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P00880 (RBL_SYNP6) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 115. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (2) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Ribulose bisphosphate carboxylase large chain

Short name=RuBisCO large subunit
EC=4.1.1.39
Gene names
Name:cbbL
Synonyms:rbcA, rbcL
Ordered Locus Names:syc0130_c
OrganismSynechococcus sp. (strain ATCC 27144 / PCC 6301 / SAUG 1402/1) (Anacystis nidulans) [Complete proteome] [HAMAP]
Taxonomic identifier269084 [NCBI]
Taxonomic lineageBacteriaCyanobacteriaOscillatoriophycideaeChroococcalesSynechococcus

Protein attributes

Sequence length472 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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. HAMAP-Rule MF_01338

Catalytic activity

2 3-phospho-D-glycerate + 2 H+ = D-ribulose 1,5-bisphosphate + CO2 + H2O. HAMAP-Rule MF_01338

3-phospho-D-glycerate + 2-phosphoglycolate = D-ribulose 1,5-bisphosphate + O2. HAMAP-Rule MF_01338

Cofactor

Binds 1 magnesium ion per subunit.

Subunit structure

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

Post-translational modification

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. HAMAP-Rule MF_01338

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".

Sequence similarities

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

Biophysicochemical properties

Kinetic parameters:

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

KM=39 µM for ribulose 1,5-bisphosphate Ref.6

KM=173 µM for CO2

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

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 472472Ribulose bisphosphate carboxylase large chain HAMAP-Rule MF_01338
PRO_0000062651

Sites

Active site1721Proton acceptor
Active site2911Proton acceptor
Metal binding1981Magnesium; via carbamate group
Metal binding2001Magnesium
Metal binding2011Magnesium
Binding site1201Substrate; in homodimeric partner
Binding site1701Substrate
Binding site1741Substrate
Binding site2921Substrate
Binding site3241Substrate
Binding site3761Substrate
Site3311Transition state stabilizer

Amino acid modifications

Modified residue1981N6-carboxylysine HAMAP-Rule MF_01338

Experimental info

Sequence conflict38 – 392RF → PV Ref.1
Sequence conflict3531A → R Ref.1

Secondary structure

.................................................................................... 472
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P00880 [UniParc].

Last modified February 15, 2005. Version 2.
Checksum: CDD8519AA9D493C9

FASTA47252,448
        10         20         30         40         50         60 
MPKTQSAAGY KAGVKDYKLT YYTPDYTPKD TDLLAAFRFS PQPGVPADEA GAAIAAESST 

        70         80         90        100        110        120 
GTWTTVWTDL LTDMDRYKGK CYHIEPVQGE ENSYFAFIAY PLDLFEEGSV TNILTSIVGN 

       130        140        150        160        170        180 
VFGFKAIRSL RLEDIRFPVA LVKTFQGPPH GIQVERDLLN KYGRPMLGCT IKPKLGLSAK 

       190        200        210        220        230        240 
NYGRAVYECL RGGLDFTKDD ENINSQPFQR WRDRFLFVAD AIHKSQAETG EIKGHYLNVT 

       250        260        270        280        290        300 
APTCEEMMKR AEFAKELGMP IIMHDFLTAG FTANTTLAKW CRDNGVLLHI HRAMHAVIDR 

       310        320        330        340        350        360 
QRNHGIHFRV LAKCLRLSGG DHLHSGTVVG KLEGDKASTL GFVDLMREDH IEADRSRGVF 

       370        380        390        400        410        420 
FTQDWASMPG VLPVASGGIH VWHMPALVEI FGDDSVLQFG GGTLGHPWGN APGATANRVA 

       430        440        450        460        470 
LEACVQARNE GRDLYREGGD ILREAGKWSP ELAAALDLWK EIKFEFETMD KL 

« Hide

References

« Hide 'large scale' references
[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].
[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).
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
K00486 Genomic DNA. No translation available.
X03220 Genomic DNA. Translation: CAA26972.1.
AP008231 Genomic DNA. Translation: BAD78320.1.
PIRRKYCL. A90941.
RefSeqYP_170840.1. NC_006576.1.

3D structure databases

PDBe
RCSB PDB
PDBj
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[»]
ProteinModelPortalP00880.
SMRP00880. Positions 6-472.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

DIPDIP-6210N.
STRING269084.syc0130_c.

Proteomic databases

PRIDEP00880.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaBAD78320; BAD78320; syc0130_c.
GeneID3200134.
KEGGsyc:syc0130_c.
PATRIC32485757. VBISynElo117686_0157.

Organism-specific databases

CMRSearch...

Phylogenomic databases

eggNOGCOG1850.
HOGENOMHOG000230831.
KOK01601.
OMAHRAMHAA.
OrthoDBEOG6ZKXMS.
ProtClustDBPRK04208.

Enzyme and pathway databases

BioCycSELO269084:GCDQ-135-MONOMER.
SABIO-RKP00880.

Family and domain databases

Gene3D3.20.20.110. 1 hit.
3.30.70.150. 1 hit.
HAMAPMF_01338. RuBisCO_L_type1.
InterProIPR020878. RuBisCo_large_chain_AS.
IPR020888. RuBisCO_lsu.
IPR000685. RuBisCO_lsu_C.
IPR017443. RuBisCO_lsu_fd_N.
IPR017444. RuBisCO_lsu_N.
[Graphical view]
PfamPF00016. RuBisCO_large. 1 hit.
PF02788. RuBisCO_large_N. 1 hit.
[Graphical view]
SUPFAMSSF51649. SSF51649. 1 hit.
SSF54966. SSF54966. 1 hit.
PROSITEPS00157. RUBISCO_LARGE. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceP00880.

Entry information

Entry nameRBL_SYNP6
AccessionPrimary (citable) accession number: P00880
Entry history
Integrated into UniProtKB/Swiss-Prot: July 21, 1986
Last sequence update: February 15, 2005
Last modified: April 16, 2014
This is version 115 of the entry and version 2 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references