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Q60028

- RBL2_THIDA

UniProt

Q60028 - RBL2_THIDA

Protein

Ribulose bisphosphate carboxylase

Gene

cbbM

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 95 (01 Oct 2014)
      Sequence version 3 (20 Dec 2005)
      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 Publication

    Catalytic activityi

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

    Cofactori

    Binds 1 magnesium ion per subunit.By similarity

    Kineticsi

    The CO2/O2 specificity factor (tau) is 14.

    1. KM=13.3 µM for ribulose 1,5-bisphosphate1 Publication
    2. KM=256 µM for CO21 Publication
    3. KM=619 µM for O21 Publication

    Vmax=3.3 µmol/min/mg enzyme with CO2 as substrate1 Publication

    Vmax=0.6 µmol/min/mg enzyme with O2 as substrate1 Publication

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei111 – 1111Substrate; in homodimeric partnerBy similarity
    Active sitei166 – 1661Proton acceptorBy similarity
    Binding sitei168 – 1681SubstrateBy similarity
    Metal bindingi191 – 1911Magnesium; via carbamate groupBy similarity
    Metal bindingi193 – 1931MagnesiumBy similarity
    Metal bindingi194 – 1941MagnesiumBy similarity
    Active sitei287 – 2871Proton acceptorBy similarity
    Binding sitei288 – 2881SubstrateBy similarity
    Binding sitei321 – 3211SubstrateBy similarity
    Sitei329 – 3291Transition state stabilizerBy similarity
    Binding sitei368 – 3681SubstrateBy similarity

    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-2688-MONOMER.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Ribulose bisphosphate carboxylase (EC:4.1.1.39)
    Short name:
    RuBisCO
    Gene namesi
    Name:cbbM
    Synonyms:cbbL2
    Ordered Locus Names:Tbd_2638
    OrganismiThiobacillus denitrificans (strain ATCC 25259)
    Taxonomic identifieri292415 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaBetaproteobacteriaHydrogenophilalesHydrogenophilaceaeThiobacillus
    ProteomesiUP000008291: Chromosome

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 459459Ribulose bisphosphate carboxylasePRO_0000062668Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei191 – 1911N6-carboxylysineBy similarity

    Interactioni

    Subunit structurei

    The complex is approximately 350 kDa when isolated from either T.denitrificans or R.sphaeroides, suggesting a homohexamer or homooctamer structure.1 Publication

    Protein-protein interaction databases

    STRINGi292415.Tbd_2638.

    Structurei

    3D structure databases

    ProteinModelPortaliQ60028.
    SMRiQ60028. Positions 2-457.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Sequence similaritiesi

    Phylogenomic databases

    eggNOGiCOG1850.
    HOGENOMiHOG000230831.
    KOiK01601.
    OMAiAKEHREF.
    OrthoDBiEOG66QKT8.

    Family and domain databases

    Gene3Di3.20.20.110. 1 hit.
    3.30.70.150. 1 hit.
    HAMAPiMF_01339. RuBisCO_L_type2.
    InterProiIPR020871. RuBisCO.
    IPR020878. RuBisCo_large_chain_AS.
    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.

    Q60028-1 [UniParc]FASTAAdd to Basket

    « Hide

    MDQSARYADL SLKEEDLIKG GRHILVAYKM KPKSGYGYLE AAAHFAAESS    50
    TGTNVEVSTT DDFTKGVDAL VYYIDEASED MRIAYPLELF DRNVTDGRFM 100
    LVSFLTLAIG NNQGMGDIEH AKMIDFYVPE RCIQMFDGPA TDISNLWRIL 150
    GRPVVNGGYI AGTIIKPKLG LRPEPFAKAA YQFWLGGDFI KNDEPQGNQV 200
    FCPLKKVLPL VYDAMKRAQD DTGQAKLFSM NITADDHYEM CARADYALEV 250
    FGPDADKLAF LVDGYVGGPG MVTTARRQYP GQYLHYHRAG HGAVTSPSAK 300
    RGYTAFVLAK MSRLQGASGI HVGTMGYGKM EGEGDDKIIA YMIERDECQG 350
    PVYFQKWYGM KPTTPIISGG MNALRLPGFF ENLGHGNVIN TAGGGSYGHI 400
    DSPAAGAISL RQSYECWKQG ADPIEFAKEH KEFARAFESF PKDADKLFPG 450
    WREKLGVHK 459
    Length:459
    Mass (Da):50,690
    Last modified:December 20, 2005 - v3
    Checksum:i4E080DCFDEA4266D
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti459 – 4591K → S in AAA99178. (PubMed:8550452)Curated

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    L37437 Genomic DNA. Translation: AAA99178.2.
    CP000116 Genomic DNA. Translation: AAZ98591.1.
    RefSeqiYP_316396.1. NC_007404.1.

    Genome annotation databases

    EnsemblBacteriaiAAZ98591; AAZ98591; Tbd_2638.
    GeneIDi3672367.
    KEGGitbd:Tbd_2638.
    PATRICi23971473. VBIThiDen82923_2623.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    L37437 Genomic DNA. Translation: AAA99178.2 .
    CP000116 Genomic DNA. Translation: AAZ98591.1 .
    RefSeqi YP_316396.1. NC_007404.1.

    3D structure databases

    ProteinModelPortali Q60028.
    SMRi Q60028. Positions 2-457.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 292415.Tbd_2638.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai AAZ98591 ; AAZ98591 ; Tbd_2638 .
    GeneIDi 3672367.
    KEGGi tbd:Tbd_2638.
    PATRICi 23971473. VBIThiDen82923_2623.

    Phylogenomic databases

    eggNOGi COG1850.
    HOGENOMi HOG000230831.
    KOi K01601.
    OMAi AKEHREF.
    OrthoDBi EOG66QKT8.

    Enzyme and pathway databases

    BioCyci TDEN292415:GHWG-2688-MONOMER.

    Family and domain databases

    Gene3Di 3.20.20.110. 1 hit.
    3.30.70.150. 1 hit.
    HAMAPi MF_01339. RuBisCO_L_type2.
    InterProi IPR020871. RuBisCO.
    IPR020878. RuBisCo_large_chain_AS.
    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.
    2. Shively J.M.
      Submitted (SEP-2000) to the EMBL/GenBank/DDBJ databases
      Cited for: SEQUENCE REVISION TO 83 AND C-TERMINUS.
    3. "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.
    4. "Ribulose diphosphate carboxylase from autotrophic microorganisms."
      McFadden B.A., Denend A.R.
      J. Bacteriol. 110:633-642(1972) [PubMed] [Europe PMC] [Abstract]
      Cited for: SUBUNIT.

    Entry informationi

    Entry nameiRBL2_THIDA
    AccessioniPrimary (citable) accession number: Q60028
    Secondary accession number(s): Q3SFL5
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: July 15, 1998
    Last sequence update: December 20, 2005
    Last modified: October 1, 2014
    This is version 95 of the entry and version 3 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 contrast to form I RuBisCO, the form II RuBisCO are composed solely of large subunits By similarity.By similarity

    Keywords - Technical termi

    Complete proteome, Reference proteome

    Documents

    1. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3