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O58677

- RBL_PYRHO

UniProt

O58677 - RBL_PYRHO

Protein

Ribulose bisphosphate carboxylase

Gene

rbcL

Organism
Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)
Status
Reviewed - Annotation score: 3 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 100 (01 Oct 2014)
      Sequence version 1 (01 Aug 1998)
      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.UniRule 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.UniRule annotation

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Active sitei160 – 1601Proton acceptorUniRule annotation
    Binding sitei162 – 1621SubstrateUniRule annotation
    Metal bindingi186 – 1861Magnesium; via carbamate groupUniRule annotation
    Metal bindingi188 – 1881MagnesiumUniRule annotation
    Metal bindingi189 – 1891MagnesiumUniRule annotation
    Active sitei278 – 2781Proton acceptorUniRule annotation
    Binding sitei279 – 2791SubstrateUniRule annotation
    Binding sitei311 – 3111SubstrateUniRule annotation
    Sitei318 – 3181Transition 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

    BioCyciPHOR70601:GJWR-933-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
    Ordered Locus Names:PH0939
    OrganismiPyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)
    Taxonomic identifieri70601 [NCBI]
    Taxonomic lineageiArchaeaEuryarchaeotaThermococciThermococcalesThermococcaceaePyrococcus
    ProteomesiUP000000752: Chromosome

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 430430Ribulose bisphosphate carboxylasePRO_0000062677Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei186 – 1861N6-carboxylysineUniRule annotation

    Interactioni

    Subunit structurei

    Homodimer or homodecamer. In contrast to form I RuBisCO, the form III RuBisCO is composed solely of large subunits.UniRule annotation

    Protein-protein interaction databases

    STRINGi70601.PH0939.

    Structurei

    Secondary structure

    1
    430
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi7 – 93
    Helixi11 – 144
    Beta strandi25 – 3713
    Helixi39 – 4911
    Turni50 – 523
    Beta strandi55 – 595
    Helixi63 – 653
    Helixi66 – 683
    Beta strandi71 – 788
    Beta strandi81 – 888
    Helixi90 – 923
    Helixi98 – 1058
    Helixi108 – 1114
    Beta strandi115 – 12410
    Helixi127 – 1304
    Helixi139 – 1479
    Beta strandi150 – 1523
    Beta strandi154 – 1574
    Beta strandi160 – 1634
    Helixi167 – 17913
    Beta strandi183 – 1864
    Helixi199 – 21719
    Beta strandi222 – 2243
    Helixi231 – 24313
    Beta strandi248 – 2525
    Helixi253 – 2564
    Helixi258 – 27114
    Beta strandi274 – 2785
    Turni280 – 2823
    Helixi283 – 2864
    Beta strandi291 – 2933
    Helixi295 – 30511
    Beta strandi308 – 3114
    Beta strandi317 – 3193
    Helixi323 – 33412
    Beta strandi344 – 3507
    Helixi353 – 3553
    Helixi356 – 3638
    Beta strandi368 – 3703
    Helixi372 – 3765
    Helixi382 – 39817
    Helixi402 – 4054
    Turni406 – 4083
    Helixi410 – 42213

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    2CWXX-ray2.00A/E1-430[»]
    2CXEX-ray3.00A/B/C/D1-430[»]
    2D69X-ray1.90A/B/D/E1-430[»]
    ProteinModelPortaliO58677.
    SMRiO58677. Positions 1-423.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiO58677.

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni348 – 3503Substrate bindingUniRule annotation
    Regioni370 – 3734Substrate bindingUniRule annotation

    Sequence similaritiesi

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

    Phylogenomic databases

    eggNOGiCOG1850.
    HOGENOMiHOG000230831.
    KOiK01601.
    OMAiCTPLKQA.

    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.

    O58677-1 [UniParc]FASTAAdd to Basket

    « Hide

    MMVLRMKVEW YLDFVDLNYE PGRDELIVEY YFEPNGVSPE EAAGRIASES    50
    SIGTWTTLWK LPEMAKRSMA KVFYLEKHGE GYIAKIAYPL TLFEEGSLVQ 100
    LFSAVAGNVF GMKALKNLRL LDFHPPYEYL RHFKGPQFGV QGIREFMGVK 150
    DRPLTATVPK PKMGWSVEEY AEIAYELWSG GIDLLKDDEN FTSFPFNRFE 200
    ERVRKLYRVR DRVEAETGET KEYLINITGP VNIMEKRAEM VANEGGQYVM 250
    IDIVVAGWSA LQYMREVTED LGLAIHAHRA MHAAFTRNPR HGITMLALAK 300
    AARMIGVDQI HTGTAVGKMA GNYEEIKRIN DFLLSKWEHI RPVFPVASGG 350
    LHPGLMPELI RLFGKDLVIQ AGGGVMGHPD GPRAGAKALR DAIDAAIEGV 400
    DLDEKAKSSP ELKKSLREVG LSKAKVGVQH 430
    Length:430
    Mass (Da):48,247
    Last modified:August 1, 1998 - v1
    Checksum:i1068CA138F019AD9
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    BA000001 Genomic DNA. Translation: BAA30036.1.
    PIRiF71084.
    RefSeqiNP_142861.1. NC_000961.1.
    WP_010885029.1. NC_000961.1.

    Genome annotation databases

    EnsemblBacteriaiBAA30036; BAA30036; BAA30036.
    GeneIDi1443264.
    KEGGipho:PH0939.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    BA000001 Genomic DNA. Translation: BAA30036.1 .
    PIRi F71084.
    RefSeqi NP_142861.1. NC_000961.1.
    WP_010885029.1. NC_000961.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    2CWX X-ray 2.00 A/E 1-430 [» ]
    2CXE X-ray 3.00 A/B/C/D 1-430 [» ]
    2D69 X-ray 1.90 A/B/D/E 1-430 [» ]
    ProteinModelPortali O58677.
    SMRi O58677. Positions 1-423.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 70601.PH0939.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai BAA30036 ; BAA30036 ; BAA30036 .
    GeneIDi 1443264.
    KEGGi pho:PH0939.

    Phylogenomic databases

    eggNOGi COG1850.
    HOGENOMi HOG000230831.
    KOi K01601.
    OMAi CTPLKQA.

    Enzyme and pathway databases

    BioCyci PHOR70601:GJWR-933-MONOMER.

    Miscellaneous databases

    EvolutionaryTracei O58677.

    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. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3.
    2. "Crystal structure of octameric ribulose-1,5-bisphosphate carboxylase/oxygenase (rubisco) from Pyrococcus horikoshii OT3 (form-1 crystal)."
      RIKEN structural genomics initiative (RSGI)
      Submitted (DEC-2005) to the PDB data bank
      Cited for: X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS).

    Entry informationi

    Entry nameiRBL_PYRHO
    AccessioniPrimary (citable) accession number: O58677
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: September 26, 2003
    Last sequence update: August 1, 1998
    Last modified: October 1, 2014
    This is version 100 of the entry and version 1 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.UniRule annotation

    Keywords - Technical termi

    3D-structure, Complete 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