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P0C512 (RBL_ORYSJ) Reviewed, UniProtKB/Swiss-Prot

Last modified May 1, 2013. Version 44. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (3) | 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
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:rbcL
ORF Names:Nip064
Encoded onPlastid; Chloroplast
OrganismOryza sativa subsp. japonica (Rice) [Reference proteome]
Taxonomic identifier39947 [NCBI]
Taxonomic lineageEukaryota › Viridiplantae › Streptophyta › Embryophyta › Tracheophyta › Spermatophyta › Magnoliophyta › Liliopsida › Poales › Poaceae › BEP clade › Ehrhartoideae › Oryzeae › Oryza ›

Protein attributes

Sequence length477 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
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.

Subcellular location

Plastid › chloroplast HAMAP-Rule MF_01338.

Post-translational modification

The disulfide bond which can form between Cys-247 in the large chain dimeric partners within the hexadecamer appears to be associated with oxidative stress and protein turnover By similarity. The disulfide bond reported in 1WDD may be the result of oxidation during crystallization. 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". HAMAP-Rule MF_01338

Sequence similarities

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

Sequence caution

The sequence AAS46127.1 differs from that shown. Reason: Erroneous initiation.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Propeptide1 – 22 By similarity
PRO_0000290101
Chain3 – 477475Ribulose bisphosphate carboxylase large chain HAMAP-Rule MF_01338
PRO_0000290102

Sites

Active site1751Proton acceptor
Active site2941Proton acceptor
Metal binding2011Magnesium; via carbamate group
Metal binding2031Magnesium
Metal binding2041Magnesium
Binding site1231Substrate; in homodimeric partner
Binding site1731Substrate
Binding site1771Substrate
Binding site2951Substrate
Binding site3271Substrate
Binding site3791Substrate
Site3341Transition state stabilizer

Amino acid modifications

Modified residue31N-acetylproline By similarity
Modified residue2011N6-carboxylysine HAMAP-Rule MF_01338
Disulfide bond247Interchain; in linked form HAMAP-Rule MF_01338

Secondary structure

1 .................................................................................... 477
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P0C512 [UniParc].

Last modified June 12, 2007. Version 1.
Checksum: 8EECF4F8F1F0A8F9

FASTA47752,881
        10         20         30         40         50         60 
MSPQTETKAS VGFKAGVKDY KLTYYTPEYE TKDTDILAAF RVTPQPGVPP EEAGAAVAAE 

        70         80         90        100        110        120 
SSTGTWTTVW TDGLTSLDRY KGRCYHIEPV VGEDNQYIAY VAYPLDLFEE GSVTNMFTSI 

       130        140        150        160        170        180 
VGNVFGFKAL RALRLEDLRI PPTYSKTFQG PPHGIQVERD KLNKYGRPLL GCTIKPKLGL 

       190        200        210        220        230        240 
SAKNYGRACY ECLRGGLDFT KDDENVNSQP FMRWRDRFVF CAEAIYKSQA ETGEIKGHYL 

       250        260        270        280        290        300 
NATAGTCEEM IKRAVFAREL GVPIVMHDYL TGGFTANTSL AHYCRDNGLL LHIHRAMHAV 

       310        320        330        340        350        360 
IDRQKNHGMH FRVLAKALRM SGGDHIHAGT VVGKLEGERE MTLGFVDLLR DDFIEKDRAR 

       370        380        390        400        410        420 
GIFFTQDWVS MPGVIPVASG GIHVWHMPAL TEIFGDDSVL QFGGGTLGHP WGNAPGAAAN 

       430        440        450        460        470 
RVALEACVQA RNEGRDLARE GNEIIRSACK WSPELAAACE IWKAIKFEFE PVDKLDS

« Hide

References

« Hide 'large scale' references
[1]"Nucleotide sequence and expression of the gene for the large subunit of rice ribulose 1,5-bisphosphate carboxylase."
Nishizawa Y., Hirai A.
Jpn. J. Genet. 62:389-395(1987)
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
Strain: cv. Nipponbare.
[2]"The complete sequence of the rice (Oryza sativa) chloroplast genome: intermolecular recombination between distinct tRNA genes accounts for a major plastid DNA inversion during the evolution of the cereals."
Hiratsuka J., Shimada H., Whittier R., Ishibashi T., Sakamoto M., Mori M., Kondo C., Honji Y., Sun C.-R., Meng B.-Y., Li Y.-Q., Kanno A., Nishizawa Y., Hirai A., Shinozaki K., Sugiura M.
Mol. Gen. Genet. 217:185-194(1989) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: cv. Nipponbare.
[3]"A comparison of rice chloroplast genomes."
Tang J., Xia H., Cao M., Zhang X., Zeng W., Hu S., Tong W., Wang J., Wang J., Yu J., Yang H., Zhu L.
Plant Physiol. 135:412-420(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: cv. Nipponbare.
[4]"Proteomic analysis of rice leaf, stem and root tissues during growth course."
Nozu Y., Tsugita A., Kamijo K.
Proteomics 6:3665-3670(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: PROTEIN SEQUENCE [LARGE SCALE ANALYSIS] OF 41-48; 180-186 AND 320-327, MASS SPECTROMETRY.
Strain: cv. Nipponbare.
[5]"Crystal structure of activated rice RuBisCO complexed with 2-carboxyarabinitol-1,5-bisphosphate."
Mizohata E., Matsumura H., Ueno T., Ishida H., Inoue T., Mae T., Kai Y.
Submitted (NOV-2004) to the PDB data bank
Cited for: X-RAY CRYSTALLOGRAPHY (1.35 ANGSTROMS).
Strain: cv. Notohikari.
Tissue: Leaf.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ		D00207 Genomic DNA. Translation: BAA00147.1.
X15901 Genomic DNA. Translation: CAA34004.1.
AY522330 Genomic DNA. Translation: AAS46127.1. Different initiation.
PIRRKRZL. JQ0231.
RefSeqNP_039391.1. NC_001320.1.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1WDDX-ray1.35A/E1-477[»]
3AXKX-ray1.90A/B1-477[»]
3AXMX-ray1.65A/B/C/D/E/F/G/H1-477[»]
ProteinModelPortalP0C512.
SMRP0C512. Positions 11-475.
ModBaseSearch...

Proteomic databases

PaxDbP0C512.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsLOC_Osp1g00420.1; LOC_Osp1g00420.1; LOC_Osp1g00420.
GeneID3131463.
KEGGosa:3131463.

Organism-specific databases

GrameneP0C512.

Phylogenomic databases

eggNOGCOG1850.
KOK01601.
OMAFPGPRFG.
ProtClustDBCHL00040.

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. RuBisCO_large. 1 hit.
SSF54966. RuBisCO_large. 1 hit.
PROSITEPS00157. RUBISCO_LARGE. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceP0C512.

Entry information

Entry nameRBL_ORYSJ
AccessionPrimary (citable) accession number: P0C512
Secondary accession number(s): P12089, Q6QY04, Q6QY68
Entry history
Integrated into UniProtKB/Swiss-Prot: June 12, 2007
Last sequence update: June 12, 2007
Last modified: May 1, 2013
This is version 44 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Relevant documents

Oryza sativa (rice)

Index of Oryza sativa entries and their corresponding gene designations

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families

to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents