RBL_PYRHO
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 03-AUG-2022, entry version 139.
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;
CC Evidence={ECO:0000255|HAMAP-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 RefSeq; WP_010885029.1; NC_000961.1.
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; 70601.3257353; -.
DR EnsemblBacteria; BAA30036; BAA30036; BAA30036.
DR GeneID; 1443264; -.
DR KEGG; pho:PH0939; -.
DR eggNOG; arCOG04443; Archaea.
DR OMA; IHGHPDG; -.
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; -; 1.
DR Gene3D; 3.30.70.150; -; 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 PANTHER; PTHR42704; PTHR42704; 1.
DR Pfam; PF00016; RuBisCO_large; 1.
DR Pfam; PF02788; RuBisCO_large_N; 1.
DR SFLD; SFLDS00014; RuBisCO; 2.
DR SUPFAM; SSF51649; SSF51649; 1.
DR SUPFAM; SSF54966; SSF54966; 1.
DR TIGRFAMs; TIGR03326; rubisco_III; 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
