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O93627

- RBL_THEKO

UniProt

O93627 - RBL_THEKO

Protein

Ribulose bisphosphate carboxylase

Gene

rbcL

Organism
Thermococcus kodakaraensis (strain ATCC BAA-918 / JCM 12380 / KOD1) (Pyrococcus kodakaraensis (strain KOD1))
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 109 (01 Oct 2014)
      Sequence version 5 (23 Jan 2007)
      Previous versions | rss
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    Functioni

    Catalyzes the addition of molecular CO2 and H2O to ribulose 1,5-bisphosphate (RuBP), generating two molecules of 3-phosphoglycerate (3-PGA). Functions in an archaeal AMP degradation pathway, together with AMP phosphorylase and R15P isomerase.3 PublicationsUniRule annotation

    Catalytic activityi

    2 3-phospho-D-glycerate + 2 H+ = D-ribulose 1,5-bisphosphate + CO2 + H2O.UniRule annotation
    3-phospho-D-glycerate + 2-phosphoglycolate = D-ribulose 1,5-bisphosphate + O2.UniRule annotation

    Cofactori

    Binds 1 magnesium ion per subunit.2 PublicationsUniRule annotation

    Temperature dependencei

    Optimum temperature is 90 degrees Celsius. Highly thermostable. Has a half-life of 220 minutes at 90 degrees Celsius.1 Publication

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Active sitei163 – 1631Proton acceptorUniRule annotation
    Binding sitei165 – 1651SubstrateCurated
    Metal bindingi189 – 1891Magnesium; via carbamate group1 PublicationUniRule annotation
    Metal bindingi191 – 1911Magnesium1 PublicationUniRule annotation
    Metal bindingi192 – 1921Magnesium1 PublicationUniRule annotation
    Active sitei281 – 2811Proton acceptorUniRule annotation
    Binding sitei282 – 2821SubstrateCurated
    Binding sitei314 – 3141SubstrateCurated
    Sitei322 – 3221Transition state stabilizerUniRule annotation

    GO - Molecular functioni

    1. magnesium ion binding Source: UniProtKB-HAMAP
    2. oxidoreductase activity Source: UniProtKB-KW
    3. ribulose-bisphosphate carboxylase activity Source: UniProtKB-HAMAP

    GO - Biological processi

    1. AMP catabolic process Source: UniProtKB-HAMAP
    2. carbon fixation Source: UniProtKB-KW

    Keywords - Molecular functioni

    Lyase, Oxidoreductase

    Keywords - Biological processi

    Carbon dioxide fixation

    Keywords - Ligandi

    Magnesium, Metal-binding

    Enzyme and pathway databases

    BioCyciMetaCyc:MONOMER-13272.
    TKOD69014:GH72-2342-MONOMER.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Ribulose bisphosphate carboxylaseUniRule annotation (EC:4.1.1.39UniRule annotation)
    Short name:
    RuBisCOUniRule annotation
    Gene namesi
    Name:rbcLUniRule annotation
    Synonyms:rbc
    Ordered Locus Names:TK2290
    OrganismiThermococcus kodakaraensis (strain ATCC BAA-918 / JCM 12380 / KOD1) (Pyrococcus kodakaraensis (strain KOD1))
    Taxonomic identifieri69014 [NCBI]
    Taxonomic lineageiArchaeaEuryarchaeotaThermococciThermococcalesThermococcaceaeThermococcus
    ProteomesiUP000000536: Chromosome

    Pathology & Biotechi

    Disruption phenotypei

    Cells lacking this gene show a slight decrease in growth as sompared to the wild-type when they are grown in nutrient-rich medium.1 Publication

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi63 – 631E → S: Decrease in activity and in thermostability. Large decrease in activity; forms dimers; when associated with S-66 and S-69. 1 Publication
    Mutagenesisi66 – 661R → S: Large decrease in activity and in thermostability. Large decrease in activity; forms dimers; when associated with S-63 and S-69. 1 Publication
    Mutagenesisi69 – 691D → S: Slight decrease in activity; no change in thermostability. Large decrease in activity; forms dimers; when associated with S-63 and S-66. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Initiator methioninei1 – 11Removed2 Publications
    Chaini2 – 444443Ribulose bisphosphate carboxylasePRO_0000062678Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei189 – 1891N6-carboxylysine1 PublicationUniRule annotation

    Expressioni

    Inductioni

    Up-regulated by nucleosides (at protein level).1 Publication

    Interactioni

    Subunit structurei

    Homodecamer, consisting of fiver dimer units which form a ring-like pentagonal structure. This arrangement is essential for its high thermostability. In contrast to form I RuBisCO, the form III RuBisCO is composed solely of large subunits.3 Publications

    Protein-protein interaction databases

    IntActiO93627. 1 interaction.
    MINTiMINT-8377356.
    STRINGi69014.TK2290.

    Structurei

    Secondary structure

    1
    444
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi10 – 123
    Turni21 – 233
    Beta strandi24 – 3310
    Helixi39 – 4911
    Turni50 – 523
    Helixi64 – 707
    Beta strandi73 – 797
    Beta strandi81 – 833
    Beta strandi85 – 928
    Helixi93 – 953
    Helixi101 – 1088
    Helixi111 – 1144
    Beta strandi118 – 12710
    Helixi130 – 1334
    Helixi142 – 1509
    Beta strandi157 – 1604
    Beta strandi163 – 1664
    Helixi170 – 18213
    Beta strandi187 – 1893
    Helixi202 – 22019
    Beta strandi225 – 2295
    Helixi234 – 24714
    Beta strandi251 – 2555
    Helixi256 – 2594
    Helixi261 – 27414
    Beta strandi277 – 2815
    Turni283 – 2853
    Helixi286 – 2894
    Beta strandi294 – 2963
    Helixi298 – 30811
    Beta strandi311 – 3144
    Beta strandi320 – 3234
    Helixi327 – 33812
    Beta strandi340 – 3423
    Beta strandi363 – 3697
    Helixi372 – 3743
    Helixi376 – 3827
    Beta strandi384 – 3896
    Helixi392 – 3954
    Helixi401 – 41515
    Helixi421 – 4255
    Helixi429 – 43810

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1GEHX-ray2.80A/B/C/D/E1-444[»]
    3A12X-ray2.30A/B/C/D/E/F/G/H/I/J1-444[»]
    3A13X-ray2.34A/B/C/D/E/F/G/H/I/J1-444[»]
    3KDNX-ray2.09A/B/C/D/E/F/G/H/I/J1-444[»]
    3KDOX-ray2.36A/B/C/D/E/F/G/H/I/J1-444[»]
    ProteinModelPortaliO93627.
    SMRiO93627. Positions 12-443.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiO93627.

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni367 – 3693Substrate bindingCurated
    Regioni389 – 3924Substrate bindingCurated

    Sequence similaritiesi

    Belongs to the RuBisCO large chain family. Type III subfamily.UniRule annotation

    Phylogenomic databases

    eggNOGiCOG1850.
    HOGENOMiHOG000230831.
    KOiK01601.

    Family and domain databases

    Gene3Di3.20.20.110. 1 hit.
    3.30.70.150. 1 hit.
    HAMAPiMF_01133. RuBisCO_L_type3.
    InterProiIPR017712. RuBisCO_III.
    IPR000685. RuBisCO_lsu_C.
    IPR017443. RuBisCO_lsu_fd_N.
    IPR017444. RuBisCO_lsu_N.
    [Graphical view]
    PfamiPF00016. RuBisCO_large. 1 hit.
    PF02788. RuBisCO_large_N. 1 hit.
    [Graphical view]
    SUPFAMiSSF51649. SSF51649. 1 hit.
    SSF54966. SSF54966. 1 hit.
    TIGRFAMsiTIGR03326. rubisco_III. 1 hit.

    Sequencei

    Sequence statusi: Complete.

    Sequence processingi: The displayed sequence is further processed into a mature form.

    O93627-1 [UniParc]FASTAAdd to Basket

    « Hide

    MVEKFDTIYD YYVDKGYEPS KKRDIIAVFR VTPAEGYTIE QAAGAVAAES    50
    STGTWTTLYP WYEQERWADL SAKAYDFHDM GDGSWIVRIA YPFHAFEEAN 100
    LPGLLASIAG NIFGMKRVKG LRLEDLYFPE KLIREFDGPA FGIEGVRKML 150
    EIKDRPIYGV VPKPKVGYSP EEFEKLAYDL LSNGADYMKD DENLTSPWYN 200
    RFEERAEIMA KIIDKVENET GEKKTWFANI TADLLEMEQR LEVLADLGLK 250
    HAMVDVVITG WGALRYIRDL AADYGLAIHG HRAMHAAFTR NPYHGISMFV 300
    LAKLYRLIGI DQLHVGTAGA GKLEGGKWDV IQNARILRES HYKPDENDVF 350
    HLEQKFYSIK AAFPTSSGGL HPGNIQPVIE ALGTDIVLQL GGGTLGHPDG 400
    PAAGARAVRQ AIDAIMQGIP LDEYAKTHKE LARALEKWGH VTPV 444
    Length:444
    Mass (Da):49,713
    Last modified:January 23, 2007 - v5
    Checksum:i6E3AFF37367DD7FE
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AB018555 Genomic DNA. Translation: BAA33863.1.
    AP006878 Genomic DNA. Translation: BAD86479.1.
    RefSeqiYP_184703.1. NC_006624.1.

    Genome annotation databases

    EnsemblBacteriaiBAD86479; BAD86479; TK2290.
    GeneIDi3234791.
    KEGGitko:TK2290.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AB018555 Genomic DNA. Translation: BAA33863.1 .
    AP006878 Genomic DNA. Translation: BAD86479.1 .
    RefSeqi YP_184703.1. NC_006624.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1GEH X-ray 2.80 A/B/C/D/E 1-444 [» ]
    3A12 X-ray 2.30 A/B/C/D/E/F/G/H/I/J 1-444 [» ]
    3A13 X-ray 2.34 A/B/C/D/E/F/G/H/I/J 1-444 [» ]
    3KDN X-ray 2.09 A/B/C/D/E/F/G/H/I/J 1-444 [» ]
    3KDO X-ray 2.36 A/B/C/D/E/F/G/H/I/J 1-444 [» ]
    ProteinModelPortali O93627.
    SMRi O93627. Positions 12-443.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    IntActi O93627. 1 interaction.
    MINTi MINT-8377356.
    STRINGi 69014.TK2290.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai BAD86479 ; BAD86479 ; TK2290 .
    GeneIDi 3234791.
    KEGGi tko:TK2290.

    Phylogenomic databases

    eggNOGi COG1850.
    HOGENOMi HOG000230831.
    KOi K01601.

    Enzyme and pathway databases

    BioCyci MetaCyc:MONOMER-13272.
    TKOD69014:GH72-2342-MONOMER.

    Miscellaneous databases

    EvolutionaryTracei O93627.

    Family and domain databases

    Gene3Di 3.20.20.110. 1 hit.
    3.30.70.150. 1 hit.
    HAMAPi MF_01133. RuBisCO_L_type3.
    InterProi IPR017712. RuBisCO_III.
    IPR000685. RuBisCO_lsu_C.
    IPR017443. RuBisCO_lsu_fd_N.
    IPR017444. RuBisCO_lsu_N.
    [Graphical view ]
    Pfami PF00016. RuBisCO_large. 1 hit.
    PF02788. RuBisCO_large_N. 1 hit.
    [Graphical view ]
    SUPFAMi SSF51649. SSF51649. 1 hit.
    SSF54966. SSF54966. 1 hit.
    TIGRFAMsi TIGR03326. rubisco_III. 1 hit.
    ProtoNeti Search...

    Publicationsi

    1. "Presence of a structurally novel type ribulose-bisphosphate carboxylase/oxygenase in the hyperthermophilic archaeon, Pyrococcus kodakaraensis KOD1."
      Ezaki S., Maeda N., Kishimoto T., Atomi H., Imanaka T.
      J. Biol. Chem. 274:5078-5082(1999) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 2-12, FUNCTION, CATALYTIC ACTIVITY.
      Strain: ATCC BAA-918 / JCM 12380 / KOD1.
    2. "Complete genome sequence of the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1 and comparison with Pyrococcus genomes."
      Fukui T., Atomi H., Kanai T., Matsumi R., Fujiwara S., Imanaka T.
      Genome Res. 15:352-363(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: ATCC BAA-918 / JCM 12380 / KOD1.
    3. "Ribulose bisphosphate carboxylase/oxygenase from the hyperthermophilic archaeon Pyrococcus kodakaraensis KOD1 is composed solely of large subunits and forms a pentagonal structure."
      Maeda N., Kitano K., Fukui T., Ezaki S., Atomi H., Miki K., Imanaka T.
      J. Mol. Biol. 293:57-66(1999) [PubMed] [Europe PMC] [Abstract]
      Cited for: PROTEIN SEQUENCE OF 2-12, CHARACTERIZATION, CRYSTALLIZATION.
      Strain: ATCC BAA-918 / JCM 12380 / KOD1.
    4. "The unique pentagonal structure of an archaeal Rubisco is essential for its high thermostability."
      Maeda N., Kanai T., Atomi H., Imanaka T.
      J. Biol. Chem. 277:31656-31662(2002) [PubMed] [Europe PMC] [Abstract]
      Cited for: SUBUNIT, MUTAGENESIS OF GLU-63; ARG-66 AND ASP-69.
      Strain: ATCC BAA-918 / JCM 12380 / KOD1.
    5. "Archaeal type III RuBisCOs function in a pathway for AMP metabolism."
      Sato T., Atomi H., Imanaka T.
      Science 315:1003-1006(2007) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, CATALYTIC ACTIVITY, DISRUPTION PHENOTYPE, PATHWAY.
      Strain: ATCC BAA-918 / JCM 12380 / KOD1.
    6. "Enzymatic characterization of AMP phosphorylase and ribose-1,5-bisphosphate isomerase functioning in an archaeal AMP metabolic pathway."
      Aono R., Sato T., Yano A., Yoshida S., Nishitani Y., Miki K., Imanaka T., Atomi H.
      J. Bacteriol. 194:6847-6855(2012) [PubMed] [Europe PMC] [Abstract]
      Cited for: INDUCTION, PATHWAY.
      Strain: ATCC BAA-918 / JCM 12380 / KOD1.
    7. "Crystal structure of a novel-type archaeal rubisco with pentagonal symmetry."
      Kitano K., Maeda N., Fukui T., Atomi H., Imanaka T., Miki K.
      Structure 9:473-481(2001) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS), COFACTOR, SUBUNIT.
      Strain: ATCC BAA-918 / JCM 12380 / KOD1.
    8. "Structure-based catalytic optimization of a type III Rubisco from a hyperthermophile."
      Nishitani Y., Yoshida S., Fujihashi M., Kitagawa K., Doi T., Atomi H., Imanaka T., Miki K.
      J. Biol. Chem. 285:39339-39347(2010) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.09 ANGSTROMS) OF WILD-TYPE AND MUTANTS IN COMPLEX WITH INHIBITOR AND MAGNESIUM, FUNCTION, COFACTOR, TEMPERATURE DEPENDENCE, CARBAMYLATION AT LYS-189.
      Strain: ATCC BAA-918 / JCM 12380 / KOD1.

    Entry informationi

    Entry nameiRBL_THEKO
    AccessioniPrimary (citable) accession number: O93627
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: September 26, 2003
    Last sequence update: January 23, 2007
    Last modified: October 1, 2014
    This is version 109 of the entry and version 5 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    Because the Archaea possessing a type III RuBisCO are all anaerobic, it is most likely that only the carboxylase activity of RuBisCO, and not the competitive oxygenase activity (by which RuBP reacts with O2 to form one molecule of 3-phosphoglycerate and one molecule of 2-phosphoglycolate), is biologically relevant in these strains.1 Publication

    Keywords - Technical termi

    3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

    Documents

    1. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    2. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3