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Protein

Ribulose bisphosphate carboxylase

Gene

rbcL

Organism
Pyrococcus yayanosii (strain CH1 / JCM 16557)
Status
Unreviewed-Annotation score: Annotation score: 3 out of 5-Protein inferred from homologyi

Functioni

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.UniRule annotation

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

Mg2+UniRule annotationNote: Binds 1 Mg2+ ion per subunit.UniRule annotation

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Active sitei156 – 1561Proton acceptorUniRule annotation
Binding sitei158 – 1581SubstrateUniRule annotation
Metal bindingi182 – 1821Magnesium; via carbamate groupUniRule annotation
Metal bindingi184 – 1841MagnesiumUniRule annotation
Metal bindingi185 – 1851MagnesiumUniRule annotation
Active sitei274 – 2741Proton acceptorUniRule annotation
Binding sitei275 – 2751SubstrateUniRule annotation
Binding sitei307 – 3071SubstrateUniRule annotation
Sitei314 – 3141Transition state stabilizerUniRule annotation

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

LyaseUniRule annotation, OxidoreductaseUniRule annotation

Keywords - Biological processi

Carbon dioxide fixationUniRule annotation

Keywords - Ligandi

MagnesiumUniRule annotation, Metal-bindingUniRule annotation

Enzyme and pathway databases

BioCyciPYAY529709:GHZ0-9-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Ribulose bisphosphate carboxylaseUniRule annotation (EC:4.1.1.39UniRule annotation)
Short name:
RuBisCOUniRule annotation
Gene namesi
Name:rbcLUniRule annotation
Ordered Locus Names:PYCH_00090Imported
OrganismiPyrococcus yayanosii (strain CH1 / JCM 16557)Imported
Taxonomic identifieri529709 [NCBI]
Taxonomic lineageiArchaeaEuryarchaeotaThermococciThermococcalesThermococcaceaePyrococcus
ProteomesiUP000008386 Componenti: Chromosome

PTM / Processingi

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei182 – 1821N6-carboxylysineUniRule annotation

Interactioni

Subunit structurei

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

Protein-protein interaction databases

STRINGi529709.PYCH_00090.

Structurei

3D structure databases

ProteinModelPortaliF8AF48.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni344 – 3463Substrate bindingUniRule annotation
Regioni366 – 3694Substrate bindingUniRule annotation

Sequence similaritiesi

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

Phylogenomic databases

KOiK01601.
OMAiHAAFTRN.

Family and domain databases

Gene3Di3.20.20.110. 1 hit.
3.30.70.150. 1 hit.
HAMAPiMF_01133. RuBisCO_L_type3.
InterProiIPR017712. RuBisCO_III.
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.
TIGRFAMsiTIGR03326. rubisco_III. 1 hit.

Sequencei

Sequence statusi: Complete.

F8AF48-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSKVEWYLDF VDLDYTPGRD ELIVEYYFEP NGVSPEEAAG RIASESSIGT
60 70 80 90 100
WTTLWKLPDM AKRSMAKVFS LEKSGEGYIA KIAYPLTLFE EGNLVQLFSA
110 120 130 140 150
IAGNIFGMKA LKNLRLLDFH PPYEYLRHFK GPQYGVKGIR EFMGIEDRPL
160 170 180 190 200
TATVPKPKMG WSVDEYAEIA YELWSGGIDL LKDDENFTSF PFNRFEERVR
210 220 230 240 250
KLYAVRDRVE AETGETKEYL INITGPAHVM EKRAQLVAAE GGQYIMIDIV
260 270 280 290 300
VVGWSALQYM REVAEDLGLA IHAHRAMHAA FTRNPRHGIS MFVLAKAARM
310 320 330 340 350
VGVDQIHTGT AVGKMAGDYE EVKRINGFLL SEWEHIKPIF PVASGGLHPG
360 370 380 390 400
LMPELIRLFG RDLVIQVGGG VMGHPDGPRA GAKALRDAIE AAIEGVSLEE
410 420
KAKESPELKK ALEKWGYLKP K
Length:421
Mass (Da):47,126
Last modified:September 21, 2011 - v1
Checksum:iDC4D0153E37B1599
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP002779 Genomic DNA. Translation: AEH23722.1.
RefSeqiWP_013904780.1. NC_015680.1.
YP_004622994.1. NC_015680.1.

Genome annotation databases

EnsemblBacteriaiAEH23722; AEH23722; PYCH_00090.
GeneIDi10836592.
KEGGipya:PYCH_00090.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP002779 Genomic DNA. Translation: AEH23722.1.
RefSeqiWP_013904780.1. NC_015680.1.
YP_004622994.1. NC_015680.1.

3D structure databases

ProteinModelPortaliF8AF48.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi529709.PYCH_00090.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAEH23722; AEH23722; PYCH_00090.
GeneIDi10836592.
KEGGipya:PYCH_00090.

Phylogenomic databases

KOiK01601.
OMAiHAAFTRN.

Enzyme and pathway databases

BioCyciPYAY529709:GHZ0-9-MONOMER.

Family and domain databases

Gene3Di3.20.20.110. 1 hit.
3.30.70.150. 1 hit.
HAMAPiMF_01133. RuBisCO_L_type3.
InterProiIPR017712. RuBisCO_III.
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.
TIGRFAMsiTIGR03326. rubisco_III. 1 hit.
ProtoNetiSearch...

Publicationsi

  1. "Complete genome sequence of the obligate piezophilic hyperthermophilic archaeon Pyrococcus yayanosii CH1."
    Jun X., Lupeng L., Minjuan X., Oger P., Fengping W., Jebbar M., Xiang X.
    J. Bacteriol. 193:4297-4298(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: CH1 / JCM 16557Imported.

Entry informationi

Entry nameiF8AF48_PYRYC
AccessioniPrimary (citable) accession number: F8AF48
Entry historyi
Integrated into UniProtKB/TrEMBL: September 21, 2011
Last sequence update: September 21, 2011
Last modified: June 24, 2015
This is version 24 of the entry and version 1 of the sequence. [Complete history]
Entry statusiUnreviewed (UniProtKB/TrEMBL)

Miscellaneousi

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.UniRule annotation

Keywords - Technical termi

Complete proteomeImported

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.