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Q60028

- RBL2_THIDA

UniProt

Q60028 - RBL2_THIDA

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Protein

Ribulose bisphosphate carboxylase

Gene
cbbM, cbbL2, Tbd_2638
Organism
Thiobacillus denitrificans (strain ATCC 25259)
Status
Reviewed - 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.UniRule annotation
3-phospho-D-glycerate + 2-phosphoglycolate = D-ribulose 1,5-bisphosphate + O2.UniRule annotation

Cofactori

Binds 1 magnesium ion per subunit By similarity.UniRule annotation

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 CO2
  3. 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

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei111 – 1111Substrate; in homodimeric partner By similarity
Active sitei166 – 1661Proton acceptor By similarity
Binding sitei168 – 1681Substrate By similarity
Metal bindingi191 – 1911Magnesium; via carbamate group By similarity
Metal bindingi193 – 1931Magnesium By similarity
Metal bindingi194 – 1941Magnesium By similarity
Active sitei287 – 2871Proton acceptor By similarity
Binding sitei288 – 2881Substrate By similarity
Binding sitei321 – 3211Substrate By similarity
Sitei329 – 3291Transition state stabilizer By similarity
Binding sitei368 – 3681Substrate By 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
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: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 459459Ribulose bisphosphate carboxylaseUniRule annotationPRO_0000062668Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei191 – 1911N6-carboxylysine By 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.

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

Sequence conflict

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti459 – 4591K → S in AAA99178. 1 Publication

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

« 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: May 14, 2014
This is version 94 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.

Keywords - Technical termi

Complete proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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