InterPro; IPR036422; RuBisCO_lsu_N_sf. DR NCBIfam; TIGR03326; rubisco_III; 1. DR PANTHER; PTHR42704; RIBULOSE BISPHOSPHATE CARBOXYLASE; 1. DR PANTHER; PTHR42704:SF9; RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN; 1. DR Pfam; PF00016; RuBisCO_large; 1. DR Pfam; PF02788; RuBisCO_large_N; 1. DR SFLD; SFLDG01052; RuBisCO; 1. DR SFLD; SFLDS00014; RuBisCO; 2. DR SFLD; SFLDG00301; RuBisCO-like_proteins; 1. DR SUPFAM; SSF51649; RuBisCo, C-terminal domain; 1. DR SUPFAM; SSF54966; RuBisCO, large subunit, small (N-terminal) domain; 1. PE 1: Evidence at protein level; KW 3D-structure; Carbon dioxide fixation; Lyase; Magnesium; Metal-binding; KW Oxidoreductase. FT CHAIN 1..430 FT /note="Ribulose bisphosphate carboxylase" FT /id="PRO_0000062677" FT ACT_SITE 160 FT /note="Proton acceptor" FT /evidence="ECO:0000255|HAMAP-Rule:MF_01133" FT ACT_SITE 278 FT /note="Proton acceptor" FT /evidence="ECO:0000255|HAMAP-Rule:MF_01133" FT BINDING 162 FT /ligand="substrate" FT /evidence="ECO:0000255|HAMAP-Rule:MF_01133" FT BINDING 186 FT /ligand="Mg(2+)" FT /ligand_id="ChEBI:CHEBI:18420" FT /note="via carbamate group" FT /evidence="ECO:0000255|HAMAP-Rule:MF_01133" FT BINDING 188 FT /ligand="Mg(2+)" FT /ligand_id="ChEBI:CHEBI:18420" FT /evidence="ECO:0000255|HAMAP-Rule:MF_01133" FT BINDING 189 FT /ligand="Mg(2+)" FT /ligand_id="ChEBI:CHEBI:18420" FT /evidence="ECO:0000255|HAMAP-Rule:MF_01133" FT BINDING 279 FT /ligand="substrate" FT /evidence="ECO:0000255|HAMAP-Rule:MF_01133" FT BINDING 311 FT /ligand="substrate" FT /evidence="ECO:0000255|HAMAP-Rule:MF_01133" FT BINDING 348..350 FT /ligand="substrate" FT /evidence="ECO:0000255|HAMAP-Rule:MF_01133" FT BINDING 370..373 FT /ligand="substrate" FT /evidence="ECO:0000255|HAMAP-Rule:MF_01133" FT SITE 318 FT /note="Transition state stabilizer" FT /evidence="ECO:0000255|HAMAP-Rule:MF_01133" FT MOD_RES 186 FT /note="N6-carboxylysine" FT /evidence="ECO:0000255|HAMAP-Rule:MF_01133" FT STRAND 7..9 FT /evidence="ECO:0007829|PDB:2D69" FT HELIX 11..14 FT /evidence="ECO:0007829|PDB:2D69" FT STRAND 25..37 FT /evidence="ECO:0007829|PDB:2D69" FT HELIX 39..49 FT /evidence="ECO:0007829|PDB:2D69" FT TURN 50..52 FT /evidence="ECO:0007829|PDB:2D69" FT STRAND 55..59 FT /evidence="ECO:0007829|PDB:2D69" FT HELIX 63..65 FT /evidence="ECO:0007829|PDB:2CXE" FT HELIX 66..68 FT /evidence="ECO:0007829|PDB:2D69" FT STRAND 71..78 FT /evidence="ECO:0007829|PDB:2D69" FT STRAND 81..88 FT /evidence="ECO:0007829|PDB:2D69" FT HELIX 90..92 FT /evidence="ECO:0007829|PDB:2D69" FT HELIX 98..105 FT /evidence="ECO:0007829|PDB:2D69" FT HELIX 108..111 FT /evidence="ECO:0007829|PDB:2D69" FT STRAND 115..124 FT /evidence="ECO:0007829|PDB:2D69" FT HELIX 127..130 FT /evidence="ECO:0007829|PDB:2D69" FT HELIX 139..147 FT /evidence="ECO:0007829|PDB:2D69" FT STRAND 150..152 FT /evidence="ECO:0007829|PDB:2CXE" FT STRAND 154..157 FT /evidence="ECO:0007829|PDB:2D69" FT STRAND 160..163 FT /evidence="ECO:0007829|PDB:2D69" FT HELIX 167..179 FT /evidence="ECO:0007829|PDB:2D69" FT STRAND 183..186 FT /evidence="ECO:0007829|PDB:2D69" FT HELIX 199..217 FT /evidence="ECO:0007829|PDB:2D69" FT STRAND 222..224 FT /evidence="ECO:0007829|PDB:2D69" FT HELIX 231..243 FT /evidence="ECO:0007829|PDB:2D69" FT STRAND 248..252 FT /evidence="ECO:0007829|PDB:2D69" FT HELIX 253..256 FT /evidence="ECO:0007829|PDB:2D69" FT HELIX 258..271 FT /evidence="ECO:0007829|PDB:2D69" FT STRAND 274..278 FT /evidence="ECO:0007829|PDB:2D69" FT TURN 280..282 FT /evidence="ECO:0007829|PDB:2D69" FT HELIX 283..286 FT /evidence="ECO:0007829|PDB:2D69" FT STRAND 291..293 FT /evidence="ECO:0007829|PDB:2D69" FT HELIX 295..305 FT /evidence="ECO:0007829|PDB:2D69" FT STRAND 308..311 FT /evidence="ECO:0007829|PDB:2D69" FT STRAND 317..319 FT /evidence="ECO:0007829|PDB:2D69" FT HELIX 323..334 FT /evidence="ECO:0007829|PDB:2D69" FT STRAND 344..350 FT /evidence="ECO:0007829|PDB:2D69" FT HELIX 353..355 FT /evidence="ECO:0007829|PDB:2D69" FT HELIX 356..363 FT /evidence="ECO:0007829|PDB:2D69" FT STRAND 368..370 FT /evidence="ECO:0007829|PDB:2D69" FT HELIX 372..376 FT /evidence="ECO:0007829|PDB:2D69" FT HELIX 382..398 FT /evidence="ECO:0007829|PDB:2D69" FT HELIX 402..405 FT /evidence="ECO:0007829|PDB:2D69" FT TURN 406..408 FT /evidence="ECO:0007829|PDB:2CXE" FT HELIX 410..422 FT /evidence="ECO:0007829|PDB:2D69" SQ SEQUENCE 430 AA; 48247 MW; 1068CA138F019AD9 CRC64; MMVLRMKVEW YLDFVDLNYE PGRDELIVEY YFEPNGVSPE EAAGRIASES SIGTWTTLWK LPEMAKRSMA KVFYLEKHGE GYIAKIAYPL TLFEEGSLVQ LFSAVAGNVF GMKALKNLRL LDFHPPYEYL RHFKGPQFGV QGIREFMGVK DRPLTATVPK PKMGWSVEEY AEIAYELWSG GIDLLKDDEN FTSFPFNRFE ERVRKLYRVR DRVEAETGET KEYLINITGP VNIMEKRAEM VANEGGQYVM IDIVVAGWSA LQYMREVTED LGLAIHAHRA MHAAFTRNPR HGITMLALAK AARMIGVDQI HTGTAVGKMA GNYEEIKRIN DFLLSKWEHI RPVFPVASGG LHPGLMPELI RLFGKDLVIQ AGGGVMGHPD GPRAGAKALR DAIDAAIEGV DLDEKAKSSP ELKKSLREVG LSKAKVGVQH //