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P00876

- RBL_TOBAC

UniProt

P00876 - RBL_TOBAC

Protein

Ribulose bisphosphate carboxylase large chain

Gene

rbcL

Organism
Nicotiana tabacum (Common tobacco)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 115 (01 Oct 2014)
      Sequence version 2 (01 Jun 2001)
      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

    Enzyme and pathway databases

    SABIO-RKP00876.

    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
    Synonyms:rbcA
    Encoded oniPlastid; Chloroplast
    OrganismiNicotiana tabacum (Common tobacco)
    Taxonomic identifieri4097 [NCBI]
    Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaeasteridslamiidsSolanalesSolanaceaeNicotianoideaeNicotianeaeNicotiana

    Subcellular locationi

    GO - Cellular componenti

    1. chloroplast Source: UniProtKB-SubCell

    Keywords - Cellular componenti

    Chloroplast, Plastid

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Propeptidei1 – 221 PublicationPRO_0000031427
    Chaini3 – 477475Ribulose bisphosphate carboxylase large chainPRO_0000031428Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei3 – 31N-acetylproline
    Modified residuei14 – 141N6,N6,N6-trimethyllysine1 Publication
    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 bonds reported in 3RUB and 4RUB may be the result of oxidation during crystallization.By similarity

    Keywords - PTMi

    Acetylation, Disulfide bond, Methylation

    Proteomic databases

    PRIDEiP00876.

    Interactioni

    Subunit structurei

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

    Protein-protein interaction databases

    DIPiDIP-42221N.
    MINTiMINT-1176576.

    Structurei

    Secondary structure

    1
    477
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi21 – 244
    Beta strandi36 – 449
    Helixi50 – 5910
    Turni60 – 623
    Helixi71 – 733
    Helixi77 – 804
    Beta strandi83 – 897
    Beta strandi91 – 955
    Beta strandi97 – 1037
    Helixi105 – 1073
    Helixi113 – 1219
    Helixi124 – 1263
    Beta strandi130 – 13910
    Helixi142 – 1454
    Beta strandi151 – 1533
    Helixi155 – 1628
    Beta strandi169 – 1735
    Beta strandi175 – 1784
    Helixi182 – 19413
    Beta strandi198 – 2014
    Beta strandi207 – 2093
    Beta strandi210 – 2123
    Helixi214 – 23219
    Beta strandi237 – 2415
    Helixi247 – 26014
    Beta strandi263 – 2686
    Helixi269 – 2724
    Helixi274 – 28714
    Beta strandi290 – 2945
    Helixi298 – 3025
    Beta strandi307 – 3093
    Helixi311 – 32111
    Beta strandi324 – 3274
    Beta strandi332 – 3343
    Helixi336 – 35015
    Beta strandi352 – 3543
    Helixi358 – 3603
    Beta strandi375 – 3817
    Helixi384 – 3863
    Helixi387 – 3948
    Beta strandi396 – 4038
    Turni404 – 4085
    Helixi413 – 43220
    Helixi437 – 45115
    Helixi453 – 46614

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1EJ7X-ray2.45L3-477[»]
    1RLCX-ray2.70L1-477[»]
    1RLDX-ray2.50A/B22-467[»]
    3RUBX-ray2.00L1-477[»]
    4RUBX-ray2.70A/B/C/D1-477[»]
    ProteinModelPortaliP00876.
    SMRiP00876. Positions 9-472.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP00876.

    Family & Domainsi

    Sequence similaritiesi

    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.

    P00876-1 [UniParc]FASTAAdd to Basket

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    MSPQTETKAS VGFKAGVKEY KLTYYTPEYQ TKDTDILAAF RVTPQPGVPP    50
    EEAGAAVAAE SSTGTWTTVW TDGLTSLDRY KGRCYRIERV VGEKDQYIAY 100
    VAYPLDLFEE GSVTNMFTSI VGNVFGFKAL RALRLEDLRI PPAYVKTFQG 150
    PPHGIQVERD KLNKYGRPLL GCTIKPKLGL SAKNYGRAVY ECLRGGLDFT 200
    KDDENVNSQP FMRWRDRFLF CAEALYKAQA ETGEIKGHYL NATAGTCEEM 250
    IKRAVFAREL GVPIVMHDYL TGGFTANTSL AHYCRDNGLL LHIHRAMHAV 300
    IDRQKNHGIH FRVLAKALRM SGGDHIHSGT VVGKLEGERD ITLGFVDLLR 350
    DDFVEQDRSR GIYFTQDWVS LPGVLPVASG GIHVWHMPAL TEIFGDDSVL 400
    QFGGGTLGHP WGNAPGAVAN RVALEACVKA RNEGRDLAQE GNEIIREACK 450
    WSPELAAACE VWKEIVFNFA AVDVLDK 477
    Length:477
    Mass (Da):52,898
    Last modified:June 1, 2001 - v2
    Checksum:i232D54E42263198F
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti284 – 2841C → G AA sequence 1 PublicationCurated
    Sequence conflicti377 – 3771V → E in AAD15025. (PubMed:7160620)Curated

    Natural variant

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Natural varianti394 – 3941F → V.1 Publication
    Natural varianti405 – 4051G → M.1 Publication

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    J01450 Genomic DNA. Translation: AAD15025.1.
    Z00044 Genomic DNA. Translation: CAA77361.1.
    PIRiA01095. RKNTL.
    RefSeqiNP_054507.1. NC_001879.2.

    Genome annotation databases

    GeneIDi800513.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    J01450 Genomic DNA. Translation: AAD15025.1 .
    Z00044 Genomic DNA. Translation: CAA77361.1 .
    PIRi A01095. RKNTL.
    RefSeqi NP_054507.1. NC_001879.2.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1EJ7 X-ray 2.45 L 3-477 [» ]
    1RLC X-ray 2.70 L 1-477 [» ]
    1RLD X-ray 2.50 A/B 22-467 [» ]
    3RUB X-ray 2.00 L 1-477 [» ]
    4RUB X-ray 2.70 A/B/C/D 1-477 [» ]
    ProteinModelPortali P00876.
    SMRi P00876. Positions 9-472.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    DIPi DIP-42221N.
    MINTi MINT-1176576.

    Proteomic databases

    PRIDEi P00876.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    GeneIDi 800513.

    Enzyme and pathway databases

    SABIO-RK P00876.

    Miscellaneous databases

    EvolutionaryTracei P00876.

    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. "The nucleotide sequence of the tobacco chloroplast gene for the large subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase."
      Shinozaki K., Sugiura M.
      Gene 20:91-102(1982) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    2. "The complete nucleotide sequence of the tobacco chloroplast genome: its gene organization and expression."
      Shinozaki K., Ohme M., Tanaka M., Wakasugi T., Hayashida N., Matsubayashi T., Zaita N., Chunwongse J., Obokata J., Yamaguchi-Shinozaki K., Ohto C., Torazawa K., Meng B.-Y., Sugita M., Deno H., Kamogashira T., Yamada K., Kusuda J.
      , Takaiwa F., Kato A., Tohdoh N., Shimada H., Sugiura M.
      EMBO J. 5:2043-2049(1986) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: cv. Bright Yellow 4.
    3. "Amino-acid sequence of the large subunit of D-ribulose bisphosphate carboxylase/oxygenase from Nicotiana tabacum."
      Amiri I., Salnikow J., Vater J.
      Biochim. Biophys. Acta 784:116-123(1984)
      Cited for: PROTEIN SEQUENCE OF 5-477, VARIANTS VAL-394 AND MET-405.
    4. "Post-translational modifications in the large subunit of ribulose bisphosphate carboxylase/oxygenase."
      Houtz R.L., Stults J.T., Mulligan R.M., Tolbert N.E.
      Proc. Natl. Acad. Sci. U.S.A. 86:1855-1859(1989) [PubMed] [Europe PMC] [Abstract]
      Cited for: PROTEIN SEQUENCE OF 3-18, METHYLATION AT LYS-14.
    5. "A crystal form of ribulose-1,5-bisphosphate carboxylase/oxygenase from Nicotiana tabacum in the activated state."
      Suh S.W., Cascio D., Chapman M.S., Eisenberg D.
      J. Mol. Biol. 197:363-365(1987) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.7 ANGSTROMS).
    6. "Crystal structure of the unactivated form of ribulose-1,5-bisphosphate carboxylase/oxygenase from tobacco refined at 2.0-A resolution."
      Curmi P.M.G., Cascio D., Sweet R.M., Eisenberg D., Schreuder H.
      J. Biol. Chem. 267:16980-16989(1992) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS).
    7. "The transition between the open and closed states of rubisco is triggered by the inter-phosphate distance of the bound bisphosphate."
      Duff A.P., Andrews T.J., Curmi P.M.G.
      J. Mol. Biol. 298:903-916(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.45 ANGSTROMS) OF 3-477, CARBAMYLATION AT LYS-201.

    Entry informationi

    Entry nameiRBL_TOBAC
    AccessioniPrimary (citable) accession number: P00876
    Secondary accession number(s): Q32716
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: July 21, 1986
    Last sequence update: June 1, 2001
    Last modified: October 1, 2014
    This is version 115 of the entry and version 2 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, Direct protein sequencing

    Documents

    1. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    2. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3