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P00877

- RBL_CHLRE

UniProt

P00877 - RBL_CHLRE

Protein

Ribulose bisphosphate carboxylase large chain

Gene

rbcL

Organism
Chlamydomonas reinhardtii (Chlamydomonas smithii)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 119 (01 Oct 2014)
      Sequence version 1 (21 Jul 1986)
      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

    BioCyciCHLAMY:CHRECP049-MONOMER.

    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
    Encoded oniPlastid; Chloroplast
    OrganismiChlamydomonas reinhardtii (Chlamydomonas smithii)
    Taxonomic identifieri3055 [NCBI]
    Taxonomic lineageiEukaryotaViridiplantaeChlorophytaChlorophyceaeChlamydomonadalesChlamydomonadaceaeChlamydomonas
    ProteomesiUP000006906: Chloroplast

    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_0000031175
    Chaini3 – 475473Ribulose bisphosphate carboxylase large chainPRO_0000031176Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei3 – 31N-acetylproline1 Publication
    Modified residuei104 – 10414-hydroxyproline1 Publication
    Modified residuei151 – 15114-hydroxyproline
    Modified residuei201 – 2011N6-carboxylysine2 Publications
    Disulfide bondi247 – 247Interchain; in linked form
    Modified residuei256 – 2561S-methylcysteine1 Publication
    Modified residuei369 – 3691S-methylcysteine1 Publication

    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 1IR2 may be the result of oxidation during crystallization.By similarity
    The electron density found in the position of Thr-471 (PubMed:11866526 only) suggests it is either O-methylthreonine, or Ile, which may be produced by RNA editing.

    Keywords - PTMi

    Acetylation, Disulfide bond, Hydroxylation, Methylation

    Proteomic databases

    PRIDEiP00877.

    Interactioni

    Subunit structurei

    Heterohexadecamer of 8 large chains and 8 small chains; disulfide-linked. The disulfide link is formed within the large subunit homodimers.2 Publications

    Structurei

    Secondary structure

    1
    475
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi21 – 244
    Beta strandi36 – 449
    Helixi50 – 6011
    Turni61 – 633
    Beta strandi66 – 683
    Helixi70 – 745
    Helixi77 – 804
    Beta strandi83 – 897
    Beta strandi93 – 953
    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 – 45115
    Helixi453 – 46210

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1GK8X-ray1.40A/C/E/G1-475[»]
    1IR2X-ray1.84A/B/C/D/E/F/G/H/S/T/U/V/W/X/Y/Z1-475[»]
    1UW9X-ray2.05A/B/E/H/K/O/R/V1-475[»]
    1UWAX-ray2.30A/B/E/H/K/O/R/V1-475[»]
    1UZDX-ray2.40A/B/E/H/K/O/R/V1-475[»]
    1UZHX-ray2.20A/B/E/H/K/O/R/V1-475[»]
    2V63X-ray1.80A/B/C/D/E/F/G/H1-475[»]
    2V67X-ray2.00A/B/C/D/E/F/G/H1-475[»]
    2V68X-ray2.30A/B/C/D/E/F/G/H1-475[»]
    2V69X-ray2.80A/B/C/D/E/F/G/H1-475[»]
    2V6AX-ray1.50A/B/C/D/E/F/G/H1-475[»]
    2VDHX-ray2.30A/B/C/D/E/F/G/H1-475[»]
    2VDIX-ray2.65A/B/C/D/E/F/G/H1-475[»]
    ProteinModelPortaliP00877.
    SMRiP00877. Positions 7-475.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP00877.

    Family & Domainsi

    Sequence similaritiesi

    Phylogenomic databases

    KOiK01601.

    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.

    P00877-1 [UniParc]FASTAAdd to Basket

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    MVPQTETKAG AGFKAGVKDY RLTYYTPDYV VRDTDILAAF RMTPQLGVPP    50
    EECGAAVAAE SSTGTWTTVW TDGLTSLDRY KGRCYDIEPV PGEDNQYIAY 100
    VAYPIDLFEE GSVTNMFTSI VGNVFGFKAL RALRLEDLRI PPAYVKTFVG 150
    PPHGIQVERD KLNKYGRGLL GCTIKPKLGL SAKNYGRAVY ECLRGGLDFT 200
    KDDENVNSQP FMRWRDRFLF VAEAIYKAQA ETGEVKGHYL NATAGTCEEM 250
    MKRAVCAKEL GVPIIMHDYL TGGFTANTSL AIYCRDNGLL LHIHRAMHAV 300
    IDRQRNHGIH FRVLAKALRM SGGDHLHSGT VVGKLEGERE VTLGFVDLMR 350
    DDYVEKDRSR GIYFTQDWCS MPGVMPVASG GIHVWHMPAL VEIFGDDACL 400
    QFGGGTLGHP WGNAPGAAAN RVALEACTQA RNEGRDLARE GGDVIRSACK 450
    WSPELAAACE VWKEIKFEFD TIDKL 475
    Length:475
    Mass (Da):52,543
    Last modified:July 21, 1986 - v1
    Checksum:i5A9BFD394CF7D4D4
    GO

    Natural variant

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Natural varianti46 – 461L → P in strain: 137c and CC-503.

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    J01399 Genomic DNA. Translation: AAA84449.1.
    FJ423446 Genomic DNA. Translation: ACJ50136.1.
    BK000554 Genomic DNA. Translation: DAA00950.1.
    PIRiA01097. RKKML.
    RefSeqiNP_958405.1. NC_005353.1.

    Genome annotation databases

    EnsemblPlantsiDAA00950; DAA00950; DAA00950.
    GeneIDi2717040.
    KEGGicre:ChreCp049.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    J01399 Genomic DNA. Translation: AAA84449.1 .
    FJ423446 Genomic DNA. Translation: ACJ50136.1 .
    BK000554 Genomic DNA. Translation: DAA00950.1 .
    PIRi A01097. RKKML.
    RefSeqi NP_958405.1. NC_005353.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1GK8 X-ray 1.40 A/C/E/G 1-475 [» ]
    1IR2 X-ray 1.84 A/B/C/D/E/F/G/H/S/T/U/V/W/X/Y/Z 1-475 [» ]
    1UW9 X-ray 2.05 A/B/E/H/K/O/R/V 1-475 [» ]
    1UWA X-ray 2.30 A/B/E/H/K/O/R/V 1-475 [» ]
    1UZD X-ray 2.40 A/B/E/H/K/O/R/V 1-475 [» ]
    1UZH X-ray 2.20 A/B/E/H/K/O/R/V 1-475 [» ]
    2V63 X-ray 1.80 A/B/C/D/E/F/G/H 1-475 [» ]
    2V67 X-ray 2.00 A/B/C/D/E/F/G/H 1-475 [» ]
    2V68 X-ray 2.30 A/B/C/D/E/F/G/H 1-475 [» ]
    2V69 X-ray 2.80 A/B/C/D/E/F/G/H 1-475 [» ]
    2V6A X-ray 1.50 A/B/C/D/E/F/G/H 1-475 [» ]
    2VDH X-ray 2.30 A/B/C/D/E/F/G/H 1-475 [» ]
    2VDI X-ray 2.65 A/B/C/D/E/F/G/H 1-475 [» ]
    ProteinModelPortali P00877.
    SMRi P00877. Positions 7-475.
    ModBasei Search...
    MobiDBi Search...

    Proteomic databases

    PRIDEi P00877.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblPlantsi DAA00950 ; DAA00950 ; DAA00950 .
    GeneIDi 2717040.
    KEGGi cre:ChreCp049.

    Phylogenomic databases

    KOi K01601.

    Enzyme and pathway databases

    BioCyci CHLAMY:CHRECP049-MONOMER.

    Miscellaneous databases

    EvolutionaryTracei P00877.

    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. "Sequence of the chloroplast DNA region of Chlamydomonas reinhardii containing the gene of the large subunit of ribulose bisphosphate carboxylase and parts of its flanking genes."
      Dron M., Rahire M., Rochaix J.-D.
      J. Mol. Biol. 162:775-793(1982) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], CARBAMYLATION AT LYS-201.
    2. "Nucleotide diversity of the Chlamydomonas reinhardtii plastid genome: addressing the mutational-hazard hypothesis."
      Smith D.R., Lee R.W.
      BMC Evol. Biol. 9:120-120(2009) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: CC-503.
    3. "Posttranslational modifications in the amino-terminal region of the large subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase from several plant species."
      Houtz R.L., Poneleit L., Jones S.B., Royer M., Stults J.T.
      Plant Physiol. 98:1170-1174(1992) [PubMed] [Europe PMC] [Abstract]
      Cited for: PROTEIN SEQUENCE OF 3-14, ACETYLATION AT PRO-3.
    4. "The Chlamydomonas reinhardtii plastid chromosome: islands of genes in a sea of repeats."
      Maul J.E., Lilly J.W., Cui L., dePamphilis C.W., Miller W., Harris E.H., Stern D.B.
      Plant Cell 14:2659-2679(2002) [PubMed] [Europe PMC] [Abstract]
      Cited for: IDENTIFICATION, COMPLETE PLASTID GENOME.
    5. "First crystal structure of Rubisco from a green alga, Chlamydomonas reinhardtii."
      Taylor T.C., Backlund A., Bjorhall K., Spreitzer R.J., Andersson I.
      J. Biol. Chem. 276:48159-48164(2001) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.4 ANGSTROMS) IN COMPLEX WITH THE TRANSITION-STATE ANALOG 2-CABP, HYDROXYLATION AT PRO-104 AND 151, CARBAMYLATION AT LYS-201, METHYLATION AT CYS-256 AND CYS-369.
      Strain: 2137.
    6. "Crystal structure of activated ribulose-1,5-bisphosphate carboxylase/oxygenase from green alga Chlamydomonas reinhardtii complexed with 2-carboxyarabinitol-1,5-bisphosphate."
      Mizohata E., Matsumura H., Okano Y., Kumei M., Takuma H., Onodera J., Kato K., Shibata N., Inoue T., Yokota A., Kai Y.
      J. Mol. Biol. 316:679-691(2002) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS) IN COMPLEX WITH THE TRANSITION-STATE ANALOG 2-CABP.
      Strain: 137c / CC-125.

    Entry informationi

    Entry nameiRBL_CHLRE
    AccessioniPrimary (citable) accession number: P00877
    Secondary accession number(s): B7U1I9
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: July 21, 1986
    Last sequence update: July 21, 1986
    Last modified: October 1, 2014
    This is version 119 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. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3