RBL_THEKO
ID RBL_THEKO Reviewed; 444 AA.
AC O93627;
DT 26-SEP-2003, integrated into UniProtKB/Swiss-Prot.
DT 23-JAN-2007, sequence version 5.
DT 03-AUG-2022, entry version 148.
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, ECO:0000269|PubMed:9988755};
GN Name=rbcL {ECO:0000255|HAMAP-Rule:MF_01133}; Synonyms=rbc;
GN OrderedLocusNames=TK2290;
OS Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)
OS (Pyrococcus kodakaraensis (strain KOD1)).
OC Archaea; Euryarchaeota; Thermococci; Thermococcales; Thermococcaceae;
OC Thermococcus.
OX NCBI_TaxID=69014;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 2-12, FUNCTION,
RP CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, AND SUBUNIT.
RC STRAIN=ATCC BAA-918 / JCM 12380 / KOD1;
RX PubMed=9988755; DOI=10.1074/jbc.274.8.5078;
RA Ezaki S., Maeda N., Kishimoto T., Atomi H., Imanaka T.;
RT "Presence of a structurally novel type ribulose-bisphosphate
RT carboxylase/oxygenase in the hyperthermophilic archaeon, Pyrococcus
RT kodakaraensis KOD1.";
RL J. Biol. Chem. 274:5078-5082(1999).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC BAA-918 / JCM 12380 / KOD1;
RX PubMed=15710748; DOI=10.1101/gr.3003105;
RA Fukui T., Atomi H., Kanai T., Matsumi R., Fujiwara S., Imanaka T.;
RT "Complete genome sequence of the hyperthermophilic archaeon Thermococcus
RT kodakaraensis KOD1 and comparison with Pyrococcus genomes.";
RL Genome Res. 15:352-363(2005).
RN [3]
RP PROTEIN SEQUENCE OF 2-12, FUNCTION, SUBUNIT, AND CRYSTALLIZATION.
RC STRAIN=ATCC BAA-918 / JCM 12380 / KOD1;
RX PubMed=10512715; DOI=10.1006/jmbi.1999.3145;
RA Maeda N., Kitano K., Fukui T., Ezaki S., Atomi H., Miki K., Imanaka T.;
RT "Ribulose bisphosphate carboxylase/oxygenase from the hyperthermophilic
RT archaeon Pyrococcus kodakaraensis KOD1 is composed solely of large subunits
RT and forms a pentagonal structure.";
RL J. Mol. Biol. 293:57-66(1999).
RN [4]
RP FUNCTION, SUBUNIT, AND MUTAGENESIS OF GLU-63; ARG-66 AND ASP-69.
RC STRAIN=ATCC BAA-918 / JCM 12380 / KOD1;
RX PubMed=12070156; DOI=10.1074/jbc.m203117200;
RA Maeda N., Kanai T., Atomi H., Imanaka T.;
RT "The unique pentagonal structure of an archaeal Rubisco is essential for
RT its high thermostability.";
RL J. Biol. Chem. 277:31656-31662(2002).
RN [5]
RP FUNCTION, CATALYTIC ACTIVITY, DISRUPTION PHENOTYPE, AND PATHWAY.
RC STRAIN=ATCC BAA-918 / JCM 12380 / KOD1;
RX PubMed=17303759; DOI=10.1126/science.1135999;
RA Sato T., Atomi H., Imanaka T.;
RT "Archaeal type III RuBisCOs function in a pathway for AMP metabolism.";
RL Science 315:1003-1006(2007).
RN [6]
RP INDUCTION, AND PATHWAY.
RC STRAIN=ATCC BAA-918 / JCM 12380 / KOD1;
RX PubMed=23065974; DOI=10.1128/jb.01335-12;
RA Aono R., Sato T., Yano A., Yoshida S., Nishitani Y., Miki K., Imanaka T.,
RA Atomi H.;
RT "Enzymatic characterization of AMP phosphorylase and ribose-1,5-
RT bisphosphate isomerase functioning in an archaeal AMP metabolic pathway.";
RL J. Bacteriol. 194:6847-6855(2012).
RN [7]
RP X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS), COFACTOR, AND SUBUNIT.
RC STRAIN=ATCC BAA-918 / JCM 12380 / KOD1;
RX PubMed=11435112; DOI=10.1016/s0969-2126(01)00608-6;
RA Kitano K., Maeda N., Fukui T., Atomi H., Imanaka T., Miki K.;
RT "Crystal structure of a novel-type archaeal rubisco with pentagonal
RT symmetry.";
RL Structure 9:473-481(2001).
RN [8]
RP X-RAY CRYSTALLOGRAPHY (2.09 ANGSTROMS) OF WILD-TYPE AND MUTANTS IN COMPLEX
RP WITH INHIBITOR AND MAGNESIUM, FUNCTION, COFACTOR, TEMPERATURE DEPENDENCE,
RP AND CARBOXYLATION AT LYS-189.
RC STRAIN=ATCC BAA-918 / JCM 12380 / KOD1;
RX PubMed=20926376; DOI=10.1074/jbc.m110.147587;
RA Nishitani Y., Yoshida S., Fujihashi M., Kitagawa K., Doi T., Atomi H.,
RA Imanaka T., Miki K.;
RT "Structure-based catalytic optimization of a type III Rubisco from a
RT hyperthermophile.";
RL J. Biol. Chem. 285:39339-39347(2010).
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) (PubMed:9988755, PubMed:10512715). Functions
CC in an archaeal AMP degradation pathway, together with AMP phosphorylase
CC and R15P isomerase (PubMed:17303759). {ECO:0000255|HAMAP-Rule:MF_01133,
CC ECO:0000269|PubMed:10512715, ECO:0000269|PubMed:12070156,
CC ECO:0000269|PubMed:17303759, ECO:0000269|PubMed:20926376,
CC ECO:0000269|PubMed:9988755}.
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, ECO:0000269|PubMed:9988755};
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 ECO:0000269|PubMed:9988755};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_01133,
CC ECO:0000269|PubMed:11435112, ECO:0000269|PubMed:20926376};
CC Note=Binds 1 Mg(2+) ion per subunit. {ECO:0000255|HAMAP-Rule:MF_01133,
CC ECO:0000269|PubMed:11435112, ECO:0000269|PubMed:20926376};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Temperature dependence:
CC Optimum temperature is 90 degrees Celsius (PubMed:9988755). Highly
CC thermostable, has a half-life of 220 minutes at 90 degrees Celsius
CC (PubMed:9988755). {ECO:0000269|PubMed:20926376,
CC ECO:0000269|PubMed:9988755};
CC -!- SUBUNIT: Homodecamer, consisting of five dimer units which form a ring-
CC like pentagonal structure. This arrangement is essential for its high
CC thermostability (PubMed:12070156). In contrast to form I RuBisCO, the
CC form III RuBisCO is composed solely of large subunits (PubMed:9988755).
CC {ECO:0000269|PubMed:10512715, ECO:0000269|PubMed:11435112,
CC ECO:0000269|PubMed:12070156, ECO:0000269|PubMed:20926376,
CC ECO:0000305|PubMed:9988755}.
CC -!- INDUCTION: Up-regulated by nucleosides (at protein level).
CC {ECO:0000269|PubMed:23065974}.
CC -!- DISRUPTION PHENOTYPE: Cells lacking this gene show a slight decrease in
CC growth as compared to the wild-type when they are grown in nutrient-
CC rich medium. {ECO:0000269|PubMed:17303759}.
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:0000305|PubMed:17303759}.
CC -!- SIMILARITY: Belongs to the RuBisCO large chain family. Type III
CC subfamily. {ECO:0000255|HAMAP-Rule:MF_01133}.
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DR EMBL; AB018555; BAA33863.1; -; Genomic_DNA.
DR EMBL; AP006878; BAD86479.1; -; Genomic_DNA.
DR RefSeq; WP_011251240.1; NC_006624.1.
DR PDB; 1GEH; X-ray; 2.80 A; A/B/C/D/E=1-444.
DR PDB; 3A12; X-ray; 2.30 A; A/B/C/D/E/F/G/H/I/J=1-444.
DR PDB; 3A13; X-ray; 2.34 A; A/B/C/D/E/F/G/H/I/J=1-444.
DR PDB; 3KDN; X-ray; 2.09 A; A/B/C/D/E/F/G/H/I/J=1-444.
DR PDB; 3KDO; X-ray; 2.36 A; A/B/C/D/E/F/G/H/I/J=1-444.
DR PDB; 3WQP; X-ray; 2.25 A; A/B/C/D/E/F/G/H/I/J=1-444.
DR PDBsum; 1GEH; -.
DR PDBsum; 3A12; -.
DR PDBsum; 3A13; -.
DR PDBsum; 3KDN; -.
DR PDBsum; 3KDO; -.
DR PDBsum; 3WQP; -.
DR AlphaFoldDB; O93627; -.
DR SMR; O93627; -.
DR IntAct; O93627; 1.
DR MINT; O93627; -.
DR STRING; 69014.TK2290; -.
DR EnsemblBacteria; BAD86479; BAD86479; TK2290.
DR GeneID; 3234791; -.
DR KEGG; tko:TK2290; -.
DR PATRIC; fig|69014.16.peg.2245; -.
DR eggNOG; arCOG04443; Archaea.
DR HOGENOM; CLU_031450_3_1_2; -.
DR InParanoid; O93627; -.
DR OMA; IHGHPDG; -.
DR OrthoDB; 9533at2157; -.
DR PhylomeDB; O93627; -.
DR BioCyc; MetaCyc:MON-13272; -.
DR BRENDA; 4.1.1.39; 5246.
DR EvolutionaryTrace; O93627; -.
DR Proteomes; UP000000536; 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; Direct protein sequencing; Lyase;
KW Magnesium; Metal-binding; Oxidoreductase; Reference proteome.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0000269|PubMed:10512715,
FT ECO:0000269|PubMed:9988755"
FT CHAIN 2..444
FT /note="Ribulose bisphosphate carboxylase"
FT /id="PRO_0000062678"
FT ACT_SITE 163
FT /note="Proton acceptor"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01133"
FT ACT_SITE 281
FT /note="Proton acceptor"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01133"
FT BINDING 165
FT /ligand="substrate"
FT /evidence="ECO:0000305"
FT BINDING 189
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /note="via carbamate group"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01133,
FT ECO:0000269|PubMed:20926376"
FT BINDING 191
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01133,
FT ECO:0000269|PubMed:20926376"
FT BINDING 192
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01133,
FT ECO:0000269|PubMed:20926376"
FT BINDING 282
FT /ligand="substrate"
FT /evidence="ECO:0000305"
FT BINDING 314
FT /ligand="substrate"
FT /evidence="ECO:0000305"
FT BINDING 367..369
FT /ligand="substrate"
FT /evidence="ECO:0000305"
FT BINDING 389..392
FT /ligand="substrate"
FT /evidence="ECO:0000305"
FT SITE 322
FT /note="Transition state stabilizer"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01133"
FT MOD_RES 189
FT /note="N6-carboxylysine"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01133,
FT ECO:0000269|PubMed:20926376"
FT MUTAGEN 63
FT /note="E->S: Decrease in activity and in thermostability.
FT Large decrease in activity; forms dimers; when associated
FT with S-66 and S-69."
FT /evidence="ECO:0000269|PubMed:12070156"
FT MUTAGEN 66
FT /note="R->S: Large decrease in activity and in
FT thermostability. Large decrease in activity; forms dimers;
FT when associated with S-63 and S-69."
FT /evidence="ECO:0000269|PubMed:12070156"
FT MUTAGEN 69
FT /note="D->S: Slight decrease in activity; no change in
FT thermostability. Large decrease in activity; forms dimers;
FT when associated with S-63 and S-66."
FT /evidence="ECO:0000269|PubMed:12070156"
FT HELIX 10..12
FT /evidence="ECO:0007829|PDB:3KDN"
FT TURN 21..23
FT /evidence="ECO:0007829|PDB:3KDN"
FT STRAND 24..33
FT /evidence="ECO:0007829|PDB:3KDN"
FT HELIX 39..49
FT /evidence="ECO:0007829|PDB:3KDN"
FT TURN 50..52
FT /evidence="ECO:0007829|PDB:3KDN"
FT HELIX 64..70
FT /evidence="ECO:0007829|PDB:3KDN"
FT STRAND 73..79
FT /evidence="ECO:0007829|PDB:3KDN"
FT STRAND 81..83
FT /evidence="ECO:0007829|PDB:3KDN"
FT STRAND 85..92
FT /evidence="ECO:0007829|PDB:3KDN"
FT HELIX 93..95
FT /evidence="ECO:0007829|PDB:3KDN"
FT HELIX 101..108
FT /evidence="ECO:0007829|PDB:3KDN"
FT HELIX 111..114
FT /evidence="ECO:0007829|PDB:3KDN"
FT STRAND 118..127
FT /evidence="ECO:0007829|PDB:3KDN"
FT HELIX 130..133
FT /evidence="ECO:0007829|PDB:3KDN"
FT HELIX 142..150
FT /evidence="ECO:0007829|PDB:3KDN"
FT STRAND 157..160
FT /evidence="ECO:0007829|PDB:3KDN"
FT STRAND 163..166
FT /evidence="ECO:0007829|PDB:3KDN"
FT HELIX 170..182
FT /evidence="ECO:0007829|PDB:3KDN"
FT STRAND 187..189
FT /evidence="ECO:0007829|PDB:3KDN"
FT HELIX 202..220
FT /evidence="ECO:0007829|PDB:3KDN"
FT STRAND 225..229
FT /evidence="ECO:0007829|PDB:3KDN"
FT HELIX 234..247
FT /evidence="ECO:0007829|PDB:3KDN"
FT STRAND 251..255
FT /evidence="ECO:0007829|PDB:3KDN"
FT HELIX 256..259
FT /evidence="ECO:0007829|PDB:3KDN"
FT HELIX 261..274
FT /evidence="ECO:0007829|PDB:3KDN"
FT STRAND 277..281
FT /evidence="ECO:0007829|PDB:3KDN"
FT TURN 283..285
FT /evidence="ECO:0007829|PDB:3KDN"
FT HELIX 286..289
FT /evidence="ECO:0007829|PDB:3KDN"
FT STRAND 294..296
FT /evidence="ECO:0007829|PDB:3KDN"
FT HELIX 298..308
FT /evidence="ECO:0007829|PDB:3KDN"
FT STRAND 311..314
FT /evidence="ECO:0007829|PDB:3KDN"
FT STRAND 320..323
FT /evidence="ECO:0007829|PDB:3KDN"
FT HELIX 327..338
FT /evidence="ECO:0007829|PDB:3KDN"
FT STRAND 340..342
FT /evidence="ECO:0007829|PDB:3KDN"
FT STRAND 363..369
FT /evidence="ECO:0007829|PDB:3KDN"
FT TURN 372..374
FT /evidence="ECO:0007829|PDB:3WQP"
FT HELIX 376..382
FT /evidence="ECO:0007829|PDB:3KDN"
FT STRAND 384..389
FT /evidence="ECO:0007829|PDB:3KDN"
FT HELIX 392..395
FT /evidence="ECO:0007829|PDB:3KDN"
FT HELIX 401..415
FT /evidence="ECO:0007829|PDB:3KDN"
FT HELIX 421..425
FT /evidence="ECO:0007829|PDB:3KDN"
FT HELIX 429..438
FT /evidence="ECO:0007829|PDB:3KDN"
SQ SEQUENCE 444 AA; 49713 MW; 6E3AFF37367DD7FE CRC64;
MVEKFDTIYD YYVDKGYEPS KKRDIIAVFR VTPAEGYTIE QAAGAVAAES STGTWTTLYP
WYEQERWADL SAKAYDFHDM GDGSWIVRIA YPFHAFEEAN LPGLLASIAG NIFGMKRVKG
LRLEDLYFPE KLIREFDGPA FGIEGVRKML EIKDRPIYGV VPKPKVGYSP EEFEKLAYDL
LSNGADYMKD DENLTSPWYN RFEERAEIMA KIIDKVENET GEKKTWFANI TADLLEMEQR
LEVLADLGLK HAMVDVVITG WGALRYIRDL AADYGLAIHG HRAMHAAFTR NPYHGISMFV
LAKLYRLIGI DQLHVGTAGA GKLEGGKWDV IQNARILRES HYKPDENDVF HLEQKFYSIK
AAFPTSSGGL HPGNIQPVIE ALGTDIVLQL GGGTLGHPDG PAAGARAVRQ AIDAIMQGIP
LDEYAKTHKE LARALEKWGH VTPV
