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Reviewed, UniProtKB/Swiss-Prot P00880 (RBL_SYNP6)

Last modified June 16, 2009. Version 85. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (2) | Third-party data | Customize display text xml rdf/xml gff fasta
Names and origin · Protein attributes · General annotation (Comments) · Ontologies · Sequence annotation (Features) · Sequences · References · Cross-references · Entry information · Relevant documents

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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 lineageBacteria › Cyanobacteria › Chroococcales › Synechococcus

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Protein attributes

Sequence length472 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is not processed.
Protein existenceEvidence at protein level.

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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 MF_01338

Catalytic activity

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

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

Cofactor

Binds 1 magnesium ion per subunit. HAMAP MF_01338

Subunit structure

Heterohexadecamer of 8 large chains and 8 small chains; disulfide-linked. The disulfide link is formed within the large subunit homodimers. HAMAP MF_01338

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.

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". HAMAP MF_01338

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

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Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 472472Ribulose bisphosphate carboxylase large chain HAMAP MF_01338
PRO_0000062651

Sites

Active site1721Proton acceptor HAMAP MF_01338
Active site2911Proton acceptor HAMAP MF_01338
Metal binding1981Magnesium; via carbamate group HAMAP MF_01338
Metal binding2001Magnesium HAMAP MF_01338
Metal binding2011Magnesium HAMAP MF_01338
Binding site1201Substrate; in homodimeric partner HAMAP MF_01338
Binding site1701Substrate HAMAP MF_01338
Binding site1741Substrate HAMAP MF_01338
Binding site2921Substrate HAMAP MF_01338
Binding site3241Substrate HAMAP MF_01338
Binding site3761Substrate HAMAP MF_01338
Site3311Transition state stabilizer HAMAP MF_01338

Amino acid modifications

Modified residue1981N6-carboxylysine HAMAP MF_01338

Experimental info

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

Secondary structure

1 .................................................................................... 472
Helix Strand Turn

Details...

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Sequences

Sequence LengthMass (Da)Tools
P00880-1 [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

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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: 6307620] [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: 16593333] [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: 17211581] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[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: 8031129] [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: 9882445] [Abstract]
Cited for: KINETIC CHARACTERIZATION.
[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: 8245022] [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: 7922027] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS).
+Additional computationally mapped references.

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Cross-references

Sequence databases

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

3D structure databases

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[»]
ModBaseSearch...

Protein-protein interaction databases

DIPDIP:6210N.

Genome annotation databases

GeneID3200134.
GenomeReviewsGene locus syc0130_c in contig AP008231_GR.
KEGGsyc:syc0130_c.

Organism-specific databases

CMRSearch...

Phylogenomic databases

HOGENOMP00880.
OMAP00880. YTPDYTP.

Enzyme and pathway databases

BioCycSELO269084:SYC0130_C-MON.

Family and domain databases

HAMAPMF_01338.
[Tree]
InterProIPR000685. RuBisCO_lsu_C.
IPR017443. RuBisCO_lsu_fd_N.
IPR017444. RuBisCO_lsu_N.
[Graphical view]
Gene3DG3DSA:3.20.20.110. RuBisCO_large. 1 hit.
G3DSA:3.30.70.150. RuBisCO_large. 1 hit.
PfamPF00016. RuBisCO_large. 1 hit.
PF02788. RuBisCO_large_N. 1 hit.
[Graphical view]
PROSITEPS00157. RUBISCO_LARGE. 1 hit.
[Graphical view]
ProtoNetSearch...

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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: June 16, 2009
This is version 85 of the entry and version 2 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation projectHAMAP (High-quality Automated and Manual Annotation of microbial Proteomes)

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Relevant documents

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families

Names and origin · Protein attributes · General annotation (Comments) · Ontologies · Sequence annotation (Features) · Sequences · References · Cross-references · Entry information · Relevant documents