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P00880

- RBL_SYNP6

UniProt

P00880 - RBL_SYNP6

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Protein
Ribulose bisphosphate carboxylase large chain
Gene
cbbL, rbcA, rbcL, syc0130_c
Organism
Synechococcus sp. (strain ATCC 27144 / PCC 6301 / SAUG 1402/1) (Anacystis nidulans)
Status
Reviewed - Annotation score: 5 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 in the photorespiration process. 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

Binds 1 magnesium ion per subunit.

Kineticsi

The CO2/O2 specificity factor (tau) is 39.

  1. KM=39 µM for ribulose 1,5-bisphosphate1 Publication
  2. KM=173 µM for CO2

Vmax=2.5 µmol/min/mg enzyme with CO2 as substrate

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei120 – 1201Substrate; in homodimeric partner
Binding sitei170 – 1701Substrate
Active sitei172 – 1721Proton acceptor
Binding sitei174 – 1741Substrate
Metal bindingi198 – 1981Magnesium; via carbamate group
Metal bindingi200 – 2001Magnesium
Metal bindingi201 – 2011Magnesium
Active sitei291 – 2911Proton acceptor
Binding sitei292 – 2921Substrate
Binding sitei324 – 3241Substrate
Sitei331 – 3311Transition state stabilizer
Binding sitei376 – 3761Substrate

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

Keywords - Molecular functioni

Lyase, Monooxygenase, Oxidoreductase

Keywords - Biological processi

Calvin cycle, Carbon dioxide fixation, Photorespiration, Photosynthesis

Keywords - Ligandi

Magnesium, Metal-binding

Enzyme and pathway databases

BioCyciSELO269084:GCDQ-135-MONOMER.
SABIO-RKP00880.

Names & Taxonomyi

Protein namesi
Recommended name:
Ribulose bisphosphate carboxylase large chain (EC:4.1.1.39)
Short name:
RuBisCO large subunit
Gene namesi
Name:cbbL
Synonyms:rbcA, rbcL
Ordered Locus Names:syc0130_c
OrganismiSynechococcus sp. (strain ATCC 27144 / PCC 6301 / SAUG 1402/1) (Anacystis nidulans)
Taxonomic identifieri269084 [NCBI]
Taxonomic lineageiBacteriaCyanobacteriaOscillatoriophycideaeChroococcalesSynechococcus
ProteomesiUP000001175: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 472472Ribulose bisphosphate carboxylase large chainUniRule annotation
PRO_0000062651Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei198 – 1981N6-carboxylysineUniRule annotation

Post-translational modificationi

The disulfide bond which can form in the large chain dimeric partners within the hexadecamer appears to be associated with oxidative stress and protein turnover By similarity. Note this disulfide bond has not been seen in these crystal structures.UniRule annotation

Keywords - PTMi

Disulfide bond

Proteomic databases

PRIDEiP00880.

Interactioni

Subunit structurei

Heterohexadecamer of 8 large chains and 8 small chains; disulfide-linked. The disulfide link is formed within the large subunit homodimers.

Protein-protein interaction databases

DIPiDIP-6210N.
STRINGi269084.syc0130_c.

Structurei

Secondary structure

Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi18 – 214
Beta strandi32 – 4110
Helixi47 – 5711
Turni58 – 603
Beta strandi63 – 653
Helixi67 – 715
Helixi74 – 774
Beta strandi80 – 867
Beta strandi94 – 1007
Helixi102 – 1043
Helixi110 – 1189
Helixi121 – 1233
Beta strandi127 – 13610
Helixi139 – 1424
Helixi152 – 1598
Beta strandi166 – 1683
Beta strandi172 – 1754
Helixi179 – 19113
Beta strandi195 – 1984
Beta strandi204 – 2063
Helixi211 – 22919
Beta strandi234 – 2385
Helixi244 – 25613
Beta strandi260 – 2656
Helixi266 – 2694
Helixi271 – 28414
Beta strandi287 – 2915
Helixi295 – 2995
Beta strandi302 – 3065
Helixi308 – 31811
Beta strandi321 – 3244
Beta strandi328 – 3325
Helixi336 – 34712
Beta strandi349 – 3513
Helixi355 – 3573
Beta strandi372 – 3787
Helixi381 – 3833
Helixi384 – 3918
Beta strandi396 – 3983
Helixi401 – 4044
Helixi410 – 43021
Helixi434 – 44815
Helixi450 – 45910

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1RBLX-ray2.20A/B/C/D/E/F/G/H6-472[»]
1RSCX-ray2.30A/B/C/D/E/F/G/H1-472[»]
2WVWelectron microscopy9.00A/B/C/D/E/F/G/H1-472[»]
3RG6X-ray3.20A/B1-472[»]
ProteinModelPortaliP00880.
SMRiP00880. Positions 6-472.

Miscellaneous databases

EvolutionaryTraceiP00880.

Family & Domainsi

Sequence similaritiesi

Phylogenomic databases

eggNOGiCOG1850.
HOGENOMiHOG000230831.
KOiK01601.
OMAiFTQDWAS.
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.

P00880-1 [UniParc]FASTAAdd to Basket

« Hide

MPKTQSAAGY KAGVKDYKLT YYTPDYTPKD TDLLAAFRFS PQPGVPADEA    50
GAAIAAESST GTWTTVWTDL LTDMDRYKGK CYHIEPVQGE ENSYFAFIAY 100
PLDLFEEGSV TNILTSIVGN VFGFKAIRSL RLEDIRFPVA LVKTFQGPPH 150
GIQVERDLLN KYGRPMLGCT IKPKLGLSAK NYGRAVYECL RGGLDFTKDD 200
ENINSQPFQR WRDRFLFVAD AIHKSQAETG EIKGHYLNVT APTCEEMMKR 250
AEFAKELGMP IIMHDFLTAG FTANTTLAKW CRDNGVLLHI HRAMHAVIDR 300
QRNHGIHFRV LAKCLRLSGG DHLHSGTVVG KLEGDKASTL GFVDLMREDH 350
IEADRSRGVF FTQDWASMPG VLPVASGGIH VWHMPALVEI FGDDSVLQFG 400
GGTLGHPWGN APGATANRVA LEACVQARNE GRDLYREGGD ILREAGKWSP 450
ELAAALDLWK EIKFEFETMD KL 472
Length:472
Mass (Da):52,448
Last modified:February 15, 2005 - v2
Checksum:iCDD8519AA9D493C9
GO

Sequence conflict

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti38 – 392RF → PV1 Publication
Sequence conflicti353 – 3531A → R1 Publication

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
K00486 Genomic DNA. No translation available.
X03220 Genomic DNA. Translation: CAA26972.1.
AP008231 Genomic DNA. Translation: BAD78320.1.
PIRiA90941. RKYCL.
RefSeqiWP_011242444.1. NC_006576.1.
YP_170840.1. NC_006576.1.

Genome annotation databases

EnsemblBacteriaiBAD78320; BAD78320; syc0130_c.
GeneIDi3200134.
KEGGisyc:syc0130_c.
PATRICi32485757. VBISynElo117686_0157.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
K00486 Genomic DNA. No translation available.
X03220 Genomic DNA. Translation: CAA26972.1 .
AP008231 Genomic DNA. Translation: BAD78320.1 .
PIRi A90941. RKYCL.
RefSeqi WP_011242444.1. NC_006576.1.
YP_170840.1. NC_006576.1.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
1RBL X-ray 2.20 A/B/C/D/E/F/G/H 6-472 [» ]
1RSC X-ray 2.30 A/B/C/D/E/F/G/H 1-472 [» ]
2WVW electron microscopy 9.00 A/B/C/D/E/F/G/H 1-472 [» ]
3RG6 X-ray 3.20 A/B 1-472 [» ]
ProteinModelPortali P00880.
SMRi P00880. Positions 6-472.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

DIPi DIP-6210N.
STRINGi 269084.syc0130_c.

Proteomic databases

PRIDEi P00880.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai BAD78320 ; BAD78320 ; syc0130_c .
GeneIDi 3200134.
KEGGi syc:syc0130_c.
PATRICi 32485757. VBISynElo117686_0157.

Phylogenomic databases

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

Enzyme and pathway databases

BioCyci SELO269084:GCDQ-135-MONOMER.
SABIO-RK P00880.

Miscellaneous databases

EvolutionaryTracei P00880.

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. "The nucleotide sequence for the large subunit of ribulose 1,5-bisphosphate carboxylase from a unicellular cyanobacterium, Synechococcus PCC6301."
    Reichelt B.Y., Delaney S.F.
    DNA 2:121-129(1983) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  2. "Molecular cloning and sequence analysis of the cyanobacterial gene for the large subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase."
    Shinozaki K., Yamada C., Takahata N., Sugiura M.
    Proc. Natl. Acad. Sci. U.S.A. 80:4050-4054(1983) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], CARBAMYLATION AT LYS-198.
  3. "Genes for the large and small subunits of ribulose-1,5-bisphosphate carboxylase/oxygenase constitute a single operon in a cyanobacterium Anacystis nidulans 6301."
    Shinozaki K., Sugiura M.
    Mol. Gen. Genet. 200:27-32(1985)
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  4. "Complete nucleotide sequence of the freshwater unicellular cyanobacterium Synechococcus elongatus PCC 6301 chromosome: gene content and organization."
    Sugita C., Ogata K., Shikata M., Jikuya H., Takano J., Furumichi M., Kanehisa M., Omata T., Sugiura M., Sugita M.
    Photosyn. Res. 93:55-67(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 27144 / PCC 6301 / SAUG 1402/1.
  5. "High substrate specificity factor ribulose bisphosphate carboxylase/oxygenase from eukaryotic marine algae and properties of recombinant cyanobacterial RubiSCO containing 'algal' residue modifications."
    Read B.A., Tabita F.R.
    Arch. Biochem. Biophys. 312:210-218(1994) [PubMed] [Europe PMC] [Abstract]
    Cited for: PROTEIN SEQUENCE OF 333-342.
  6. "Closely related form I ribulose bisphosphate carboxylase/oxygenase molecules that possess different CO2/O2 substrate specificities."
    Horken K.M., Tabita F.R.
    Arch. Biochem. Biophys. 361:183-194(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: KINETIC PARAMETERS.
  7. "The X-ray structure of Synechococcus ribulose-bisphosphate carboxylase/oxygenase-activated quaternary complex at 2.2-A resolution."
    Newman J., Gutteridge S.
    J. Biol. Chem. 268:25876-25886(1993) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS).
  8. "Structure of an effector-induced inactivated state of ribulose 1,5-bisphosphate carboxylase/oxygenase: the binary complex between enzyme and xylulose 1,5-bisphosphate."
    Newman J., Gutteridge S.
    Structure 2:495-502(1994) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS).

Entry informationi

Entry nameiRBL_SYNP6
AccessioniPrimary (citable) accession number: P00880
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 21, 1986
Last sequence update: February 15, 2005
Last modified: September 3, 2014
This is version 118 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".

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing

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

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