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Protein

Ribulose bisphosphate carboxylase

Gene

rbcL

Organism
Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Experimental evidence at protein leveli

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)DescriptionActionsGraphical viewLength
Active sitei160Proton acceptorUniRule annotation1
Binding sitei162SubstrateUniRule annotation1
Metal bindingi186Magnesium; via carbamate groupUniRule annotation1
Metal bindingi188MagnesiumUniRule annotation1
Metal bindingi189MagnesiumUniRule annotation1
Active sitei278Proton acceptorUniRule annotation1
Binding sitei279SubstrateUniRule annotation1
Binding sitei311SubstrateUniRule annotation1
Sitei318Transition state stabilizerUniRule annotation1

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Lyase, Oxidoreductase

Keywords - Biological processi

Carbon dioxide fixation

Keywords - Ligandi

Magnesium, Metal-binding

Enzyme and pathway databases

BRENDAi4.1.1.39. 5244.

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:PH0939
OrganismiPyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)
Taxonomic identifieri70601 [NCBI]
Taxonomic lineageiArchaeaEuryarchaeotaThermococciThermococcalesThermococcaceaePyrococcus
Proteomesi
  • UP000000752 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000626771 – 430Ribulose bisphosphate carboxylaseAdd BLAST430

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei186N6-carboxylysineUniRule annotation1

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

STRINGi70601.PH0939.

Structurei

Secondary structure

1430
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi7 – 9Combined sources3
Helixi11 – 14Combined sources4
Beta strandi25 – 37Combined sources13
Helixi39 – 49Combined sources11
Turni50 – 52Combined sources3
Beta strandi55 – 59Combined sources5
Helixi63 – 65Combined sources3
Helixi66 – 68Combined sources3
Beta strandi71 – 78Combined sources8
Beta strandi81 – 88Combined sources8
Helixi90 – 92Combined sources3
Helixi98 – 105Combined sources8
Helixi108 – 111Combined sources4
Beta strandi115 – 124Combined sources10
Helixi127 – 130Combined sources4
Helixi139 – 147Combined sources9
Beta strandi150 – 152Combined sources3
Beta strandi154 – 157Combined sources4
Beta strandi160 – 163Combined sources4
Helixi167 – 179Combined sources13
Beta strandi183 – 186Combined sources4
Helixi199 – 217Combined sources19
Beta strandi222 – 224Combined sources3
Helixi231 – 243Combined sources13
Beta strandi248 – 252Combined sources5
Helixi253 – 256Combined sources4
Helixi258 – 271Combined sources14
Beta strandi274 – 278Combined sources5
Turni280 – 282Combined sources3
Helixi283 – 286Combined sources4
Beta strandi291 – 293Combined sources3
Helixi295 – 305Combined sources11
Beta strandi308 – 311Combined sources4
Beta strandi317 – 319Combined sources3
Helixi323 – 334Combined sources12
Beta strandi344 – 350Combined sources7
Helixi353 – 355Combined sources3
Helixi356 – 363Combined sources8
Beta strandi368 – 370Combined sources3
Helixi372 – 376Combined sources5
Helixi382 – 398Combined sources17
Helixi402 – 405Combined sources4
Turni406 – 408Combined sources3
Helixi410 – 422Combined sources13

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2CWXX-ray2.00A/E1-430[»]
2CXEX-ray3.00A/B/C/D1-430[»]
2D69X-ray1.90A/B/D/E1-430[»]
ProteinModelPortaliO58677.
SMRiO58677.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiO58677.

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni348 – 350Substrate bindingUniRule annotation3
Regioni370 – 373Substrate bindingUniRule annotation4

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiarCOG04443. Archaea.
COG1850. LUCA.
HOGENOMiHOG000230831.
KOiK01601.
OMAiFTQDWAS.

Family and domain databases

CDDicd08213. RuBisCO_large_III. 1 hit.
Gene3Di3.20.20.110. 1 hit.
3.30.70.150. 1 hit.
HAMAPiMF_01133. RuBisCO_L_type3. 1 hit.
InterProiIPR033966. RuBisCO.
IPR017712. RuBisCO_III.
IPR000685. RuBisCO_lsu_C.
IPR017443. RuBisCO_lsu_fd_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.

O58677-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MMVLRMKVEW YLDFVDLNYE PGRDELIVEY YFEPNGVSPE EAAGRIASES
60 70 80 90 100
SIGTWTTLWK LPEMAKRSMA KVFYLEKHGE GYIAKIAYPL TLFEEGSLVQ
110 120 130 140 150
LFSAVAGNVF GMKALKNLRL LDFHPPYEYL RHFKGPQFGV QGIREFMGVK
160 170 180 190 200
DRPLTATVPK PKMGWSVEEY AEIAYELWSG GIDLLKDDEN FTSFPFNRFE
210 220 230 240 250
ERVRKLYRVR DRVEAETGET KEYLINITGP VNIMEKRAEM VANEGGQYVM
260 270 280 290 300
IDIVVAGWSA LQYMREVTED LGLAIHAHRA MHAAFTRNPR HGITMLALAK
310 320 330 340 350
AARMIGVDQI HTGTAVGKMA GNYEEIKRIN DFLLSKWEHI RPVFPVASGG
360 370 380 390 400
LHPGLMPELI RLFGKDLVIQ AGGGVMGHPD GPRAGAKALR DAIDAAIEGV
410 420 430
DLDEKAKSSP ELKKSLREVG LSKAKVGVQH
Length:430
Mass (Da):48,247
Last modified:August 1, 1998 - v1
Checksum:i1068CA138F019AD9
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BA000001 Genomic DNA. Translation: BAA30036.1.
PIRiF71084.
RefSeqiWP_010885029.1. NC_000961.1.

Genome annotation databases

EnsemblBacteriaiBAA30036; BAA30036; BAA30036.
GeneIDi1443264.
KEGGipho:PH0939.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BA000001 Genomic DNA. Translation: BAA30036.1.
PIRiF71084.
RefSeqiWP_010885029.1. NC_000961.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2CWXX-ray2.00A/E1-430[»]
2CXEX-ray3.00A/B/C/D1-430[»]
2D69X-ray1.90A/B/D/E1-430[»]
ProteinModelPortaliO58677.
SMRiO58677.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi70601.PH0939.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiBAA30036; BAA30036; BAA30036.
GeneIDi1443264.
KEGGipho:PH0939.

Phylogenomic databases

eggNOGiarCOG04443. Archaea.
COG1850. LUCA.
HOGENOMiHOG000230831.
KOiK01601.
OMAiFTQDWAS.

Enzyme and pathway databases

BRENDAi4.1.1.39. 5244.

Miscellaneous databases

EvolutionaryTraceiO58677.

Family and domain databases

CDDicd08213. RuBisCO_large_III. 1 hit.
Gene3Di3.20.20.110. 1 hit.
3.30.70.150. 1 hit.
HAMAPiMF_01133. RuBisCO_L_type3. 1 hit.
InterProiIPR033966. RuBisCO.
IPR017712. RuBisCO_III.
IPR000685. RuBisCO_lsu_C.
IPR017443. RuBisCO_lsu_fd_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...

Entry informationi

Entry nameiRBL_PYRHO
AccessioniPrimary (citable) accession number: O58677
Entry historyi
Integrated into UniProtKB/Swiss-Prot: September 26, 2003
Last sequence update: August 1, 1998
Last modified: November 30, 2016
This is version 113 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

3D-structure, Complete proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families

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 one 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.