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O93627 (RBL_THEKO) Reviewed, UniProtKB/Swiss-Prot

Last modified May 14, 2014. Version 107. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (2) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Ribulose bisphosphate carboxylase

Short name=RuBisCO
EC=4.1.1.39
Gene names
Name:rbcL
Synonyms:rbc
Ordered Locus Names:TK2290
OrganismThermococcus kodakaraensis (strain ATCC BAA-918 / JCM 12380 / KOD1) (Pyrococcus kodakaraensis (strain KOD1)) [Reference proteome] [HAMAP]
Taxonomic identifier69014 [NCBI]
Taxonomic lineageArchaeaEuryarchaeotaThermococciThermococcalesThermococcaceaeThermococcus

Protein attributes

Sequence length444 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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. Ref.5 Ref.8

Catalytic activity

2 3-phospho-D-glycerate + 2 H+ = D-ribulose 1,5-bisphosphate + CO2 + H2O. Ref.5

3-phospho-D-glycerate + 2-phosphoglycolate = D-ribulose 1,5-bisphosphate + O2. Ref.5

Cofactor

Binds 1 magnesium ion per subunit. Ref.7 Ref.8

Subunit structure

Homodecamer, consisting of fiver dimer units which form a ring-like pentagonal structure. This arrangement is essential for its high thermostability. In contrast to form I RuBisCO, the form III RuBisCO is composed solely of large subunits. Ref.4 Ref.7

Induction

Up-regulated by nucleosides (at protein level). Ref.6

Disruption phenotype

Cells lacking this gene show a slight decrease in growth as sompared to the wild-type when they are grown in nutrient-rich medium. Ref.5

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 (Ref.5).

Sequence similarities

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

Biophysicochemical properties

Temperature dependence:

Optimum temperature is 90 degrees Celsius. Highly thermostable. Has a half-life of 220 minutes at 90 degrees Celsius. HAMAP-Rule MF_01133

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Initiator methionine11Removed Ref.1 Ref.3
Chain2 – 444443Ribulose bisphosphate carboxylase HAMAP-Rule MF_01133
PRO_0000062678

Regions

Region367 – 3693Substrate binding Probable
Region389 – 3924Substrate binding Probable

Sites

Active site1631Proton acceptor By similarity
Active site2811Proton acceptor By similarity
Metal binding1891Magnesium; via carbamate group
Metal binding1911Magnesium
Metal binding1921Magnesium
Binding site1651Substrate Probable
Binding site2821Substrate Probable
Binding site3141Substrate Probable
Site3221Transition state stabilizer By similarity

Amino acid modifications

Modified residue1891N6-carboxylysine HAMAP-Rule MF_01133

Experimental info

Mutagenesis631E → S: Decrease in activity and in thermostability. Large decrease in activity; forms dimers; when associated with S-66 and S-69. Ref.4
Mutagenesis661R → S: Large decrease in activity and in thermostability. Large decrease in activity; forms dimers; when associated with S-63 and S-69. Ref.4
Mutagenesis691D → S: Slight decrease in activity; no change in thermostability. Large decrease in activity; forms dimers; when associated with S-63 and S-66. Ref.4

Secondary structure

................................................................................ 444
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
O93627 [UniParc].

Last modified January 23, 2007. Version 5.
Checksum: 6E3AFF37367DD7FE

FASTA44449,713
        10         20         30         40         50         60 
MVEKFDTIYD YYVDKGYEPS KKRDIIAVFR VTPAEGYTIE QAAGAVAAES STGTWTTLYP 

        70         80         90        100        110        120 
WYEQERWADL SAKAYDFHDM GDGSWIVRIA YPFHAFEEAN LPGLLASIAG NIFGMKRVKG 

       130        140        150        160        170        180 
LRLEDLYFPE KLIREFDGPA FGIEGVRKML EIKDRPIYGV VPKPKVGYSP EEFEKLAYDL 

       190        200        210        220        230        240 
LSNGADYMKD DENLTSPWYN RFEERAEIMA KIIDKVENET GEKKTWFANI TADLLEMEQR 

       250        260        270        280        290        300 
LEVLADLGLK HAMVDVVITG WGALRYIRDL AADYGLAIHG HRAMHAAFTR NPYHGISMFV 

       310        320        330        340        350        360 
LAKLYRLIGI DQLHVGTAGA GKLEGGKWDV IQNARILRES HYKPDENDVF HLEQKFYSIK 

       370        380        390        400        410        420 
AAFPTSSGGL HPGNIQPVIE ALGTDIVLQL GGGTLGHPDG PAAGARAVRQ AIDAIMQGIP 

       430        440 
LDEYAKTHKE LARALEKWGH VTPV 

« Hide

References

« Hide 'large scale' references
[1]"Presence of a structurally novel type ribulose-bisphosphate carboxylase/oxygenase in the hyperthermophilic archaeon, Pyrococcus kodakaraensis KOD1."
Ezaki S., Maeda N., Kishimoto T., Atomi H., Imanaka T.
J. Biol. Chem. 274:5078-5082(1999) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 2-12, CHARACTERIZATION.
Strain: ATCC BAA-918 / JCM 12380 / KOD1.
[2]"Complete genome sequence of the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1 and comparison with Pyrococcus genomes."
Fukui T., Atomi H., Kanai T., Matsumi R., Fujiwara S., Imanaka T.
Genome Res. 15:352-363(2005) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: ATCC BAA-918 / JCM 12380 / KOD1.
[3]"Ribulose bisphosphate carboxylase/oxygenase from the hyperthermophilic archaeon Pyrococcus kodakaraensis KOD1 is composed solely of large subunits and forms a pentagonal structure."
Maeda N., Kitano K., Fukui T., Ezaki S., Atomi H., Miki K., Imanaka T.
J. Mol. Biol. 293:57-66(1999) [PubMed] [Europe PMC] [Abstract]
Cited for: PROTEIN SEQUENCE OF 2-12, CHARACTERIZATION, CRYSTALLIZATION.
Strain: ATCC BAA-918 / JCM 12380 / KOD1.
[4]"The unique pentagonal structure of an archaeal Rubisco is essential for its high thermostability."
Maeda N., Kanai T., Atomi H., Imanaka T.
J. Biol. Chem. 277:31656-31662(2002) [PubMed] [Europe PMC] [Abstract]
Cited for: SUBUNIT, MUTAGENESIS OF GLU-63; ARG-66 AND ASP-69.
Strain: ATCC BAA-918 / JCM 12380 / KOD1.
[5]"Archaeal type III RuBisCOs function in a pathway for AMP metabolism."
Sato T., Atomi H., Imanaka T.
Science 315:1003-1006(2007) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION, CATALYTIC ACTIVITY, DISRUPTION PHENOTYPE, PATHWAY.
Strain: ATCC BAA-918 / JCM 12380 / KOD1.
[6]"Enzymatic characterization of AMP phosphorylase and ribose-1,5-bisphosphate isomerase functioning in an archaeal AMP metabolic pathway."
Aono R., Sato T., Yano A., Yoshida S., Nishitani Y., Miki K., Imanaka T., Atomi H.
J. Bacteriol. 194:6847-6855(2012) [PubMed] [Europe PMC] [Abstract]
Cited for: INDUCTION, PATHWAY.
Strain: ATCC BAA-918 / JCM 12380 / KOD1.
[7]"Crystal structure of a novel-type archaeal rubisco with pentagonal symmetry."
Kitano K., Maeda N., Fukui T., Atomi H., Imanaka T., Miki K.
Structure 9:473-481(2001) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS), COFACTOR, SUBUNIT.
Strain: ATCC BAA-918 / JCM 12380 / KOD1.
[8]"Structure-based catalytic optimization of a type III Rubisco from a hyperthermophile."
Nishitani Y., Yoshida S., Fujihashi M., Kitagawa K., Doi T., Atomi H., Imanaka T., Miki K.
J. Biol. Chem. 285:39339-39347(2010) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.09 ANGSTROMS) OF WILD-TYPE AND MUTANTS IN COMPLEX WITH INHIBITOR AND MAGNESIUM, FUNCTION, COFACTOR, TEMPERATURE DEPENDENCE, CARBOXYLATION AT LYS-189.
Strain: ATCC BAA-918 / JCM 12380 / KOD1.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
AB018555 Genomic DNA. Translation: BAA33863.1.
AP006878 Genomic DNA. Translation: BAD86479.1.
RefSeqYP_184703.1. NC_006624.1.

3D structure databases

PDBe
RCSB-PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1GEHX-ray2.80A/B/C/D/E1-444[»]
3A12X-ray2.30A/B/C/D/E/F/G/H/I/J1-444[»]
3A13X-ray2.34A/B/C/D/E/F/G/H/I/J1-444[»]
3KDNX-ray2.09A/B/C/D/E/F/G/H/I/J1-444[»]
3KDOX-ray2.36A/B/C/D/E/F/G/H/I/J1-444[»]
ProteinModelPortalO93627.
SMRO93627. Positions 12-443.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

IntActO93627. 1 interaction.
MINTMINT-8377356.
STRING69014.TK2290.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaBAD86479; BAD86479; TK2290.
GeneID3234791.
KEGGtko:TK2290.

Phylogenomic databases

eggNOGCOG1850.
HOGENOMHOG000230831.
KOK01601.

Enzyme and pathway databases

BioCycMetaCyc:MONOMER-13272.
TKOD69014:GH72-2342-MONOMER.

Family and domain databases

Gene3D3.20.20.110. 1 hit.
3.30.70.150. 1 hit.
HAMAPMF_01133. RuBisCO_L_type3.
InterProIPR017712. RuBisCO_III.
IPR000685. RuBisCO_lsu_C.
IPR017443. RuBisCO_lsu_fd_N.
IPR017444. RuBisCO_lsu_N.
[Graphical view]
PfamPF00016. RuBisCO_large. 1 hit.
PF02788. RuBisCO_large_N. 1 hit.
[Graphical view]
SUPFAMSSF51649. SSF51649. 1 hit.
SSF54966. SSF54966. 1 hit.
TIGRFAMsTIGR03326. rubisco_III. 1 hit.
ProtoNetSearch...

Other

EvolutionaryTraceO93627.

Entry information

Entry nameRBL_THEKO
AccessionPrimary (citable) accession number: O93627
Entry history
Integrated into UniProtKB/Swiss-Prot: September 26, 2003
Last sequence update: January 23, 2007
Last modified: May 14, 2014
This is version 107 of the entry and version 5 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references