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Q0DI31

- CYC_ORYSJ

UniProt

Q0DI31 - CYC_ORYSJ

Protein

Cytochrome c

Gene

CC-1

Organism
Oryza sativa subsp. japonica (Rice)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
  1. Functioni

    Electron carrier protein. The oxidized form of the cytochrome c heme group can accept an electron from the heme group of the cytochrome c1 subunit of cytochrome reductase. Cytochrome c then transfers this electron to the cytochrome oxidase complex, the final protein carrier in the mitochondrial electron-transport chain.

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei23 – 231Heme (covalent)
    Binding sitei26 – 261Heme (covalent)
    Metal bindingi27 – 271Iron (heme axial ligand)
    Metal bindingi89 – 891Iron (heme axial ligand)

    GO - Molecular functioni

    1. copper ion binding Source: EnsemblPlants/Gramene
    2. electron carrier activity Source: InterPro
    3. heme binding Source: InterPro
    4. iron ion binding Source: InterPro

    GO - Biological processi

    1. oxidation-reduction process Source: UniProtKB-KW

    Keywords - Biological processi

    Electron transport, Respiratory chain, Transport

    Keywords - Ligandi

    Heme, Iron, Metal-binding

    Enzyme and pathway databases

    ReactomeiREACT_175687. Detoxification of Reactive Oxygen Species.
    REACT_176102. Release of apoptotic factors from the mitochondria.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Cytochrome c
    Gene namesi
    Name:CC-1
    Ordered Locus Names:Os05g0420600, LOC_Os05g34770
    ORF Names:OsJ_017825, OSJNBb0092E21.3, P0426G01.18
    OrganismiOryza sativa subsp. japonica (Rice)
    Taxonomic identifieri39947 [NCBI]
    Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaLiliopsidaPoalesPoaceaeBEP cladeEhrhartoideaeOryzeaeOryza
    ProteomesiUP000000763: Chromosome 5

    Organism-specific databases

    GrameneiQ0DI31.

    Subcellular locationi

    Mitochondrion intermembrane space
    Note: Loosely associated with the inner membrane.

    GO - Cellular componenti

    1. cytosol Source: EnsemblPlants/Gramene
    2. mitochondrial intermembrane space Source: UniProtKB-SubCell
    3. respiratory chain Source: UniProtKB-KW
    4. vacuolar membrane Source: EnsemblPlants/Gramene

    Keywords - Cellular componenti

    Mitochondrion

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Initiator methioninei1 – 11Removed1 Publication
    Chaini2 – 112111Cytochrome cPRO_0000108303Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei2 – 21N-acetylalanine
    Modified residuei81 – 811N6,N6,N6-trimethyllysine
    Modified residuei95 – 951N6,N6,N6-trimethyllysine

    Post-translational modificationi

    Binds 1 heme group per subunit.

    Keywords - PTMi

    Acetylation, Methylation

    Structurei

    Secondary structure

    1
    112
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi4 – 63
    Helixi12 – 2211
    Turni23 – 264
    Beta strandi36 – 383
    Helixi59 – 646
    Helixi70 – 789
    Helixi80 – 834
    Helixi97 – 11014

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1CCRX-ray1.50A2-112[»]
    ProteinModelPortaliQ0DI31.
    SMRiQ0DI31. Positions 2-112.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ0DI31.

    Family & Domainsi

    Sequence similaritiesi

    Belongs to the cytochrome c family.Curated

    Phylogenomic databases

    eggNOGiCOG3474.
    KOiK08738.
    OMAiWILADVE.

    Family and domain databases

    Gene3Di1.10.760.10. 1 hit.
    InterProiIPR009056. Cyt_c-like_dom.
    IPR002327. Cyt_c_1A/1B.
    IPR003088. Cyt_c_dom.
    [Graphical view]
    PANTHERiPTHR11961. PTHR11961. 1 hit.
    PfamiPF00034. Cytochrom_C. 1 hit.
    [Graphical view]
    PRINTSiPR00604. CYTCHRMECIAB.
    SUPFAMiSSF46626. SSF46626. 1 hit.
    PROSITEiPS51007. CYTC. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

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

    Q0DI31-1 [UniParc]FASTAAdd to Basket

    « Hide

    MASFSEAPPG NPKAGEKIFK TKCAQCHTVD KGAGHKQGPN LNGLFGRQSG    50
    TTPGYSYSTA NKNMAVIWEE NTLYDYLLNP KKYIPGTKMV FPGLKKPQER 100
    ADLISYLKEA TS 112
    Length:112
    Mass (Da):12,271
    Last modified:October 17, 2006 - v1
    Checksum:iC17D2B4628C77146
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    D12634 mRNA. Translation: BAA02159.1.
    AC124836 Genomic DNA. Translation: AAT44244.1.
    AC137623 Genomic DNA. Translation: AAV25652.1.
    AP008211 Genomic DNA. Translation: BAF17492.1.
    CM000142 Genomic DNA. Translation: EAZ34342.1.
    PIRiJS0709. CCRZ.
    RefSeqiNP_001055578.1. NM_001062113.1.
    UniGeneiOs.57469.

    Genome annotation databases

    EnsemblPlantsiOS05T0420600-01; OS05T0420600-01; OS05G0420600.
    GeneIDi4338825.
    KEGGiosa:4338825.

    Cross-referencesi

    Web resourcesi

    Protein Spotlight

    Life shuttle - Issue 76 of November 2006

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    D12634 mRNA. Translation: BAA02159.1 .
    AC124836 Genomic DNA. Translation: AAT44244.1 .
    AC137623 Genomic DNA. Translation: AAV25652.1 .
    AP008211 Genomic DNA. Translation: BAF17492.1 .
    CM000142 Genomic DNA. Translation: EAZ34342.1 .
    PIRi JS0709. CCRZ.
    RefSeqi NP_001055578.1. NM_001062113.1.
    UniGenei Os.57469.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1CCR X-ray 1.50 A 2-112 [» ]
    ProteinModelPortali Q0DI31.
    SMRi Q0DI31. Positions 2-112.
    ModBasei Search...
    MobiDBi Search...

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblPlantsi OS05T0420600-01 ; OS05T0420600-01 ; OS05G0420600 .
    GeneIDi 4338825.
    KEGGi osa:4338825.

    Organism-specific databases

    Gramenei Q0DI31.

    Phylogenomic databases

    eggNOGi COG3474.
    KOi K08738.
    OMAi WILADVE.

    Enzyme and pathway databases

    Reactomei REACT_175687. Detoxification of Reactive Oxygen Species.
    REACT_176102. Release of apoptotic factors from the mitochondria.

    Miscellaneous databases

    EvolutionaryTracei Q0DI31.

    Family and domain databases

    Gene3Di 1.10.760.10. 1 hit.
    InterProi IPR009056. Cyt_c-like_dom.
    IPR002327. Cyt_c_1A/1B.
    IPR003088. Cyt_c_dom.
    [Graphical view ]
    PANTHERi PTHR11961. PTHR11961. 1 hit.
    Pfami PF00034. Cytochrom_C. 1 hit.
    [Graphical view ]
    PRINTSi PR00604. CYTCHRMECIAB.
    SUPFAMi SSF46626. SSF46626. 1 hit.
    PROSITEi PS51007. CYTC. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "cDNA cloning and sequence analysis of rice cytochrome c gene."
      Nishi R., Uchimiya H., Kato A.
      Submitted (JUL-1992) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [MRNA].
      Strain: cv. Yamahoushi.
    2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: cv. Nipponbare.
    3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: cv. Nipponbare.
    4. "The rice annotation project database (RAP-DB): 2008 update."
      The rice annotation project (RAP)
      Nucleic Acids Res. 36:D1028-D1033(2008) [PubMed] [Europe PMC] [Abstract]
      Cited for: GENOME REANNOTATION.
      Strain: cv. Nipponbare.
    5. "The genomes of Oryza sativa: a history of duplications."
      Yu J., Wang J., Lin W., Li S., Li H., Zhou J., Ni P., Dong W., Hu S., Zeng C., Zhang J., Zhang Y., Li R., Xu Z., Li S., Li X., Zheng H., Cong L.
      , Lin L., Yin J., Geng J., Li G., Shi J., Liu J., Lv H., Li J., Wang J., Deng Y., Ran L., Shi X., Wang X., Wu Q., Li C., Ren X., Wang J., Wang X., Li D., Liu D., Zhang X., Ji Z., Zhao W., Sun Y., Zhang Z., Bao J., Han Y., Dong L., Ji J., Chen P., Wu S., Liu J., Xiao Y., Bu D., Tan J., Yang L., Ye C., Zhang J., Xu J., Zhou Y., Yu Y., Zhang B., Zhuang S., Wei H., Liu B., Lei M., Yu H., Li Y., Xu H., Wei S., He X., Fang L., Zhang Z., Zhang Y., Huang X., Su Z., Tong W., Li J., Tong Z., Li S., Ye J., Wang L., Fang L., Lei T., Chen C.-S., Chen H.-C., Xu Z., Li H., Huang H., Zhang F., Xu H., Li N., Zhao C., Li S., Dong L., Huang Y., Li L., Xi Y., Qi Q., Li W., Zhang B., Hu W., Zhang Y., Tian X., Jiao Y., Liang X., Jin J., Gao L., Zheng W., Hao B., Liu S.-M., Wang W., Yuan L., Cao M., McDermott J., Samudrala R., Wang J., Wong G.K.-S., Yang H.
      PLoS Biol. 3:266-281(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: cv. Nipponbare.
    6. "Amino acid sequence of cytochrome c from rice."
      Mori E., Morita Y.
      J. Biochem. 87:249-266(1980) [PubMed] [Europe PMC] [Abstract]
      Cited for: PROTEIN SEQUENCE OF 2-112.
    7. "Structure of rice ferricytochrome c at 2.0-A resolution."
      Ochi H., Hata Y., Tanaka N., Kakudo M., Sakurai T., Aihara S., Morita Y.
      J. Mol. Biol. 166:407-418(1983) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS).

    Entry informationi

    Entry nameiCYC_ORYSJ
    AccessioniPrimary (citable) accession number: Q0DI31
    Secondary accession number(s): P00055, Q6L4Z1
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: July 10, 2007
    Last sequence update: October 17, 2006
    Last modified: October 1, 2014
    This is version 69 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programPlant Protein Annotation Program

    Miscellaneousi

    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. Protein Spotlight
      Protein Spotlight articles and cited UniProtKB/Swiss-Prot entries
    3. Oryza sativa (rice)
      Index of Oryza sativa entries and their corresponding gene designations
    4. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3