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P0C512

- RBL_ORYSJ

UniProt

P0C512 - RBL_ORYSJ

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
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    • History
      Entry version 52 (01 Oct 2014)
      Sequence version 1 (12 Jun 2007)
      Previous versions | rss
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    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

    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-SubCell
    2. plastid Source: Gramene

    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.

    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.
    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

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    MSPQTETKAS VGFKAGVKDY KLTYYTPEYE TKDTDILAAF RVTPQPGVPP    50
    EEAGAAVAAE SSTGTWTTVW TDGLTSLDRY KGRCYHIEPV VGEDNQYIAY 100
    VAYPLDLFEE GSVTNMFTSI VGNVFGFKAL RALRLEDLRI PPTYSKTFQG 150
    PPHGIQVERD KLNKYGRPLL GCTIKPKLGL SAKNYGRACY ECLRGGLDFT 200
    KDDENVNSQP FMRWRDRFVF CAEAIYKSQA ETGEIKGHYL NATAGTCEEM 250
    IKRAVFAREL GVPIVMHDYL TGGFTANTSL AHYCRDNGLL LHIHRAMHAV 300
    IDRQKNHGMH FRVLAKALRM SGGDHIHAGT VVGKLEGERE MTLGFVDLLR 350
    DDFIEKDRAR GIFFTQDWVS MPGVIPVASG GIHVWHMPAL TEIFGDDSVL 400
    QFGGGTLGHP WGNAPGAAAN RVALEACVQA RNEGRDLARE GNEIIRSACK 450
    WSPELAAACE IWKAIKFEFE PVDKLDS 477
    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.
    KOi K01601.
    OMAi DDEICAN.

    Miscellaneous databases

    EvolutionaryTracei P0C512.

    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

    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 1, 2014
    This is version 52 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