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Protein

Ribulose bisphosphate carboxylase

Gene

rbcL

Organism
Pyrococcus abyssi (strain GE5 / Orsay)
Status
Reviewed-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 sitei159 – 1591Proton acceptorUniRule annotation
Binding sitei161 – 1611SubstrateUniRule annotation
Metal bindingi185 – 1851Magnesium; via carbamate groupUniRule annotation
Metal bindingi187 – 1871MagnesiumUniRule annotation
Metal bindingi188 – 1881MagnesiumUniRule annotation
Active sitei277 – 2771Proton acceptorUniRule annotation
Binding sitei278 – 2781SubstrateUniRule annotation
Binding sitei310 – 3101SubstrateUniRule annotation
Sitei317 – 3171Transition 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

Lyase, Oxidoreductase

Keywords - Biological processi

Carbon dioxide fixation

Keywords - Ligandi

Magnesium, Metal-binding

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:PYRAB12110
ORF Names:PAB1580
OrganismiPyrococcus abyssi (strain GE5 / Orsay)
Taxonomic identifieri272844 [NCBI]
Taxonomic lineageiArchaeaEuryarchaeotaThermococciThermococcalesThermococcaceaePyrococcus
ProteomesiUP000000810 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 424424Ribulose bisphosphate carboxylasePRO_0000062675Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei185 – 1851N6-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

STRINGi272844.PAB1580.

Structurei

3D structure databases

ProteinModelPortaliQ9UZD7.
SMRiQ9UZD7. Positions 8-415.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni347 – 3493Substrate bindingUniRule annotation
Regioni369 – 3724Substrate bindingUniRule annotation

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiCOG1850.
HOGENOMiHOG000230831.
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.

Q9UZD7-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MVSSMKVEWY LDFVDLNYEP GRDELIVEYY FEPNGVSPEE AAGRIASESS
60 70 80 90 100
IGTWTTLWKL PEMAKRSMAK VFYLEKHGEG YIAKIAYPLT LFEEGSLVQL
110 120 130 140 150
FSAIAGNVFG MKALKNLRLL DFHPPYEYLR HFKGPQFGVK GIREFMGIKD
160 170 180 190 200
RPLTATVPKP KMGWSVEEYA EIAYELWSGG IDLLKDDENF TSFPFNRFEE
210 220 230 240 250
RVKKLYRVRD RVEAETGETK EYLINITGPV NVMEKRAELV ANEGGQYVMI
260 270 280 290 300
DIVVAGWSAL QYMREVTEDL GLAIHAHRAM HAAFTRNPKH GITMFALAKA
310 320 330 340 350
ARMIGVDQIH TGTAVGKMAG DYEEIKKIND FLLSKWEHIR PVFPVASGGL
360 370 380 390 400
HPGLMPELIR LFGKDLVIQA GGGVMGHPDG PRAGAKALRD AIDAAIEGLD
410 420
LEEKAKSSPE LKKALDKWGY LKPK
Length:424
Mass (Da):47,606
Last modified:May 1, 2000 - v1
Checksum:iCFBC3EEDB1D16A1F
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AJ248286 Genomic DNA. Translation: CAB50122.1.
HE613800 Genomic DNA. Translation: CCE70647.1.
PIRiE75102.
RefSeqiNP_126892.1. NC_000868.1.
WP_010868329.1. NC_000868.1.

Genome annotation databases

GeneIDi1496593.
KEGGipab:PAB1580.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AJ248286 Genomic DNA. Translation: CAB50122.1.
HE613800 Genomic DNA. Translation: CCE70647.1.
PIRiE75102.
RefSeqiNP_126892.1. NC_000868.1.
WP_010868329.1. NC_000868.1.

3D structure databases

ProteinModelPortaliQ9UZD7.
SMRiQ9UZD7. Positions 8-415.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi272844.PAB1580.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

GeneIDi1496593.
KEGGipab:PAB1580.

Phylogenomic databases

eggNOGiCOG1850.
HOGENOMiHOG000230831.
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.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: GE5 / Orsay.
  2. "Re-annotation of two hyperthermophilic archaea Pyrococcus abyssi GE5 and Pyrococcus furiosus DSM 3638."
    Gao J., Wang J.
    Curr. Microbiol. 64:118-129(2012) [PubMed] [Europe PMC] [Abstract]
    Cited for: GENOME REANNOTATION.
    Strain: GE5 / Orsay.

Entry informationi

Entry nameiRBL_PYRAB
AccessioniPrimary (citable) accession number: Q9UZD7
Secondary accession number(s): G8ZKK4
Entry historyi
Integrated into UniProtKB/Swiss-Prot: September 26, 2003
Last sequence update: May 1, 2000
Last modified: April 1, 2015
This is version 96 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

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 proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families

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.