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Q60028 (RBL2_THIDA) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 93. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (1) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Ribulose bisphosphate carboxylase

Short name=RuBisCO
EC=4.1.1.39
Gene names
Name:cbbM
Synonyms:cbbL2
Ordered Locus Names:Tbd_2638
OrganismThiobacillus denitrificans (strain ATCC 25259) [Complete proteome] [HAMAP]
Taxonomic identifier292415 [NCBI]
Taxonomic lineageBacteriaProteobacteriaBetaproteobacteriaHydrogenophilalesHydrogenophilaceaeThiobacillus

Protein attributes

Sequence length459 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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. Ref.1

Catalytic activity

2 3-phospho-D-glycerate + 2 H+ = D-ribulose 1,5-bisphosphate + CO2 + H2O. HAMAP-Rule MF_01339

3-phospho-D-glycerate + 2-phosphoglycolate = D-ribulose 1,5-bisphosphate + O2. HAMAP-Rule MF_01339

Cofactor

Binds 1 magnesium ion per subunit By similarity. HAMAP-Rule MF_01339

Subunit structure

The complex is approximately 350 kDa when isolated from either T.denitrificans or R.sphaeroides, suggesting a homohexamer or homooctamer structure. Ref.4

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.

Sequence similarities

Belongs to the RuBisCO large chain family. Type II subfamily.

Biophysicochemical properties

Kinetic parameters:

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

KM=13.3 µM for ribulose 1,5-bisphosphate Ref.1

KM=256 µM for CO2

KM=619 µM for O2

Vmax=3.3 µmol/min/mg enzyme with CO2 as substrate

Vmax=0.6 µmol/min/mg enzyme with O2 as substrate

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 459459Ribulose bisphosphate carboxylase HAMAP-Rule MF_01339
PRO_0000062668

Sites

Active site1661Proton acceptor By similarity
Active site2871Proton acceptor By similarity
Metal binding1911Magnesium; via carbamate group By similarity
Metal binding1931Magnesium By similarity
Metal binding1941Magnesium By similarity
Binding site1111Substrate; in homodimeric partner By similarity
Binding site1681Substrate By similarity
Binding site2881Substrate By similarity
Binding site3211Substrate By similarity
Binding site3681Substrate By similarity
Site3291Transition state stabilizer By similarity

Amino acid modifications

Modified residue1911N6-carboxylysine By similarity

Experimental info

Sequence conflict4591K → S in AAA99178. Ref.1

Sequences

Sequence LengthMass (Da)Tools
Q60028 [UniParc].

Last modified December 20, 2005. Version 3.
Checksum: 4E080DCFDEA4266D

FASTA45950,690
        10         20         30         40         50         60 
MDQSARYADL SLKEEDLIKG GRHILVAYKM KPKSGYGYLE AAAHFAAESS TGTNVEVSTT 

        70         80         90        100        110        120 
DDFTKGVDAL VYYIDEASED MRIAYPLELF DRNVTDGRFM LVSFLTLAIG NNQGMGDIEH 

       130        140        150        160        170        180 
AKMIDFYVPE RCIQMFDGPA TDISNLWRIL GRPVVNGGYI AGTIIKPKLG LRPEPFAKAA 

       190        200        210        220        230        240 
YQFWLGGDFI KNDEPQGNQV FCPLKKVLPL VYDAMKRAQD DTGQAKLFSM NITADDHYEM 

       250        260        270        280        290        300 
CARADYALEV FGPDADKLAF LVDGYVGGPG MVTTARRQYP GQYLHYHRAG HGAVTSPSAK 

       310        320        330        340        350        360 
RGYTAFVLAK MSRLQGASGI HVGTMGYGKM EGEGDDKIIA YMIERDECQG PVYFQKWYGM 

       370        380        390        400        410        420 
KPTTPIISGG MNALRLPGFF ENLGHGNVIN TAGGGSYGHI DSPAAGAISL RQSYECWKQG 

       430        440        450 
ADPIEFAKEH KEFARAFESF PKDADKLFPG WREKLGVHK 

« Hide

References

« Hide 'large scale' references
[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.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
L37437 Genomic DNA. Translation: AAA99178.2.
CP000116 Genomic DNA. Translation: AAZ98591.1.
RefSeqYP_316396.1. NC_007404.1.

3D structure databases

ProteinModelPortalQ60028.
SMRQ60028. Positions 2-457.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

STRING292415.Tbd_2638.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaAAZ98591; AAZ98591; Tbd_2638.
GeneID3672367.
KEGGtbd:Tbd_2638.
PATRIC23971473. VBIThiDen82923_2623.

Organism-specific databases

CMRSearch...

Phylogenomic databases

eggNOGCOG1850.
HOGENOMHOG000230831.
KOK01601.
OMANQYLHYH.
OrthoDBEOG66QKT8.
ProtClustDBPRK13475.

Enzyme and pathway databases

BioCycTDEN292415:GHWG-2688-MONOMER.

Family and domain databases

Gene3D3.20.20.110. 1 hit.
3.30.70.150. 1 hit.
HAMAPMF_01339. RuBisCO_L_type2.
InterProIPR020871. RuBisCO.
IPR020878. RuBisCo_large_chain_AS.
IPR000685. RuBisCO_lsu_C.
IPR017443. RuBisCO_lsu_fd_N.
IPR017444. RuBisCO_lsu_N.
[Graphical view]
PfamPF00016. RuBisCO_large. 1 hit.
PF02788. RuBisCO_large_N. 1 hit.
[Graphical view]
SUPFAMSSF51649. SSF51649. 1 hit.
SSF54966. SSF54966. 1 hit.
PROSITEPS00157. RUBISCO_LARGE. 1 hit.
[Graphical view]
ProtoNetSearch...

Entry information

Entry nameRBL2_THIDA
AccessionPrimary (citable) accession number: Q60028
Secondary accession number(s): Q3SFL5
Entry history
Integrated into UniProtKB/Swiss-Prot: July 15, 1998
Last sequence update: December 20, 2005
Last modified: April 16, 2014
This is version 93 of the entry and version 3 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families