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O58677 (RBL_PYRHO) Reviewed, UniProtKB/Swiss-Prot

Last modified May 14, 2014. Version 98. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (2) | 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:rbcL
Ordered Locus Names:PH0939
OrganismPyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3) [Complete proteome] [HAMAP]
Taxonomic identifier70601 [NCBI]
Taxonomic lineageArchaeaEuryarchaeotaThermococciThermococcalesThermococcaceaePyrococcus

Protein attributes

Sequence length430 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Catalyzes the addition of molecular CO2 and H2O to ribulose 1,5-bisphosphate (RuBP), generating two molecules of 3-phosphoglycerate (3-PGA). Functions in an archaeal AMP degradation pathway, together with AMP phosphorylase and R15P isomerase By similarity. HAMAP-Rule MF_01133

Catalytic activity

2 3-phospho-D-glycerate + 2 H+ = D-ribulose 1,5-bisphosphate + CO2 + H2O. HAMAP-Rule MF_01133

3-phospho-D-glycerate + 2-phosphoglycolate = D-ribulose 1,5-bisphosphate + O2. HAMAP-Rule MF_01133

Cofactor

Binds 1 magnesium ion per subunit By similarity. HAMAP-Rule MF_01133

Subunit structure

Homodimer or homodecamer. In contrast to form I RuBisCO, the form III RuBisCO is composed solely of large subunits By similarity.

Miscellaneous

Because the Archaea possessing a type III RuBisCO are all anaerobic, it is most likely that only the carboxylase activity of RuBisCO, and not the competitive oxygenase activity (by which RuBP reacts with O2 to form one molecule of 3-phosphoglycerate and one molecule of 2-phosphoglycolate), is biologically relevant in these strains (PubMed:17303759).

Sequence similarities

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

Ontologies

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 430430Ribulose bisphosphate carboxylase HAMAP-Rule MF_01133
PRO_0000062677

Regions

Region348 – 3503Substrate binding By similarity
Region370 – 3734Substrate binding By similarity

Sites

Active site1601Proton acceptor By similarity
Active site2781Proton acceptor By similarity
Metal binding1861Magnesium; via carbamate group By similarity
Metal binding1881Magnesium By similarity
Metal binding1891Magnesium By similarity
Binding site1621Substrate By similarity
Binding site2791Substrate By similarity
Binding site3111Substrate By similarity
Site3181Transition state stabilizer By similarity

Amino acid modifications

Modified residue1861N6-carboxylysine By similarity

Secondary structure

................................................................................... 430
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
O58677 [UniParc].

Last modified August 1, 1998. Version 1.
Checksum: 1068CA138F019AD9

FASTA43048,247
        10         20         30         40         50         60 
MMVLRMKVEW YLDFVDLNYE PGRDELIVEY YFEPNGVSPE EAAGRIASES SIGTWTTLWK 

        70         80         90        100        110        120 
LPEMAKRSMA KVFYLEKHGE GYIAKIAYPL TLFEEGSLVQ LFSAVAGNVF GMKALKNLRL 

       130        140        150        160        170        180 
LDFHPPYEYL RHFKGPQFGV QGIREFMGVK DRPLTATVPK PKMGWSVEEY AEIAYELWSG 

       190        200        210        220        230        240 
GIDLLKDDEN FTSFPFNRFE ERVRKLYRVR DRVEAETGET KEYLINITGP VNIMEKRAEM 

       250        260        270        280        290        300 
VANEGGQYVM IDIVVAGWSA LQYMREVTED LGLAIHAHRA MHAAFTRNPR HGITMLALAK 

       310        320        330        340        350        360 
AARMIGVDQI HTGTAVGKMA GNYEEIKRIN DFLLSKWEHI RPVFPVASGG LHPGLMPELI 

       370        380        390        400        410        420 
RLFGKDLVIQ AGGGVMGHPD GPRAGAKALR DAIDAAIEGV DLDEKAKSSP ELKKSLREVG 

       430 
LSKAKVGVQH 

« Hide

References

« Hide 'large scale' references
[1]"Complete sequence and gene organization of the genome of a hyper-thermophilic archaebacterium, Pyrococcus horikoshii OT3."
Kawarabayasi Y., Sawada M., Horikawa H., Haikawa Y., Hino Y., Yamamoto S., Sekine M., Baba S., Kosugi H., Hosoyama A., Nagai Y., Sakai M., Ogura K., Otsuka R., Nakazawa H., Takamiya M., Ohfuku Y., Funahashi T. expand/collapse author list , Tanaka T., Kudoh Y., Yamazaki J., Kushida N., Oguchi A., Aoki K., Yoshizawa T., Nakamura Y., Robb F.T., Horikoshi K., Masuchi Y., Shizuya H., Kikuchi H.
DNA Res. 5:55-76(1998) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3.
[2]"Crystal structure of octameric ribulose-1,5-bisphosphate carboxylase/oxygenase (rubisco) from Pyrococcus horikoshii OT3 (form-1 crystal)."
RIKEN structural genomics initiative (RSGI)
Submitted (DEC-2005) to the PDB data bank
Cited for: X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS).

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
BA000001 Genomic DNA. Translation: BAA30036.1.
PIRF71084.
RefSeqNP_142861.1. NC_000961.1.

3D structure databases

PDBe
RCSB-PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
2CWXX-ray2.00A/E1-430[»]
2CXEX-ray3.00A/B/C/D1-430[»]
2D69X-ray1.90A/B/D/E1-430[»]
ProteinModelPortalO58677.
SMRO58677. Positions 1-423.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

STRING70601.PH0939.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaBAA30036; BAA30036; BAA30036.
GeneID1443264.
KEGGpho:PH0939.

Organism-specific databases

CMRSearch...

Phylogenomic databases

eggNOGCOG1850.
HOGENOMHOG000230831.
KOK01601.
OMACTPLKQA.

Enzyme and pathway databases

BioCycPHOR70601:GJWR-933-MONOMER.

Family and domain databases

Gene3D3.20.20.110. 1 hit.
3.30.70.150. 1 hit.
HAMAPMF_01133. RuBisCO_L_type3.
InterProIPR017712. RuBisCO_III.
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.
TIGRFAMsTIGR03326. rubisco_III. 1 hit.
ProtoNetSearch...

Other

EvolutionaryTraceO58677.

Entry information

Entry nameRBL_PYRHO
AccessionPrimary (citable) accession number: O58677
Entry history
Integrated into UniProtKB/Swiss-Prot: September 26, 2003
Last sequence update: August 1, 1998
Last modified: May 14, 2014
This is version 98 of the entry and version 1 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

PDB cross-references

Index of Protein Data Bank (PDB) cross-references