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Protein

Ribulose bisphosphate carboxylase

Gene

cbbM

Organism
Thiobacillus denitrificans (strain ATCC 25259)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

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

Mg2+By similarityNote: Binds 1 Mg2+ 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
  1. Vmax=3.3 µmol/min/mg enzyme with CO2 as substrate1 Publication
  2. 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

GO - Biological processi

Complete GO annotation...

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 Componenti: 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.
OMAiNQYLHYH.
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

        10         20         30         40         50
MDQSARYADL SLKEEDLIKG GRHILVAYKM KPKSGYGYLE AAAHFAAESS
60 70 80 90 100
TGTNVEVSTT DDFTKGVDAL VYYIDEASED MRIAYPLELF DRNVTDGRFM
110 120 130 140 150
LVSFLTLAIG NNQGMGDIEH AKMIDFYVPE RCIQMFDGPA TDISNLWRIL
160 170 180 190 200
GRPVVNGGYI AGTIIKPKLG LRPEPFAKAA YQFWLGGDFI KNDEPQGNQV
210 220 230 240 250
FCPLKKVLPL VYDAMKRAQD DTGQAKLFSM NITADDHYEM CARADYALEV
260 270 280 290 300
FGPDADKLAF LVDGYVGGPG MVTTARRQYP GQYLHYHRAG HGAVTSPSAK
310 320 330 340 350
RGYTAFVLAK MSRLQGASGI HVGTMGYGKM EGEGDDKIIA YMIERDECQG
360 370 380 390 400
PVYFQKWYGM KPTTPIISGG MNALRLPGFF ENLGHGNVIN TAGGGSYGHI
410 420 430 440 450
DSPAAGAISL RQSYECWKQG ADPIEFAKEH KEFARAFESF PKDADKLFPG

WREKLGVHK
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:
EMBLi
GenBanki
DDBJi
Links Updated
L37437 Genomic DNA. Translation: AAA99178.2.
CP000116 Genomic DNA. Translation: AAZ98591.1.
RefSeqiWP_011313150.1. NC_007404.1.

Genome annotation databases

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

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L37437 Genomic DNA. Translation: AAA99178.2.
CP000116 Genomic DNA. Translation: AAZ98591.1.
RefSeqiWP_011313150.1. NC_007404.1.

3D structure databases

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

Protein-protein interaction databases

STRINGi292415.Tbd_2638.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

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

Phylogenomic databases

eggNOGiCOG1850.
HOGENOMiHOG000230831.
KOiK01601.
OMAiNQYLHYH.
OrthoDBiEOG66QKT8.

Enzyme and pathway databases

BioCyciTDEN292415:GHWG-2688-MONOMER.

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]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  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: July 22, 2015
This is version 101 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

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.