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Protein

Ribulose bisphosphate carboxylase

Gene

rbcL

Organism
Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1) (Pyrococcus kodakaraensis (strain KOD1))
Status
Reviewed-Annotation score: Annotation score: 5 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) (PubMed:9988755, PubMed:10512715). Functions in an archaeal AMP degradation pathway, together with AMP phosphorylase and R15P isomerase (PubMed:17303759).UniRule annotation5 Publications

Catalytic activityi

2 3-phospho-D-glycerate + 2 H+ = D-ribulose 1,5-bisphosphate + CO2 + H2O.UniRule annotation1 Publication
3-phospho-D-glycerate + 2-phosphoglycolate = D-ribulose 1,5-bisphosphate + O2.UniRule annotation1 Publication

Cofactori

Mg2+UniRule annotation2 PublicationsNote: Binds 1 Mg2+ ion per subunit.UniRule annotation2 Publications

Temperature dependencei

Optimum temperature is 90 degrees Celsius (PubMed:9988755). Highly thermostable, has a half-life of 220 minutes at 90 degrees Celsius (PubMed:9988755).2 Publications

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Active sitei163Proton acceptorUniRule annotation1
Binding sitei165SubstrateCurated1
Metal bindingi189Magnesium; via carbamate groupUniRule annotation1 Publication1
Metal bindingi191MagnesiumUniRule annotation1 Publication1
Metal bindingi192MagnesiumUniRule annotation1 Publication1
Active sitei281Proton acceptorUniRule annotation1
Binding sitei282SubstrateCurated1
Binding sitei314SubstrateCurated1
Sitei322Transition 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

BioCyciMetaCyc:MONOMER-13272.
BRENDAi4.1.1.39. 5246.

Names & Taxonomyi

Protein namesi
Recommended name:
Ribulose bisphosphate carboxylaseUniRule annotation (EC:4.1.1.39UniRule annotation1 Publication)
Short name:
RuBisCOUniRule annotation
Gene namesi
Name:rbcLUniRule annotation
Synonyms:rbc
Ordered Locus Names:TK2290
OrganismiThermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1) (Pyrococcus kodakaraensis (strain KOD1))
Taxonomic identifieri69014 [NCBI]
Taxonomic lineageiArchaeaEuryarchaeotaThermococciThermococcalesThermococcaceaeThermococcus
Proteomesi
  • UP000000536 Componenti: Chromosome

Pathology & Biotechi

Disruption phenotypei

Cells lacking this gene show a slight decrease in growth as compared to the wild-type when they are grown in nutrient-rich medium.1 Publication

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi63E → S: Decrease in activity and in thermostability. Large decrease in activity; forms dimers; when associated with S-66 and S-69. 1 Publication1
Mutagenesisi66R → S: Large decrease in activity and in thermostability. Large decrease in activity; forms dimers; when associated with S-63 and S-69. 1 Publication1
Mutagenesisi69D → S: Slight decrease in activity; no change in thermostability. Large decrease in activity; forms dimers; when associated with S-63 and S-66. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemoved2 Publications
ChainiPRO_00000626782 – 444Ribulose bisphosphate carboxylaseAdd BLAST443

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei189N6-carboxylysineUniRule annotation1 Publication1

Expressioni

Inductioni

Up-regulated by nucleosides (at protein level).1 Publication

Interactioni

Subunit structurei

Homodecamer, consisting of five dimer units which form a ring-like pentagonal structure. This arrangement is essential for its high thermostability (PubMed:12070156). In contrast to form I RuBisCO, the form III RuBisCO is composed solely of large subunits (PubMed:9988755).1 Publication4 Publications

Protein-protein interaction databases

IntActiO93627. 1 interactor.
MINTiMINT-8377356.
STRINGi69014.TK2290.

Structurei

Secondary structure

1444
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi10 – 12Combined sources3
Turni21 – 23Combined sources3
Beta strandi24 – 33Combined sources10
Helixi39 – 49Combined sources11
Turni50 – 52Combined sources3
Helixi64 – 70Combined sources7
Beta strandi73 – 79Combined sources7
Beta strandi81 – 83Combined sources3
Beta strandi85 – 92Combined sources8
Helixi93 – 95Combined sources3
Helixi101 – 108Combined sources8
Helixi111 – 114Combined sources4
Beta strandi118 – 127Combined sources10
Helixi130 – 133Combined sources4
Helixi142 – 150Combined sources9
Beta strandi157 – 160Combined sources4
Beta strandi163 – 166Combined sources4
Helixi170 – 182Combined sources13
Beta strandi187 – 189Combined sources3
Helixi202 – 220Combined sources19
Beta strandi225 – 229Combined sources5
Helixi234 – 247Combined sources14
Beta strandi251 – 255Combined sources5
Helixi256 – 259Combined sources4
Helixi261 – 274Combined sources14
Beta strandi277 – 281Combined sources5
Turni283 – 285Combined sources3
Helixi286 – 289Combined sources4
Beta strandi294 – 296Combined sources3
Helixi298 – 308Combined sources11
Beta strandi311 – 314Combined sources4
Beta strandi320 – 323Combined sources4
Helixi327 – 338Combined sources12
Beta strandi340 – 342Combined sources3
Beta strandi363 – 369Combined sources7
Turni372 – 374Combined sources3
Helixi376 – 382Combined sources7
Beta strandi384 – 389Combined sources6
Helixi392 – 395Combined sources4
Helixi401 – 415Combined sources15
Helixi421 – 425Combined sources5
Helixi429 – 438Combined sources10

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB 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[»]
3WQPX-ray2.25A/B/C/D/E/F/G/H/I/J1-444[»]
ProteinModelPortaliO93627.
SMRiO93627.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiO93627.

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni367 – 369Substrate bindingCurated3
Regioni389 – 392Substrate bindingCurated4

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiarCOG04443. Archaea.
COG1850. LUCA.
HOGENOMiHOG000230831.
InParanoidiO93627.
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.

Sequence processingi: The displayed sequence is further processed into a mature form.

O93627-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MVEKFDTIYD YYVDKGYEPS KKRDIIAVFR VTPAEGYTIE QAAGAVAAES
60 70 80 90 100
STGTWTTLYP WYEQERWADL SAKAYDFHDM GDGSWIVRIA YPFHAFEEAN
110 120 130 140 150
LPGLLASIAG NIFGMKRVKG LRLEDLYFPE KLIREFDGPA FGIEGVRKML
160 170 180 190 200
EIKDRPIYGV VPKPKVGYSP EEFEKLAYDL LSNGADYMKD DENLTSPWYN
210 220 230 240 250
RFEERAEIMA KIIDKVENET GEKKTWFANI TADLLEMEQR LEVLADLGLK
260 270 280 290 300
HAMVDVVITG WGALRYIRDL AADYGLAIHG HRAMHAAFTR NPYHGISMFV
310 320 330 340 350
LAKLYRLIGI DQLHVGTAGA GKLEGGKWDV IQNARILRES HYKPDENDVF
360 370 380 390 400
HLEQKFYSIK AAFPTSSGGL HPGNIQPVIE ALGTDIVLQL GGGTLGHPDG
410 420 430 440
PAAGARAVRQ AIDAIMQGIP LDEYAKTHKE LARALEKWGH VTPV
Length:444
Mass (Da):49,713
Last modified:January 23, 2007 - v5
Checksum:i6E3AFF37367DD7FE
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB018555 Genomic DNA. Translation: BAA33863.1.
AP006878 Genomic DNA. Translation: BAD86479.1.
RefSeqiWP_011251240.1. NC_006624.1.

Genome annotation databases

EnsemblBacteriaiBAD86479; BAD86479; TK2290.
GeneIDi3234791.
KEGGitko:TK2290.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB018555 Genomic DNA. Translation: BAA33863.1.
AP006878 Genomic DNA. Translation: BAD86479.1.
RefSeqiWP_011251240.1. NC_006624.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB 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[»]
3WQPX-ray2.25A/B/C/D/E/F/G/H/I/J1-444[»]
ProteinModelPortaliO93627.
SMRiO93627.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

IntActiO93627. 1 interactor.
MINTiMINT-8377356.
STRINGi69014.TK2290.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiBAD86479; BAD86479; TK2290.
GeneIDi3234791.
KEGGitko:TK2290.

Phylogenomic databases

eggNOGiarCOG04443. Archaea.
COG1850. LUCA.
HOGENOMiHOG000230831.
InParanoidiO93627.
KOiK01601.
OMAiFTQDWAS.

Enzyme and pathway databases

BioCyciMetaCyc:MONOMER-13272.
BRENDAi4.1.1.39. 5246.

Miscellaneous databases

EvolutionaryTraceiO93627.

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_THEKO
AccessioniPrimary (citable) accession number: O93627
Entry historyi
Integrated into UniProtKB/Swiss-Prot: September 26, 2003
Last sequence update: January 23, 2007
Last modified: November 30, 2016
This is version 124 of the entry and version 5 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.1 Publication

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference 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.