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Protein

Ribulose bisphosphate carboxylase

Gene

rbcL

Organism
Methanothermococcus okinawensis (strain DSM 14208 / JCM 11175 / IH1)
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 sitei153 – 1531Proton acceptorUniRule annotation
Binding sitei155 – 1551SubstrateUniRule annotation
Metal bindingi179 – 1791Magnesium; via carbamate groupUniRule annotation
Metal bindingi181 – 1811MagnesiumUniRule annotation
Metal bindingi182 – 1821MagnesiumUniRule annotation
Active sitei269 – 2691Proton acceptorUniRule annotation
Binding sitei270 – 2701SubstrateUniRule annotation
Binding sitei302 – 3021SubstrateUniRule annotation
Sitei309 – 3091Transition state stabilizerUniRule annotation

GO - Molecular functioni

  1. magnesium ion binding Source: UniProtKB-HAMAP
  2. oxidoreductase activity Source: UniProtKB-KW
  3. ribulose-bisphosphate carboxylase activity Source: UniProtKB-HAMAP

GO - Biological processi

  1. AMP catabolic process Source: UniProtKB-HAMAP
  2. carbon fixation Source: UniProtKB-KW
Complete GO annotation...

Keywords - Molecular functioni

LyaseUniRule annotationImported, OxidoreductaseUniRule annotation

Keywords - Biological processi

Carbon dioxide fixationUniRule annotation

Keywords - Ligandi

MagnesiumUniRule annotation, Metal-bindingUniRule annotation

Enzyme and pathway databases

BioCyciMOKI647113:GHB9-744-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:Metok_0719Imported
OrganismiMethanothermococcus okinawensis (strain DSM 14208 / JCM 11175 / IH1)Imported
Taxonomic identifieri647113 [NCBI]
Taxonomic lineageiArchaeaEuryarchaeotaMethanococciMethanococcalesMethanococcaceaeMethanothermococcus
ProteomesiUP000009296 Componenti: Chromosome

PTM / Processingi

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei179 – 1791N6-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

Structurei

3D structure databases

ProteinModelPortaliF8AM17.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni353 – 3553Substrate bindingUniRule annotation
Regioni375 – 3784Substrate 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.
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.

F8AM17-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MDYLELGYEP KDNELLSCMV VKAENLKKAA NDIAGESSIG TWTELKTMKS
60 70 80 90 100
EIYKKLKPRV YEINEMGKEG DTNIGLIKIA YPLDTFEPNN MPGTLAGIAG
110 120 130 140 150
NIFGMKSLNG LRILDFRFPK EFIKCYSGPK YGIKGIRKLL NVMERPLVGT
160 170 180 190 200
IVKPKVGLNS EEHAKVAYNS WIGGCDIVKD DENLVSQDFN KFEGRLHKVL
210 220 230 240 250
ECRDKAESET GEKKIYMPNI TAPYREMVRR AELVEDAGCE YAMIDVVVLG
260 270 280 290 300
FSAVQQIREE GFNFAIHAHR AMHAAITRSR EWGISMLALA KIYRLLGVDQ
310 320 330 340 350
LHIGTVVGKM EGGKDEVCSI RDEIVLEDVK EDNKNKFFNQ KWHGLNNTFP
360 370 380 390 400
VSSGGVYPKL VPEIVNIFGK DVIIQAGGGI HGHPEGTVAG ARAMRASVEA
410 420
SIEGIPLSEK AEEVSELKKA LEYWK
Length:425
Mass (Da):47,362
Last modified:September 20, 2011 - v1
Checksum:iE2A1A4B6BF3F5829
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP002792 Genomic DNA. Translation: AEH06696.1.
RefSeqiYP_004576474.1. NC_015636.1.

Genome annotation databases

EnsemblBacteriaiAEH06696; AEH06696; Metok_0719.
GeneIDi10772860.
KEGGimok:Metok_0719.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP002792 Genomic DNA. Translation: AEH06696.1.
RefSeqiYP_004576474.1. NC_015636.1.

3D structure databases

ProteinModelPortaliF8AM17.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAEH06696; AEH06696; Metok_0719.
GeneIDi10772860.
KEGGimok:Metok_0719.

Phylogenomic databases

KOiK01601.
OMAiHAAFTRN.

Enzyme and pathway databases

BioCyciMOKI647113:GHB9-744-MONOMER.

Family and domain databases

Gene3Di3.20.20.110. 1 hit.
3.30.70.150. 1 hit.
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 sequence of chromosome of Methanothermococcus okinawensis IH1."
    Lucas S., Han J., Lapidus A., Cheng J.-F., Goodwin L., Pitluck S., Peters L., Mikhailova N., Held B., Han C., Tapia R., Land M., Hauser L., Kyrpides N., Ivanova N., Pagani I., Sieprawska-Lupa M., Takai K.
    , Miyazaki J., Whitman W., Woyke T.
    Submitted (APR-2011) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: DSM 14208 / JCM 11175 / IH1Imported.

Entry informationi

Entry nameiF8AM17_METOI
AccessioniPrimary (citable) accession number: F8AM17
Entry historyi
Integrated into UniProtKB/TrEMBL: September 20, 2011
Last sequence update: September 20, 2011
Last modified: March 31, 2015
This is version 27 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.