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O58677

- RBL_PYRHO

UniProt

O58677 - RBL_PYRHO

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Protein
Ribulose bisphosphate carboxylase
Gene
rbcL, PH0939
Organism
Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)
Status
Reviewed - Annotation score: 4 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 By similarity.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

Binds 1 magnesium ion per subunit By similarity.UniRule annotation

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Active sitei160 – 1601Proton acceptor By similarity
Binding sitei162 – 1621Substrate By similarity
Metal bindingi186 – 1861Magnesium; via carbamate group By similarity
Metal bindingi188 – 1881Magnesium By similarity
Metal bindingi189 – 1891Magnesium By similarity
Active sitei278 – 2781Proton acceptor By similarity
Binding sitei279 – 2791Substrate By similarity
Binding sitei311 – 3111Substrate By similarity
Sitei318 – 3181Transition state stabilizer By similarity

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

Enzyme and pathway databases

BioCyciPHOR70601:GJWR-933-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Ribulose bisphosphate carboxylase (EC:4.1.1.39)
Short name:
RuBisCO
Gene namesi
Name:rbcL
Ordered Locus Names:PH0939
OrganismiPyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)
Taxonomic identifieri70601 [NCBI]
Taxonomic lineageiArchaeaEuryarchaeotaThermococciThermococcalesThermococcaceaePyrococcus
ProteomesiUP000000752: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 430430Ribulose bisphosphate carboxylaseUniRule annotation
PRO_0000062677Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei186 – 1861N6-carboxylysine By similarity

Interactioni

Subunit structurei

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

Protein-protein interaction databases

STRINGi70601.PH0939.

Structurei

Secondary structure

Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi7 – 93
Helixi11 – 144
Beta strandi25 – 3713
Helixi39 – 4911
Turni50 – 523
Beta strandi55 – 595
Helixi63 – 653
Helixi66 – 683
Beta strandi71 – 788
Beta strandi81 – 888
Helixi90 – 923
Helixi98 – 1058
Helixi108 – 1114
Beta strandi115 – 12410
Helixi127 – 1304
Helixi139 – 1479
Beta strandi150 – 1523
Beta strandi154 – 1574
Beta strandi160 – 1634
Helixi167 – 17913
Beta strandi183 – 1864
Helixi199 – 21719
Beta strandi222 – 2243
Helixi231 – 24313
Beta strandi248 – 2525
Helixi253 – 2564
Helixi258 – 27114
Beta strandi274 – 2785
Turni280 – 2823
Helixi283 – 2864
Beta strandi291 – 2933
Helixi295 – 30511
Beta strandi308 – 3114
Beta strandi317 – 3193
Helixi323 – 33412
Beta strandi344 – 3507
Helixi353 – 3553
Helixi356 – 3638
Beta strandi368 – 3703
Helixi372 – 3765
Helixi382 – 39817
Helixi402 – 4054
Turni406 – 4083
Helixi410 – 42213

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2CWXX-ray2.00A/E1-430[»]
2CXEX-ray3.00A/B/C/D1-430[»]
2D69X-ray1.90A/B/D/E1-430[»]
ProteinModelPortaliO58677.
SMRiO58677. Positions 1-423.

Miscellaneous databases

EvolutionaryTraceiO58677.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni348 – 3503Substrate binding By similarity
Regioni370 – 3734Substrate binding By similarity

Sequence similaritiesi

Phylogenomic databases

eggNOGiCOG1850.
HOGENOMiHOG000230831.
KOiK01601.
OMAiCTPLKQA.

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.

O58677-1 [UniParc]FASTAAdd to Basket

« Hide

MMVLRMKVEW YLDFVDLNYE PGRDELIVEY YFEPNGVSPE EAAGRIASES    50
SIGTWTTLWK LPEMAKRSMA KVFYLEKHGE GYIAKIAYPL TLFEEGSLVQ 100
LFSAVAGNVF GMKALKNLRL LDFHPPYEYL RHFKGPQFGV QGIREFMGVK 150
DRPLTATVPK PKMGWSVEEY AEIAYELWSG GIDLLKDDEN FTSFPFNRFE 200
ERVRKLYRVR DRVEAETGET KEYLINITGP VNIMEKRAEM VANEGGQYVM 250
IDIVVAGWSA LQYMREVTED LGLAIHAHRA MHAAFTRNPR HGITMLALAK 300
AARMIGVDQI HTGTAVGKMA GNYEEIKRIN DFLLSKWEHI RPVFPVASGG 350
LHPGLMPELI RLFGKDLVIQ AGGGVMGHPD GPRAGAKALR DAIDAAIEGV 400
DLDEKAKSSP ELKKSLREVG LSKAKVGVQH 430
Length:430
Mass (Da):48,247
Last modified:August 1, 1998 - v1
Checksum:i1068CA138F019AD9
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
BA000001 Genomic DNA. Translation: BAA30036.1.
PIRiF71084.
RefSeqiNP_142861.1. NC_000961.1.
WP_010885029.1. NC_000961.1.

Genome annotation databases

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

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
BA000001 Genomic DNA. Translation: BAA30036.1 .
PIRi F71084.
RefSeqi NP_142861.1. NC_000961.1.
WP_010885029.1. NC_000961.1.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
2CWX X-ray 2.00 A/E 1-430 [» ]
2CXE X-ray 3.00 A/B/C/D 1-430 [» ]
2D69 X-ray 1.90 A/B/D/E 1-430 [» ]
ProteinModelPortali O58677.
SMRi O58677. Positions 1-423.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

STRINGi 70601.PH0939.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai BAA30036 ; BAA30036 ; BAA30036 .
GeneIDi 1443264.
KEGGi pho:PH0939.

Phylogenomic databases

eggNOGi COG1850.
HOGENOMi HOG000230831.
KOi K01601.
OMAi CTPLKQA.

Enzyme and pathway databases

BioCyci PHOR70601:GJWR-933-MONOMER.

Miscellaneous databases

EvolutionaryTracei O58677.

Family and domain databases

Gene3Di 3.20.20.110. 1 hit.
3.30.70.150. 1 hit.
HAMAPi MF_01133. RuBisCO_L_type3.
InterProi IPR017712. RuBisCO_III.
IPR000685. RuBisCO_lsu_C.
IPR017443. RuBisCO_lsu_fd_N.
IPR017444. RuBisCO_lsu_N.
[Graphical view ]
Pfami PF00016. RuBisCO_large. 1 hit.
PF02788. RuBisCO_large_N. 1 hit.
[Graphical view ]
SUPFAMi SSF51649. SSF51649. 1 hit.
SSF54966. SSF54966. 1 hit.
TIGRFAMsi TIGR03326. rubisco_III. 1 hit.
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  1. 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).

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: September 3, 2014
This is version 99 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 By similarity.

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

External Data

Dasty 3

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