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P0C512

- RBL_ORYSJ

UniProt

P0C512 - RBL_ORYSJ

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Protein

Ribulose bisphosphate carboxylase large chain

Gene

rbcL

Organism
Oryza sativa subsp. japonica (Rice)
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.

Catalytic activityi

2 3-phospho-D-glycerate + 2 H+ = D-ribulose 1,5-bisphosphate + CO2 + H2O.
3-phospho-D-glycerate + 2-phosphoglycolate = D-ribulose 1,5-bisphosphate + O2.

Cofactori

Binds 1 magnesium ion per subunit.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei123 – 1231Substrate; in homodimeric partner
Binding sitei173 – 1731Substrate
Active sitei175 – 1751Proton acceptor
Binding sitei177 – 1771Substrate
Metal bindingi201 – 2011Magnesium; via carbamate group
Metal bindingi203 – 2031Magnesium
Metal bindingi204 – 2041Magnesium
Active sitei294 – 2941Proton acceptor
Binding sitei295 – 2951Substrate
Binding sitei327 – 3271Substrate
Sitei334 – 3341Transition state stabilizer
Binding sitei379 – 3791Substrate

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

Names & Taxonomyi

Protein namesi
Recommended name:
Ribulose bisphosphate carboxylase large chain (EC:4.1.1.39)
Short name:
RuBisCO large subunit
Gene namesi
Name:rbcL
Ordered Locus Names:LOC_Osp1g00420
ORF Names:Nip064
Encoded oniPlastid; Chloroplast
OrganismiOryza sativa subsp. japonica (Rice)
Taxonomic identifieri39947 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaLiliopsidaPoalesPoaceaeBEP cladeEhrhartoideaeOryzeaeOryza
ProteomesiUP000000763: Chloroplast

Organism-specific databases

GrameneiP0C512.

Subcellular locationi

GO - Cellular componenti

  1. chloroplast Source: UniProtKB-HAMAP
  2. plastid Source: Gramene
Complete GO annotation...

Keywords - Cellular componenti

Chloroplast, Plastid

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Propeptidei1 – 22By similarityPRO_0000290101
Chaini3 – 477475Ribulose bisphosphate carboxylase large chainPRO_0000290102Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei3 – 31N-acetylprolineBy similarity
Modified residuei201 – 2011N6-carboxylysine1 Publication
Disulfide bondi247 – 247Interchain; in linked form

Post-translational modificationi

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.By similarity

Keywords - PTMi

Acetylation, Disulfide bond

Proteomic databases

PaxDbiP0C512.
PRIDEiP0C512.

Expressioni

Gene expression databases

ExpressionAtlasiP0C512. baseline.

Interactioni

Subunit structurei

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

Structurei

Secondary structure

1
477
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi21 – 244
Beta strandi35 – 4410
Helixi50 – 6011
Turni61 – 633
Helixi70 – 745
Helixi77 – 804
Beta strandi83 – 897
Beta strandi91 – 933
Beta strandi97 – 1037
Helixi105 – 1073
Helixi113 – 1219
Helixi124 – 1263
Beta strandi130 – 13910
Helixi142 – 1454
Helixi155 – 1628
Beta strandi169 – 1713
Beta strandi175 – 1784
Helixi182 – 19413
Beta strandi198 – 2014
Beta strandi207 – 2093
Helixi214 – 23219
Beta strandi237 – 2415
Helixi247 – 26014
Beta strandi263 – 2686
Helixi269 – 2724
Helixi274 – 28714
Beta strandi290 – 2945
Helixi298 – 3025
Beta strandi305 – 3095
Helixi311 – 32111
Beta strandi324 – 3274
Beta strandi331 – 3355
Helixi339 – 35012
Beta strandi352 – 3543
Helixi358 – 3603
Beta strandi375 – 3817
Helixi384 – 3863
Helixi387 – 3948
Beta strandi396 – 4016
Helixi404 – 4074
Helixi413 – 43220
Helixi437 – 44913
Helixi453 – 46210

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1WDDX-ray1.35A/E1-477[»]
3AXKX-ray1.90A/B1-477[»]
3AXMX-ray1.65A/B/C/D/E/F/G/H1-477[»]
ProteinModelPortaliP0C512.
SMRiP0C512. Positions 11-475.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP0C512.

Family & Domainsi

Sequence similaritiesi

Phylogenomic databases

eggNOGiCOG1850.
InParanoidiP0C512.
KOiK01601.
OMAiDDEICAN.

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.

Sequence processingi: The displayed sequence is further processed into a mature form.

P0C512-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MSPQTETKAS VGFKAGVKDY KLTYYTPEYE TKDTDILAAF RVTPQPGVPP
60 70 80 90 100
EEAGAAVAAE SSTGTWTTVW TDGLTSLDRY KGRCYHIEPV VGEDNQYIAY
110 120 130 140 150
VAYPLDLFEE GSVTNMFTSI VGNVFGFKAL RALRLEDLRI PPTYSKTFQG
160 170 180 190 200
PPHGIQVERD KLNKYGRPLL GCTIKPKLGL SAKNYGRACY ECLRGGLDFT
210 220 230 240 250
KDDENVNSQP FMRWRDRFVF CAEAIYKSQA ETGEIKGHYL NATAGTCEEM
260 270 280 290 300
IKRAVFAREL GVPIVMHDYL TGGFTANTSL AHYCRDNGLL LHIHRAMHAV
310 320 330 340 350
IDRQKNHGMH FRVLAKALRM SGGDHIHAGT VVGKLEGERE MTLGFVDLLR
360 370 380 390 400
DDFIEKDRAR GIFFTQDWVS MPGVIPVASG GIHVWHMPAL TEIFGDDSVL
410 420 430 440 450
QFGGGTLGHP WGNAPGAAAN RVALEACVQA RNEGRDLARE GNEIIRSACK
460 470
WSPELAAACE IWKAIKFEFE PVDKLDS
Length:477
Mass (Da):52,881
Last modified:June 12, 2007 - v1
Checksum:i8EECF4F8F1F0A8F9
GO

Sequence cautioni

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

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
D00207 Genomic DNA. Translation: BAA00147.1.
X15901 Genomic DNA. Translation: CAA34004.1.
AY522330 Genomic DNA. Translation: AAS46127.1. Different initiation.
PIRiJQ0231. RKRZL.
RefSeqiNP_039391.1. NC_001320.1.

Genome annotation databases

GeneIDi3131463.
KEGGiosa:3131463.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
D00207 Genomic DNA. Translation: BAA00147.1 .
X15901 Genomic DNA. Translation: CAA34004.1 .
AY522330 Genomic DNA. Translation: AAS46127.1 . Different initiation.
PIRi JQ0231. RKRZL.
RefSeqi NP_039391.1. NC_001320.1.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
1WDD X-ray 1.35 A/E 1-477 [» ]
3AXK X-ray 1.90 A/B 1-477 [» ]
3AXM X-ray 1.65 A/B/C/D/E/F/G/H 1-477 [» ]
ProteinModelPortali P0C512.
SMRi P0C512. Positions 11-475.
ModBasei Search...
MobiDBi Search...

Proteomic databases

PaxDbi P0C512.
PRIDEi P0C512.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

GeneIDi 3131463.
KEGGi osa:3131463.

Organism-specific databases

Gramenei P0C512.

Phylogenomic databases

eggNOGi COG1850.
InParanoidi P0C512.
KOi K01601.
OMAi DDEICAN.

Miscellaneous databases

EvolutionaryTracei P0C512.

Gene expression databases

ExpressionAtlasi P0C512. baseline.

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. "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. 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, IDENTIFICATION BY 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), CARBAMYLATION AT LYS-201.
    Strain: cv. Notohikari.
    Tissue: Leaf.

Entry informationi

Entry nameiRBL_ORYSJ
AccessioniPrimary (citable) accession number: P0C512
Secondary accession number(s): P12089, Q6QY04, Q6QY68
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 12, 2007
Last sequence update: June 12, 2007
Last modified: October 29, 2014
This is version 53 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant 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, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. Oryza sativa (rice)
    Index of Oryza sativa entries and their corresponding gene designations
  3. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3