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Q56259

- RBL1_THIDA

UniProt

Q56259 - RBL1_THIDA

Protein

Ribulose bisphosphate carboxylase large chain

Gene

cbbL

Organism
Thiobacillus denitrificans (strain ATCC 25259)
Status
Reviewed - Annotation score: 4 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 94 (01 Oct 2014)
      Sequence version 2 (01 Jan 1998)
      Previous versions | rss
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    Functioni

    RuBisCO catalyzes two reactions: the carboxylation of D-ribulose 1,5-bisphosphate, the primary event in carbon dioxide fixation, as well as the oxidative fragmentation of the pentose substrate. Both reactions occur simultaneously and in competition at the same active site.1 PublicationUniRule 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

    Kineticsi

    The CO2/O2 specificity factor (tau) is 46.

    1. KM=43 µM for ribulose 1,5-bisphosphate1 Publication
    2. KM=138 µM for CO21 Publication
    3. KM=1637 µM for O21 Publication

    Vmax=1.8 µmol/min/mg enzyme with CO2 as substrate1 Publication

    Vmax=0.5 µmol/min/mg enzyme with O2 as substrate1 Publication

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei116 – 1161Substrate; in homodimeric partnerUniRule annotation
    Binding sitei166 – 1661SubstrateUniRule annotation
    Active sitei168 – 1681Proton acceptorUniRule annotation
    Binding sitei170 – 1701SubstrateUniRule annotation
    Metal bindingi194 – 1941Magnesium; via carbamate groupUniRule annotation
    Metal bindingi196 – 1961MagnesiumUniRule annotation
    Metal bindingi197 – 1971MagnesiumUniRule annotation
    Active sitei287 – 2871Proton acceptorUniRule annotation
    Binding sitei288 – 2881SubstrateUniRule annotation
    Binding sitei320 – 3201SubstrateUniRule annotation
    Sitei327 – 3271Transition state stabilizerUniRule annotation
    Binding sitei372 – 3721SubstrateUniRule annotation

    GO - Molecular functioni

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

    GO - Biological processi

    1. reductive pentose-phosphate cycle Source: UniProtKB-KW

    Keywords - Molecular functioni

    Lyase, Monooxygenase, Oxidoreductase

    Keywords - Biological processi

    Calvin cycle, Carbon dioxide fixation

    Keywords - Ligandi

    Magnesium, Metal-binding

    Enzyme and pathway databases

    BioCyciTDEN292415:GHWG-2674-MONOMER.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Ribulose bisphosphate carboxylase large chainUniRule annotation (EC:4.1.1.39UniRule annotation)
    Short name:
    RuBisCO large subunitUniRule annotation
    Gene namesi
    Name:cbbLUniRule annotation
    Synonyms:cbbL1
    Ordered Locus Names:Tbd_2624
    OrganismiThiobacillus denitrificans (strain ATCC 25259)
    Taxonomic identifieri292415 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaBetaproteobacteriaHydrogenophilalesHydrogenophilaceaeThiobacillus
    ProteomesiUP000008291: Chromosome

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 473473Ribulose bisphosphate carboxylase large chainPRO_0000062656Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei194 – 1941N6-carboxylysineUniRule annotation

    Interactioni

    Subunit structurei

    Heterohexadecamer of 8 large chains and 8 small chains By similarity. In R.sphaeroides the complex is approximately 500 kDa.1 PublicationUniRule annotation

    Protein-protein interaction databases

    STRINGi292415.Tbd_2624.

    Structurei

    3D structure databases

    ProteinModelPortaliQ56259.
    SMRiQ56259. Positions 16-460.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Sequence similaritiesi

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

    Phylogenomic databases

    eggNOGiCOG1850.
    HOGENOMiHOG000230831.
    KOiK01601.
    OMAiMETWKEV.
    OrthoDBiEOG6ZKXMS.

    Family and domain databases

    Gene3Di3.20.20.110. 1 hit.
    3.30.70.150. 1 hit.
    HAMAPiMF_01338. RuBisCO_L_type1.
    InterProiIPR020878. RuBisCo_large_chain_AS.
    IPR020888. RuBisCO_lsu.
    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.
    PROSITEiPS00157. RUBISCO_LARGE. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    Q56259-1 [UniParc]FASTAAdd to Basket

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    MAVKTYSAGV KEYRQTYWMP EYTPLDTDIL ACFKITPQAG VDREEAAAAV    50
    AAESSTGTWT TVWTDLLTDL DYYKGRAYAI EDVPGDDTCF YAFIAYPIDL 100
    FEEGSVVNVF TSLVGNVFGF KAVRALRLED VRFPIAYVKT CGGPPHGIQV 150
    ERDVMNKYGR PLLGCTIKPK LGLSAKNYGR AVYECLRGGL DFTKDDENVN 200
    SQPFMRWRQR FDFVMEAIQK SERETGERKG HYLNVTAPTP EEMYKRAEYA 250
    KEIGAPIIMH DYITGGFCAN TGLANWCRDN GMLLHIHRAM HAVLDRNPHH 300
    GIHFRVLTKI LRLSGGDHLH SGTVVGKLEG DREATLGWID MMRDSFVKED 350
    RSRGIFFDQD WGSMPGVFPV ASGGIHVWHM PALVTIFGDD SVLQFGGGTL 400
    GHPWGNAAGA AANRVALEAC VEARNKGVAI EKEGKTVLTE AAKNSPELKI 450
    AMETWKEIKF EFDTVDKLDV AHK 473
    Length:473
    Mass (Da):52,694
    Last modified:January 1, 1998 - v2
    Checksum:i470DC11519D580A7
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    L42940 Genomic DNA. Translation: AAB70697.1.
    CP000116 Genomic DNA. Translation: AAZ98577.1.
    RefSeqiWP_011313136.1. NC_007404.1.
    YP_316382.1. NC_007404.1.

    Genome annotation databases

    EnsemblBacteriaiAAZ98577; AAZ98577; Tbd_2624.
    GeneIDi3672353.
    KEGGitbd:Tbd_2624.
    PATRICi23971443. VBIThiDen82923_2608.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    L42940 Genomic DNA. Translation: AAB70697.1 .
    CP000116 Genomic DNA. Translation: AAZ98577.1 .
    RefSeqi WP_011313136.1. NC_007404.1.
    YP_316382.1. NC_007404.1.

    3D structure databases

    ProteinModelPortali Q56259.
    SMRi Q56259. Positions 16-460.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 292415.Tbd_2624.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai AAZ98577 ; AAZ98577 ; Tbd_2624 .
    GeneIDi 3672353.
    KEGGi tbd:Tbd_2624.
    PATRICi 23971443. VBIThiDen82923_2608.

    Phylogenomic databases

    eggNOGi COG1850.
    HOGENOMi HOG000230831.
    KOi K01601.
    OMAi METWKEV.
    OrthoDBi EOG6ZKXMS.

    Enzyme and pathway databases

    BioCyci TDEN292415:GHWG-2674-MONOMER.

    Family and domain databases

    Gene3Di 3.20.20.110. 1 hit.
    3.30.70.150. 1 hit.
    HAMAPi MF_01338. RuBisCO_L_type1.
    InterProi IPR020878. RuBisCo_large_chain_AS.
    IPR020888. RuBisCO_lsu.
    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.
    PROSITEi PS00157. RUBISCO_LARGE. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "Deduced amino acid sequence, functional expression, and unique enzymatic properties of the form I and form II ribulose bisphosphate carboxylase/oxygenase from the chemoautotrophic bacterium Thiobacillus denitrificans."
      Hernandez J.M., Baker S.H., Lorbach S.C., Shively J.M., Tabita F.R.
      J. Bacteriol. 178:347-356(1996) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], KINETIC PARAMETERS, FUNCTION, SUBUNIT.
    2. "The genome sequence of the obligately chemolithoautotrophic, facultatively anaerobic bacterium Thiobacillus denitrificans."
      Beller H.R., Chain P.S., Letain T.E., Chakicherla A., Larimer F.W., Richardson P.M., Coleman M.A., Wood A.P., Kelly D.P.
      J. Bacteriol. 188:1473-1488(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: ATCC 25259.

    Entry informationi

    Entry nameiRBL1_THIDA
    AccessioniPrimary (citable) accession number: Q56259
    Secondary accession number(s): Q3SFM9
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: July 15, 1998
    Last sequence update: January 1, 1998
    Last modified: October 1, 2014
    This is version 94 of the entry and version 2 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    The basic functional RuBisCO is composed of a large chain homodimer in a "head-to-tail" conformation. In form I RuBisCO this homodimer is arranged in a barrel-like tetramer with the small subunits forming a tetrameric "cap" on each end of the "barrel".UniRule annotation

    Keywords - Technical termi

    Complete proteome, Reference proteome

    Documents

    1. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3