Ribulose bisphosphate carboxylase large chain precursor - Oryza sativa subsp. japonica (Rice)

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Reviewed, UniProtKB/Swiss-Prot P0C512 (RBL_ORYSJ)

Last modified September 22, 2009. Version 18. History...

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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 names

Recommended name:
    Ribulose bisphosphate carboxylase large chain
      Short name=RuBisCO large subunit
    EC=4.1.1.39

Gene names

Name:	rbcL
ORF Names:	Nip064

Encoded on

Plastid; Chloroplast

Organism

Oryza sativa subsp. japonica (Rice)

Taxonomic identifier

39947 [NCBI]

Taxonomic lineage

Eukaryota › Viridiplantae › Streptophyta › Embryophyta › Tracheophyta › Spermatophyta › Magnoliophyta › Liliopsida › Poales › Poaceae › BEP clade › Ehrhartoideae › Oryzeae › Oryza

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Protein attributes

Sequence length	477 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence 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
Subcellular location	Plastid › chloroplast. HAMAP 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.
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.

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Ontologies

Keywords
Biological process	Calvin cycle Carbon dioxide fixation Photorespiration Photosynthesis
Cellular component	Chloroplast Plastid
Ligand	Magnesium Metal-binding
Molecular function	Lyase Monooxygenase Oxidoreductase
PTM	Acetylation Disulfide bond
Technical term	3D-structure Direct protein sequencing
Gene Ontology (GO)
Biological process	oxidation reduction Inferred from electronic annotation. Source: UniProtKB-KW photorespiration Inferred from electronic annotation. Source: UniProtKB-KW reductive pentose-phosphate cycle Inferred from electronic annotation. Source: UniProtKB-KW
Cellular component	chloroplast Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular function	magnesium ion binding Inferred from electronic annotation. Source: UniProtKB-KW monooxygenase activity Inferred from electronic annotation. Source: UniProtKB-KW ribulose-bisphosphate carboxylase activity Inferred from electronic annotation. Source: HAMAP
Complete GO annotation...

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Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Propeptide

1 – 2

By similarity

PRO_0000290101

Chain

3 – 477

475

Ribulose bisphosphate carboxylase large chain HAMAP MF_01338

PRO_0000290102

Sites

Active site

175

Proton acceptor HAMAP MF_01338

Active site

294

Proton acceptor HAMAP MF_01338

Metal binding

201

Magnesium; via carbamate group HAMAP MF_01338

Metal binding

203

Magnesium HAMAP MF_01338

Metal binding

204

Magnesium HAMAP MF_01338

Binding site

123

Substrate; in homodimeric partner HAMAP MF_01338

Binding site

173

Substrate HAMAP MF_01338

Binding site

177

Substrate HAMAP MF_01338

Binding site

295

Substrate HAMAP MF_01338

Binding site

327

Substrate HAMAP MF_01338

Binding site

379

Substrate HAMAP MF_01338

Site

334

Transition state stabilizer HAMAP MF_01338

Amino acid modifications

Modified residue

N-acetylproline By similarity

Modified residue

201

N6-carboxylysine HAMAP MF_01338

Disulfide bond

247

Interchain; in linked form HAMAP MF_01338

Secondary structure

477

Helix Strand Turn

Details...

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Sequences

Sequence

Length

Mass (Da)

Tools

P0C512-1 [UniParc].

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

477

52,881

        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

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References

	« Hide 'large scale' referencesShow '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: 2770692] [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: 15122023] [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: 16758443] [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.

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Cross-references

Sequence databases

D00207 Genomic DNA. Translation: BAA00147.1.
X15901 Genomic DNA. Translation: CAA34004.1.
AY522330 Genomic DNA. Translation: AAS46127.1. Different initiation.

PIR

RKRZL. JQ0231.

RefSeq

NP_039391.1.

3D structure databases

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1WDD	X-ray	1.35	A/E	1-477	[»]

ModBase

Search...

Genome annotation databases

GeneID

3131463.

GenomeReviews

Gene locus rbcL in contig AY522330_GR.

KEGG

osa:3131463.

NMPDR

fig|39947.1.peg.32.

Organism-specific databases

Gramene

P12089.

Family and domain databases

HAMAP

MF_01338.
[Tree]

InterPro

IPR000685. RuBisCO_lsu_C.
IPR017443. RuBisCO_lsu_fd_N.
IPR017444. RuBisCO_lsu_N.
[Graphical view]

Gene3D

G3DSA:3.20.20.110. RuBisCO_large. 1 hit.
G3DSA:3.30.70.150. RuBisCO_large. 1 hit.

Pfam

PF00016. RuBisCO_large. 1 hit.
PF02788. RuBisCO_large_N. 1 hit.
[Graphical view]

PROSITE

PS00157. RUBISCO_LARGE. 1 hit.
[Graphical view]

ProtoNet

Search...

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Entry information

Entry name

RBL_ORYSJ

Accession

Primary (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:	September 22, 2009
This is version 18 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

HAMAP (High-quality Automated and Manual Annotation of microbial Proteomes)

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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