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Database: UniProt/SWISS-PROT
Entry: RBL_THEKO
LinkDB: RBL_THEKO
Original site: 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   05-DEC-2018, entry version 134.
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
RT   Thermococcus kodakaraensis KOD1 and comparison with Pyrococcus
RT   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.,
RA   Imanaka T.;
RT   "Ribulose bisphosphate carboxylase/oxygenase from the
RT   hyperthermophilic archaeon Pyrococcus kodakaraensis KOD1 is composed
RT   solely of large subunits 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
RT   for 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
RT   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.,
RA   Imanaka T., Atomi H.;
RT   "Enzymatic characterization of AMP phosphorylase and ribose-1,5-
RT   bisphosphate isomerase functioning in an archaeal AMP metabolic
RT   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
RP   COMPLEX WITH INHIBITOR AND MAGNESIUM, FUNCTION, COFACTOR, TEMPERATURE
RP   DEPENDENCE, AND CARBAMYLATION 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).
CC       Functions in an archaeal AMP degradation pathway, together with
CC       AMP phosphorylase and R15P isomerase (PubMed:17303759).
CC       {ECO:0000255|HAMAP-Rule:MF_01133, ECO:0000269|PubMed:10512715,
CC       ECO:0000269|PubMed:12070156, ECO:0000269|PubMed:17303759,
CC       ECO:0000269|PubMed:20926376, ECO:0000269|PubMed:9988755}.
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=2 3-phospho-D-glycerate + 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 = 2-phosphoglycolate +
CC         3-phospho-D-glycerate + 2 H(+); Xref=Rhea:RHEA:36631,
CC         ChEBI:CHEBI:15378, ChEBI:CHEBI:15379, ChEBI:CHEBI:57870,
CC         ChEBI:CHEBI:58033, ChEBI:CHEBI:58272;
CC         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-
CC       Rule:MF_01133, ECO:0000269|PubMed:11435112,
CC       ECO:0000269|PubMed:20926376};
CC   -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC       Temperature dependence:
CC         Optimum temperature is 90 degrees Celsius (PubMed:9988755).
CC         Highly thermostable, has a half-life of 220 minutes at 90
CC         degrees Celsius (PubMed:9988755). {ECO:0000269|PubMed:20926376,
CC         ECO:0000269|PubMed:9988755};
CC   -!- SUBUNIT: Homodecamer, consisting of five dimer units which form a
CC       ring-like pentagonal structure. This arrangement is essential for
CC       its high thermostability (PubMed:12070156). In contrast to form I
CC       RuBisCO, the form III RuBisCO is composed solely of large subunits
CC       (PubMed:9988755). {ECO:0000269|PubMed:10512715,
CC       ECO:0000269|PubMed:11435112, ECO:0000269|PubMed:12070156,
CC       ECO:0000269|PubMed:20926376, 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
CC       decrease in growth as compared to the wild-type when they are
CC       grown in nutrient-rich medium. {ECO:0000269|PubMed:17303759}.
CC   -!- MISCELLANEOUS: Because the Archaea possessing a type III RuBisCO
CC       are all anaerobic, it is most likely that only the carboxylase
CC       activity of RuBisCO, and not the competitive oxygenase activity
CC       (by which RuBP reacts with O(2) to form one molecule of 3-
CC       phosphoglycerate and one molecule of 2-phosphoglycolate), is
CC       biologically relevant in these strains.
CC       {ECO:0000305|PubMed:17303759}.
CC   -!- SIMILARITY: Belongs to the RuBisCO large chain family. Type III
CC       subfamily. {ECO:0000255|HAMAP-Rule:MF_01133}.
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   ProteinModelPortal; 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   eggNOG; COG1850; LUCA.
DR   HOGENOM; HOG000230831; -.
DR   InParanoid; O93627; -.
DR   KO; K01601; -.
DR   OMA; FTQDWAS; -.
DR   OrthoDB; POG093Z02MJ; -.
DR   BioCyc; MetaCyc:MONOMER-13272; -.
DR   BioCyc; TKOD69014:G1G2A-2316-MONOMER; -.
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; Complete proteome;
KW   Direct protein sequencing; Lyase; Magnesium; Metal-binding;
KW   Oxidoreductase; Reference proteome.
FT   INIT_MET      1      1       Removed. {ECO:0000269|PubMed:10512715,
FT                                ECO:0000269|PubMed:9988755}.
FT   CHAIN         2    444       Ribulose bisphosphate carboxylase.
FT                                /FTId=PRO_0000062678.
FT   REGION      367    369       Substrate binding. {ECO:0000305}.
FT   REGION      389    392       Substrate binding. {ECO:0000305}.
FT   ACT_SITE    163    163       Proton acceptor. {ECO:0000255|HAMAP-
FT                                Rule:MF_01133}.
FT   ACT_SITE    281    281       Proton acceptor. {ECO:0000255|HAMAP-
FT                                Rule:MF_01133}.
FT   METAL       189    189       Magnesium; via carbamate group.
FT                                {ECO:0000255|HAMAP-Rule:MF_01133,
FT                                ECO:0000269|PubMed:20926376}.
FT   METAL       191    191       Magnesium. {ECO:0000255|HAMAP-
FT                                Rule:MF_01133,
FT                                ECO:0000269|PubMed:20926376}.
FT   METAL       192    192       Magnesium. {ECO:0000255|HAMAP-
FT                                Rule:MF_01133,
FT                                ECO:0000269|PubMed:20926376}.
FT   BINDING     165    165       Substrate. {ECO:0000305}.
FT   BINDING     282    282       Substrate. {ECO:0000305}.
FT   BINDING     314    314       Substrate. {ECO:0000305}.
FT   SITE        322    322       Transition state stabilizer.
FT                                {ECO:0000255|HAMAP-Rule:MF_01133}.
FT   MOD_RES     189    189       N6-carboxylysine. {ECO:0000255|HAMAP-
FT                                Rule:MF_01133,
FT                                ECO:0000269|PubMed:20926376}.
FT   MUTAGEN      63     63       E->S: Decrease in activity and in
FT                                thermostability. Large decrease in
FT                                activity; forms dimers; when associated
FT                                with S-66 and S-69.
FT                                {ECO:0000269|PubMed:12070156}.
FT   MUTAGEN      66     66       R->S: Large decrease in activity and in
FT                                thermostability. Large decrease in
FT                                activity; forms dimers; when associated
FT                                with S-63 and S-69.
FT                                {ECO:0000269|PubMed:12070156}.
FT   MUTAGEN      69     69       D->S: Slight decrease in activity; no
FT                                change in thermostability. Large decrease
FT                                in activity; forms dimers; when
FT                                associated with S-63 and S-66.
FT                                {ECO:0000269|PubMed:12070156}.
FT   HELIX        10     12       {ECO:0000244|PDB:3KDN}.
FT   TURN         21     23       {ECO:0000244|PDB:3KDN}.
FT   STRAND       24     33       {ECO:0000244|PDB:3KDN}.
FT   HELIX        39     49       {ECO:0000244|PDB:3KDN}.
FT   TURN         50     52       {ECO:0000244|PDB:3KDN}.
FT   HELIX        64     70       {ECO:0000244|PDB:3KDN}.
FT   STRAND       73     79       {ECO:0000244|PDB:3KDN}.
FT   STRAND       81     83       {ECO:0000244|PDB:3KDN}.
FT   STRAND       85     92       {ECO:0000244|PDB:3KDN}.
FT   HELIX        93     95       {ECO:0000244|PDB:3KDN}.
FT   HELIX       101    108       {ECO:0000244|PDB:3KDN}.
FT   HELIX       111    114       {ECO:0000244|PDB:3KDN}.
FT   STRAND      118    127       {ECO:0000244|PDB:3KDN}.
FT   HELIX       130    133       {ECO:0000244|PDB:3KDN}.
FT   HELIX       142    150       {ECO:0000244|PDB:3KDN}.
FT   STRAND      157    160       {ECO:0000244|PDB:3KDN}.
FT   STRAND      163    166       {ECO:0000244|PDB:3KDN}.
FT   HELIX       170    182       {ECO:0000244|PDB:3KDN}.
FT   STRAND      187    189       {ECO:0000244|PDB:3KDN}.
FT   HELIX       202    220       {ECO:0000244|PDB:3KDN}.
FT   STRAND      225    229       {ECO:0000244|PDB:3KDN}.
FT   HELIX       234    247       {ECO:0000244|PDB:3KDN}.
FT   STRAND      251    255       {ECO:0000244|PDB:3KDN}.
FT   HELIX       256    259       {ECO:0000244|PDB:3KDN}.
FT   HELIX       261    274       {ECO:0000244|PDB:3KDN}.
FT   STRAND      277    281       {ECO:0000244|PDB:3KDN}.
FT   TURN        283    285       {ECO:0000244|PDB:3KDN}.
FT   HELIX       286    289       {ECO:0000244|PDB:3KDN}.
FT   STRAND      294    296       {ECO:0000244|PDB:3KDN}.
FT   HELIX       298    308       {ECO:0000244|PDB:3KDN}.
FT   STRAND      311    314       {ECO:0000244|PDB:3KDN}.
FT   STRAND      320    323       {ECO:0000244|PDB:3KDN}.
FT   HELIX       327    338       {ECO:0000244|PDB:3KDN}.
FT   STRAND      340    342       {ECO:0000244|PDB:3KDN}.
FT   STRAND      363    369       {ECO:0000244|PDB:3KDN}.
FT   TURN        372    374       {ECO:0000244|PDB:3WQP}.
FT   HELIX       376    382       {ECO:0000244|PDB:3KDN}.
FT   STRAND      384    389       {ECO:0000244|PDB:3KDN}.
FT   HELIX       392    395       {ECO:0000244|PDB:3KDN}.
FT   HELIX       401    415       {ECO:0000244|PDB:3KDN}.
FT   HELIX       421    425       {ECO:0000244|PDB:3KDN}.
FT   HELIX       429    438       {ECO:0000244|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
//
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