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Database: UniProt/TrEMBL
Entry: F8AF48_PYRYC
LinkDB: F8AF48_PYRYC
Original site: F8AF48_PYRYC 
ID   F8AF48_PYRYC            Unreviewed;       421 AA.
AC   F8AF48;
DT   21-SEP-2011, integrated into UniProtKB/TrEMBL.
DT   21-SEP-2011, sequence version 1.
DT   24-JAN-2024, entry version 59.
DE   RecName: Full=Ribulose bisphosphate carboxylase {ECO:0000256|HAMAP-Rule:MF_01133};
DE            Short=RuBisCO {ECO:0000256|HAMAP-Rule:MF_01133};
DE            EC=4.1.1.39 {ECO:0000256|HAMAP-Rule:MF_01133};
GN   Name=rbcL {ECO:0000256|HAMAP-Rule:MF_01133};
GN   OrderedLocusNames=PYCH_00090 {ECO:0000313|EMBL:AEH23722.1};
OS   Pyrococcus yayanosii (strain CH1 / JCM 16557).
OC   Archaea; Euryarchaeota; Thermococci; Thermococcales; Thermococcaceae;
OC   Pyrococcus.
OX   NCBI_TaxID=529709 {ECO:0000313|EMBL:AEH23722.1, ECO:0000313|Proteomes:UP000008386};
RN   [1] {ECO:0000313|EMBL:AEH23722.1, ECO:0000313|Proteomes:UP000008386}
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=CH1 / JCM 16557 {ECO:0000313|Proteomes:UP000008386};
RX   PubMed=21705594; DOI=10.1128/JB.05345-11;
RA   Jun X., Lupeng L., Minjuan X., Oger P., Fengping W., Jebbar M., Xiang X.;
RT   "Complete genome sequence of the obligate piezophilic hyperthermophilic
RT   archaeon Pyrococcus yayanosii CH1.";
RL   J. Bacteriol. 193:4297-4298(2011).
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:0000256|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:0000256|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:0000256|HAMAP-Rule:MF_01133};
CC   -!- COFACTOR:
CC       Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC         Evidence={ECO:0000256|HAMAP-Rule:MF_01133};
CC       Note=Binds 1 Mg(2+) ion per subunit. {ECO:0000256|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:0000256|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:0000256|HAMAP-Rule:MF_01133}.
CC   -!- SIMILARITY: Belongs to the RuBisCO large chain family. Type III
CC       subfamily. {ECO:0000256|HAMAP-Rule:MF_01133}.
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DR   EMBL; CP002779; AEH23722.1; -; Genomic_DNA.
DR   RefSeq; WP_013904780.1; NC_015680.1.
DR   AlphaFoldDB; F8AF48; -.
DR   STRING; 529709.PYCH_00090; -.
DR   GeneID; 10836592; -.
DR   KEGG; pya:PYCH_00090; -.
DR   eggNOG; arCOG04443; Archaea.
DR   HOGENOM; CLU_031450_3_1_2; -.
DR   OMA; IHGHPDG; -.
DR   OrthoDB; 52787at2157; -.
DR   Proteomes; UP000008386; 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   3: Inferred from homology;
KW   Carbon dioxide fixation {ECO:0000256|HAMAP-Rule:MF_01133};
KW   Lyase {ECO:0000256|HAMAP-Rule:MF_01133};
KW   Magnesium {ECO:0000256|HAMAP-Rule:MF_01133};
KW   Metal-binding {ECO:0000256|HAMAP-Rule:MF_01133};
KW   Oxidoreductase {ECO:0000256|HAMAP-Rule:MF_01133}.
FT   DOMAIN          9..125
FT                   /note="Ribulose bisphosphate carboxylase large subunit
FT                   ferrodoxin-like N-terminal"
FT                   /evidence="ECO:0000259|Pfam:PF02788"
FT   DOMAIN          135..415
FT                   /note="Ribulose bisphosphate carboxylase large subunit C-
FT                   terminal"
FT                   /evidence="ECO:0000259|Pfam:PF00016"
FT   ACT_SITE        156
FT                   /note="Proton acceptor"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_01133"
FT   ACT_SITE        274
FT                   /note="Proton acceptor"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_01133"
FT   BINDING         158
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_01133"
FT   BINDING         182
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /note="via carbamate group"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_01133"
FT   BINDING         184
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_01133"
FT   BINDING         185
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_01133"
FT   BINDING         275
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_01133"
FT   BINDING         307
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_01133"
FT   BINDING         344..346
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_01133"
FT   BINDING         366..369
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_01133"
FT   SITE            314
FT                   /note="Transition state stabilizer"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_01133"
FT   MOD_RES         182
FT                   /note="N6-carboxylysine"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_01133"
SQ   SEQUENCE   421 AA;  47126 MW;  DC4D0153E37B1599 CRC64;
     MSKVEWYLDF VDLDYTPGRD ELIVEYYFEP NGVSPEEAAG RIASESSIGT WTTLWKLPDM
     AKRSMAKVFS LEKSGEGYIA KIAYPLTLFE EGNLVQLFSA IAGNIFGMKA LKNLRLLDFH
     PPYEYLRHFK GPQYGVKGIR EFMGIEDRPL TATVPKPKMG WSVDEYAEIA YELWSGGIDL
     LKDDENFTSF PFNRFEERVR KLYAVRDRVE AETGETKEYL INITGPAHVM EKRAQLVAAE
     GGQYIMIDIV VVGWSALQYM REVAEDLGLA IHAHRAMHAA FTRNPRHGIS MFVLAKAARM
     VGVDQIHTGT AVGKMAGDYE EVKRINGFLL SEWEHIKPIF PVASGGLHPG LMPELIRLFG
     RDLVIQVGGG VMGHPDGPRA GAKALRDAIE AAIEGVSLEE KAKESPELKK ALEKWGYLKP
     K
//
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