Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.

O93627

- RBL_THEKO

UniProt

O93627 - RBL_THEKO

(max 400 entries)x

Your basket is currently empty.

Select item(s) and click on "Add to basket" to create your own collection here
(400 entries max)

Protein

Ribulose bisphosphate carboxylase

Gene

rbcL

Organism
Thermococcus kodakaraensis (strain ATCC BAA-918 / JCM 12380 / KOD1) (Pyrococcus kodakaraensis (strain KOD1))
Status
Reviewed - 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). Functions in an archaeal AMP degradation pathway, together with AMP phosphorylase and R15P isomerase.3 PublicationsUniRule 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.2 PublicationsUniRule annotation

Temperature dependencei

Optimum temperature is 90 degrees Celsius. Highly thermostable. Has a half-life of 220 minutes at 90 degrees Celsius.1 Publication

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Active sitei163 – 1631Proton acceptorUniRule annotation
Binding sitei165 – 1651SubstrateCurated
Metal bindingi189 – 1891Magnesium; via carbamate group1 PublicationUniRule annotation
Metal bindingi191 – 1911Magnesium1 PublicationUniRule annotation
Metal bindingi192 – 1921Magnesium1 PublicationUniRule annotation
Active sitei281 – 2811Proton acceptorUniRule annotation
Binding sitei282 – 2821SubstrateCurated
Binding sitei314 – 3141SubstrateCurated
Sitei322 – 3221Transition 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

Enzyme and pathway databases

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

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
Synonyms:rbc
Ordered Locus Names:TK2290
OrganismiThermococcus kodakaraensis (strain ATCC BAA-918 / JCM 12380 / KOD1) (Pyrococcus kodakaraensis (strain KOD1))
Taxonomic identifieri69014 [NCBI]
Taxonomic lineageiArchaeaEuryarchaeotaThermococciThermococcalesThermococcaceaeThermococcus
ProteomesiUP000000536: Chromosome

Pathology & Biotechi

Disruption phenotypei

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

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi63 – 631E → S: Decrease in activity and in thermostability. Large decrease in activity; forms dimers; when associated with S-66 and S-69. 1 Publication
Mutagenesisi66 – 661R → S: Large decrease in activity and in thermostability. Large decrease in activity; forms dimers; when associated with S-63 and S-69. 1 Publication
Mutagenesisi69 – 691D → S: Slight decrease in activity; no change in thermostability. Large decrease in activity; forms dimers; when associated with S-63 and S-66. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methioninei1 – 11Removed2 Publications
Chaini2 – 444443Ribulose bisphosphate carboxylasePRO_0000062678Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei189 – 1891N6-carboxylysine1 PublicationUniRule annotation

Expressioni

Inductioni

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

Interactioni

Subunit structurei

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.3 Publications

Protein-protein interaction databases

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

Structurei

Secondary structure

1
444
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi10 – 123
Turni21 – 233
Beta strandi24 – 3310
Helixi39 – 4911
Turni50 – 523
Helixi64 – 707
Beta strandi73 – 797
Beta strandi81 – 833
Beta strandi85 – 928
Helixi93 – 953
Helixi101 – 1088
Helixi111 – 1144
Beta strandi118 – 12710
Helixi130 – 1334
Helixi142 – 1509
Beta strandi157 – 1604
Beta strandi163 – 1664
Helixi170 – 18213
Beta strandi187 – 1893
Helixi202 – 22019
Beta strandi225 – 2295
Helixi234 – 24714
Beta strandi251 – 2555
Helixi256 – 2594
Helixi261 – 27414
Beta strandi277 – 2815
Turni283 – 2853
Helixi286 – 2894
Beta strandi294 – 2963
Helixi298 – 30811
Beta strandi311 – 3144
Beta strandi320 – 3234
Helixi327 – 33812
Beta strandi340 – 3423
Beta strandi363 – 3697
Helixi372 – 3743
Helixi376 – 3827
Beta strandi384 – 3896
Helixi392 – 3954
Helixi401 – 41515
Helixi421 – 4255
Helixi429 – 43810

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
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[»]
ProteinModelPortaliO93627.
SMRiO93627. Positions 12-443.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiO93627.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni367 – 3693Substrate bindingCurated
Regioni389 – 3924Substrate bindingCurated

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiCOG1850.
HOGENOMiHOG000230831.
InParanoidiO93627.
KOiK01601.

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.

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:
EMBL
GenBank
DDBJ
Links Updated
AB018555 Genomic DNA. Translation: BAA33863.1.
AP006878 Genomic DNA. Translation: BAD86479.1.
RefSeqiYP_184703.1. NC_006624.1.

Genome annotation databases

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

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
AB018555 Genomic DNA. Translation: BAA33863.1 .
AP006878 Genomic DNA. Translation: BAD86479.1 .
RefSeqi YP_184703.1. NC_006624.1.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
1GEH X-ray 2.80 A/B/C/D/E 1-444 [» ]
3A12 X-ray 2.30 A/B/C/D/E/F/G/H/I/J 1-444 [» ]
3A13 X-ray 2.34 A/B/C/D/E/F/G/H/I/J 1-444 [» ]
3KDN X-ray 2.09 A/B/C/D/E/F/G/H/I/J 1-444 [» ]
3KDO X-ray 2.36 A/B/C/D/E/F/G/H/I/J 1-444 [» ]
ProteinModelPortali O93627.
SMRi O93627. Positions 12-443.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

IntActi O93627. 1 interaction.
MINTi MINT-8377356.
STRINGi 69014.TK2290.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai BAD86479 ; BAD86479 ; TK2290 .
GeneIDi 3234791.
KEGGi tko:TK2290.

Phylogenomic databases

eggNOGi COG1850.
HOGENOMi HOG000230831.
InParanoidi O93627.
KOi K01601.

Enzyme and pathway databases

BioCyci MetaCyc:MONOMER-13272.
TKOD69014:GH72-2342-MONOMER.

Miscellaneous databases

EvolutionaryTracei O93627.

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. "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, FUNCTION, CATALYTIC ACTIVITY.
    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, CARBAMYLATION AT LYS-189.
    Strain: ATCC BAA-918 / JCM 12380 / KOD1.

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: October 29, 2014
This is version 110 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

External Data

Dasty 3