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O85040

- RBL1_HALNC

UniProt

O85040 - RBL1_HALNC

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Protein

Ribulose bisphosphate carboxylase large chain

Gene

cbbL

Organism
Halothiobacillus neapolitanus (strain ATCC 23641 / c2) (Thiobacillus neapolitanus)
Status
Reviewed - Annotation score: 3 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.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

Mg2+UniRule annotationNote: Binds 1 Mg(2+) ion per subunit.UniRule annotation

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

BioCyciHNEA555778:GIVV-951-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
Ordered Locus Names:Hneap_0922
OrganismiHalothiobacillus neapolitanus (strain ATCC 23641 / c2) (Thiobacillus neapolitanus)
Taxonomic identifieri555778 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaChromatialesHalothiobacillaceaeHalothiobacillus
ProteomesiUP000009102: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 473473Ribulose bisphosphate carboxylase large chainPRO_0000062660Add
BLAST

Amino acid modifications

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

Expressioni

Inductioni

Produced when grown in air or in air supplemented with 5% CO2.

Interactioni

Subunit structurei

Heterohexadecamer of 8 large chains and 8 small chains.UniRule annotation

Protein-protein interaction databases

STRINGi555778.Hneap_0922.

Structurei

Secondary structure

1
473
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi28 – 3710Combined sources
Helixi43 – 5311Combined sources
Turni54 – 563Combined sources
Helixi63 – 675Combined sources
Turni70 – 723Combined sources
Beta strandi76 – 838Combined sources
Beta strandi86 – 9611Combined sources
Helixi98 – 1003Combined sources
Helixi106 – 1149Combined sources
Helixi117 – 1193Combined sources
Beta strandi123 – 13210Combined sources
Helixi135 – 1384Combined sources
Helixi148 – 1558Combined sources
Beta strandi162 – 1665Combined sources
Beta strandi170 – 1723Combined sources
Helixi175 – 18713Combined sources
Beta strandi191 – 1944Combined sources
Beta strandi200 – 2023Combined sources
Helixi207 – 22519Combined sources
Beta strandi230 – 2345Combined sources
Helixi240 – 25314Combined sources
Beta strandi257 – 2615Combined sources
Turni262 – 2654Combined sources
Helixi267 – 28014Combined sources
Beta strandi283 – 2875Combined sources
Helixi291 – 2955Combined sources
Beta strandi300 – 3023Combined sources
Helixi304 – 31411Combined sources
Beta strandi317 – 3204Combined sources
Helixi329 – 3313Combined sources
Helixi333 – 34311Combined sources
Beta strandi345 – 3473Combined sources
Helixi351 – 3533Combined sources
Beta strandi368 – 3747Combined sources
Helixi377 – 3793Combined sources
Helixi380 – 3878Combined sources
Beta strandi389 – 3946Combined sources
Helixi397 – 4004Combined sources
Helixi406 – 42520Combined sources
Turni430 – 4334Combined sources
Helixi434 – 4429Combined sources
Helixi446 – 45510Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1SVDX-ray1.80A1-473[»]
ProteinModelPortaliO85040.
SMRiO85040. Positions 16-460.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiO85040.

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.

O85040-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MAVKKYSAGV KEYRQTYWMP EYTPLDSDIL ACFKITPQPG VDREEAAAAV
60 70 80 90 100
AAESSTGTWT TVWTDLLTDM DYYKGRAYRI EDVPGDDAAF YAFIAYPIDL
110 120 130 140 150
FEEGSVVNVF TSLVGNVFGF KAVRGLRLED VRFPLAYVKT CGGPPHGIQV
160 170 180 190 200
ERDKMNKYGR PLLGCTIKPK LGLSAKNYGR AVYECLRGGL DFTKDDENIN
210 220 230 240 250
SQPFMRWRDR FLFVQDATET AEAQTGERKG HYLNVTAPTP EEMYKRAEFA
260 270 280 290 300
KEIGAPIIMH DYITGGFTAN TGLAKWCQDN GVLLHIHRAM HAVIDRNPNH
310 320 330 340 350
GIHFRVLTKI LRLSGGDHLH TGTVVGKLEG DRASTLGWID LLRESFIPED
360 370 380 390 400
RSRGIFFDQD WGSMPGVFAV ASGGIHVWHM PALVNIFGDD SVLQFGGGTL
410 420 430 440 450
GHPWGNAAGA AANRVALEAC VEARNQGRDI EKEGKEILTA AAQHSPELKI
460 470
AMETWKEIKF EFDTVDKLDT QNR
Length:473
Mass (Da):52,636
Last modified:November 1, 1998 - v1
Checksum:iB84D2EDE46CAF7D8
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF038430 Genomic DNA. Translation: AAC32549.1.
CP001801 Genomic DNA. Translation: ACX95765.1.
RefSeqiWP_012823801.1. NC_013422.1.
YP_003262812.1. NC_013422.1.

Genome annotation databases

EnsemblBacteriaiACX95765; ACX95765; Hneap_0922.
GeneIDi8534063.
KEGGihna:Hneap_0922.
PATRICi32205718. VBIHalNea120669_0941.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF038430 Genomic DNA. Translation: AAC32549.1 .
CP001801 Genomic DNA. Translation: ACX95765.1 .
RefSeqi WP_012823801.1. NC_013422.1.
YP_003262812.1. NC_013422.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
1SVD X-ray 1.80 A 1-473 [» ]
ProteinModelPortali O85040.
SMRi O85040. Positions 16-460.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

STRINGi 555778.Hneap_0922.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai ACX95765 ; ACX95765 ; Hneap_0922 .
GeneIDi 8534063.
KEGGi hna:Hneap_0922.
PATRICi 32205718. VBIHalNea120669_0941.

Phylogenomic databases

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

Enzyme and pathway databases

BioCyci HNEA555778:GIVV-951-MONOMER.

Miscellaneous databases

EvolutionaryTracei O85040.

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. "Insertion mutation of the form I cbbL gene encoding ribulose bisphosphate carboxylase/oxygenase (RuBisCO) in Thiobacillus neapolitanus results in expression of form II RuBisCO, loss of carboxysomes, and an increased CO2 requirement for growth."
    Baker S.H., Jin S., Aldrich H.C., Howard G.T., Shively J.M.
    J. Bacteriol. 180:4133-4139(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], EXPRESSION.
  2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 23641 / c2.
  3. "The structure of Halothiobacillus neapolitanus Rubisco."
    Kerfeld C.A., Sawaya M.R., Pashkov I., Cannon G., Williams E., Tran K., Yeates T.O.
    Submitted (APR-2005) to the PDB data bank
    Cited for: X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS).

Entry informationi

Entry nameiRBL1_HALNC
AccessioniPrimary (citable) accession number: O85040
Secondary accession number(s): D0KZ92
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 22, 2005
Last sequence update: November 1, 1998
Last modified: November 26, 2014
This is version 78 of the entry and version 1 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

3D-structure, Complete proteome, 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