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Q56259

- RBL1_THIDA

UniProt

Q56259 - RBL1_THIDA

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Protein

Ribulose bisphosphate carboxylase large chain

Gene

cbbL

Organism
Thiobacillus denitrificans (strain ATCC 25259)
Status
Reviewed - Annotation score: 4 out of 5- Experimental evidence at protein leveli

Functioni

RuBisCO catalyzes two reactions: the carboxylation of D-ribulose 1,5-bisphosphate, the primary event in carbon dioxide fixation, as well as the oxidative fragmentation of the pentose substrate. Both reactions occur simultaneously and in competition at the same active site.1 PublicationUniRule 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 Mg(2+) ion per subunit.UniRule annotation

Kineticsi

The CO2/O2 specificity factor (tau) is 46.

  1. KM=43 µM for ribulose 1,5-bisphosphate1 Publication
  2. KM=138 µM for CO21 Publication
  3. KM=1637 µM for O21 Publication

Vmax=1.8 µmol/min/mg enzyme with CO2 as substrate1 Publication

Vmax=0.5 µmol/min/mg enzyme with O2 as substrate1 Publication

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei116 – 1161Substrate; in homodimeric partnerUniRule annotation
Binding sitei166 – 1661SubstrateUniRule annotation
Active sitei168 – 1681Proton acceptorUniRule annotation
Binding sitei170 – 1701SubstrateUniRule annotation
Metal bindingi194 – 1941Magnesium; via carbamate groupUniRule annotation
Metal bindingi196 – 1961MagnesiumUniRule annotation
Metal bindingi197 – 1971MagnesiumUniRule annotation
Active sitei287 – 2871Proton acceptorUniRule annotation
Binding sitei288 – 2881SubstrateUniRule annotation
Binding sitei320 – 3201SubstrateUniRule annotation
Sitei327 – 3271Transition state stabilizerUniRule annotation
Binding sitei372 – 3721SubstrateUniRule annotation

GO - Molecular functioni

  1. magnesium ion binding Source: UniProtKB-HAMAP
  2. monooxygenase activity Source: UniProtKB-KW
  3. ribulose-bisphosphate carboxylase activity Source: UniProtKB-HAMAP

GO - Biological processi

  1. reductive pentose-phosphate cycle Source: UniProtKB-KW
Complete GO annotation...

Keywords - Molecular functioni

Lyase, Monooxygenase, Oxidoreductase

Keywords - Biological processi

Calvin cycle, Carbon dioxide fixation

Keywords - Ligandi

Magnesium, Metal-binding

Enzyme and pathway databases

BioCyciTDEN292415:GHWG-2674-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Ribulose bisphosphate carboxylase large chainUniRule annotation (EC:4.1.1.39UniRule annotation)
Short name:
RuBisCO large subunitUniRule annotation
Gene namesi
Name:cbbLUniRule annotation
Synonyms:cbbL1
Ordered Locus Names:Tbd_2624
OrganismiThiobacillus denitrificans (strain ATCC 25259)
Taxonomic identifieri292415 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaBetaproteobacteriaHydrogenophilalesHydrogenophilaceaeThiobacillus
ProteomesiUP000008291: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 473473Ribulose bisphosphate carboxylase large chainPRO_0000062656Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei194 – 1941N6-carboxylysineUniRule annotation

Interactioni

Subunit structurei

Heterohexadecamer of 8 large chains and 8 small chains (By similarity). In R.sphaeroides the complex is approximately 500 kDa.1 PublicationUniRule annotation

Protein-protein interaction databases

STRINGi292415.Tbd_2624.

Structurei

3D structure databases

ProteinModelPortaliQ56259.
SMRiQ56259. Positions 16-460.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiCOG1850.
HOGENOMiHOG000230831.
KOiK01601.
OMAiMETWKEV.
OrthoDBiEOG6ZKXMS.

Family and domain databases

Gene3Di3.20.20.110. 1 hit.
3.30.70.150. 1 hit.
HAMAPiMF_01338. RuBisCO_L_type1.
InterProiIPR020878. RuBisCo_large_chain_AS.
IPR020888. RuBisCO_lsu.
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.
PROSITEiPS00157. RUBISCO_LARGE. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q56259-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MAVKTYSAGV KEYRQTYWMP EYTPLDTDIL ACFKITPQAG VDREEAAAAV
60 70 80 90 100
AAESSTGTWT TVWTDLLTDL DYYKGRAYAI EDVPGDDTCF YAFIAYPIDL
110 120 130 140 150
FEEGSVVNVF TSLVGNVFGF KAVRALRLED VRFPIAYVKT CGGPPHGIQV
160 170 180 190 200
ERDVMNKYGR PLLGCTIKPK LGLSAKNYGR AVYECLRGGL DFTKDDENVN
210 220 230 240 250
SQPFMRWRQR FDFVMEAIQK SERETGERKG HYLNVTAPTP EEMYKRAEYA
260 270 280 290 300
KEIGAPIIMH DYITGGFCAN TGLANWCRDN GMLLHIHRAM HAVLDRNPHH
310 320 330 340 350
GIHFRVLTKI LRLSGGDHLH SGTVVGKLEG DREATLGWID MMRDSFVKED
360 370 380 390 400
RSRGIFFDQD WGSMPGVFPV ASGGIHVWHM PALVTIFGDD SVLQFGGGTL
410 420 430 440 450
GHPWGNAAGA AANRVALEAC VEARNKGVAI EKEGKTVLTE AAKNSPELKI
460 470
AMETWKEIKF EFDTVDKLDV AHK
Length:473
Mass (Da):52,694
Last modified:January 1, 1998 - v2
Checksum:i470DC11519D580A7
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L42940 Genomic DNA. Translation: AAB70697.1.
CP000116 Genomic DNA. Translation: AAZ98577.1.
RefSeqiWP_011313136.1. NC_007404.1.
YP_316382.1. NC_007404.1.

Genome annotation databases

EnsemblBacteriaiAAZ98577; AAZ98577; Tbd_2624.
GeneIDi3672353.
KEGGitbd:Tbd_2624.
PATRICi23971443. VBIThiDen82923_2608.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L42940 Genomic DNA. Translation: AAB70697.1 .
CP000116 Genomic DNA. Translation: AAZ98577.1 .
RefSeqi WP_011313136.1. NC_007404.1.
YP_316382.1. NC_007404.1.

3D structure databases

ProteinModelPortali Q56259.
SMRi Q56259. Positions 16-460.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

STRINGi 292415.Tbd_2624.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai AAZ98577 ; AAZ98577 ; Tbd_2624 .
GeneIDi 3672353.
KEGGi tbd:Tbd_2624.
PATRICi 23971443. VBIThiDen82923_2608.

Phylogenomic databases

eggNOGi COG1850.
HOGENOMi HOG000230831.
KOi K01601.
OMAi METWKEV.
OrthoDBi EOG6ZKXMS.

Enzyme and pathway databases

BioCyci TDEN292415:GHWG-2674-MONOMER.

Family and domain databases

Gene3Di 3.20.20.110. 1 hit.
3.30.70.150. 1 hit.
HAMAPi MF_01338. RuBisCO_L_type1.
InterProi IPR020878. RuBisCo_large_chain_AS.
IPR020888. RuBisCO_lsu.
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.
PROSITEi PS00157. RUBISCO_LARGE. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  1. "Deduced amino acid sequence, functional expression, and unique enzymatic properties of the form I and form II ribulose bisphosphate carboxylase/oxygenase from the chemoautotrophic bacterium Thiobacillus denitrificans."
    Hernandez J.M., Baker S.H., Lorbach S.C., Shively J.M., Tabita F.R.
    J. Bacteriol. 178:347-356(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], KINETIC PARAMETERS, FUNCTION, SUBUNIT.
  2. "The genome sequence of the obligately chemolithoautotrophic, facultatively anaerobic bacterium Thiobacillus denitrificans."
    Beller H.R., Chain P.S., Letain T.E., Chakicherla A., Larimer F.W., Richardson P.M., Coleman M.A., Wood A.P., Kelly D.P.
    J. Bacteriol. 188:1473-1488(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 25259.

Entry informationi

Entry nameiRBL1_THIDA
AccessioniPrimary (citable) accession number: Q56259
Secondary accession number(s): Q3SFM9
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 15, 1998
Last sequence update: January 1, 1998
Last modified: November 26, 2014
This is version 95 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Miscellaneous

The basic functional RuBisCO is composed of a large chain homodimer in a "head-to-tail" conformation. In form I RuBisCO this homodimer is arranged in a barrel-like tetramer with the small subunits forming a tetrameric "cap" on each end of the "barrel".UniRule annotation

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3