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P00044

- CYC1_YEAST

UniProt

P00044 - CYC1_YEAST

Protein

Cytochrome c iso-1

Gene

CYC1

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
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 sitei20 – 201Heme (covalent)
    Binding sitei23 – 231Heme (covalent)
    Metal bindingi24 – 241Iron (heme axial ligand)
    Metal bindingi86 – 861Iron (heme axial ligand)

    GO - Molecular functioni

    1. electron carrier activity Source: SGD
    2. heme binding Source: InterPro
    3. iron ion binding Source: InterPro
    4. protein binding Source: IntAct

    GO - Biological processi

    1. mitochondrial electron transport, cytochrome c to oxygen Source: SGD
    2. mitochondrial electron transport, ubiquinol to cytochrome c Source: SGD

    Keywords - Biological processi

    Electron transport, Respiratory chain, Transport

    Keywords - Ligandi

    Heme, Iron, Metal-binding

    Enzyme and pathway databases

    BioCyciYEAST:G3O-31683-MONOMER.
    ReactomeiREACT_188673. Release of apoptotic factors from the mitochondria.
    REACT_191152. Detoxification of Reactive Oxygen Species.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Cytochrome c iso-1
    Gene namesi
    Name:CYC1
    Ordered Locus Names:YJR048W
    ORF Names:J1653
    OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
    Taxonomic identifieri559292 [NCBI]
    Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
    ProteomesiUP000002311: Chromosome X

    Organism-specific databases

    SGDiS000003809. CYC1.

    Subcellular locationi

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

    GO - Cellular componenti

    1. mitochondrial intermembrane space Source: SGD
    2. respiratory chain Source: UniProtKB-KW

    Keywords - Cellular componenti

    Mitochondrion

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi78 – 781K → R: Loss of methylation by CTM1. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Initiator methioninei1 – 11Removed1 Publication
    Chaini2 – 109108Cytochrome c iso-1PRO_0000108337Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei78 – 781N6,N6,N6-trimethyllysine; by CTM12 Publications
    Modified residuei79 – 791N6,N6,N6-trimethyllysine3 Publications

    Post-translational modificationi

    Binds 1 heme group per subunit.
    Methylation may enhance its transport into mitochondria. Methylation occurs in fungi, plants, and some protozoa, but not in animals. The precise role of methylation at Lys-79 is unknown, but it seems to preclude pro-apoptotic activity, possibly by lowering affinity for APAF1.4 Publications

    Keywords - PTMi

    Methylation

    Proteomic databases

    MaxQBiP00044.
    PaxDbiP00044.
    PeptideAtlasiP00044.

    Expressioni

    Developmental stagei

    Iso-1 is the predominant cytochrome c in aerobically grown cells.

    Inductioni

    By oxygen.

    Gene expression databases

    GenevestigatoriP00044.

    Interactioni

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    CCP1P004313EBI-5393,EBI-4389

    Protein-protein interaction databases

    BioGridi33801. 72 interactions.
    DIPiDIP-4265N.
    IntActiP00044. 5 interactions.
    MINTiMINT-8285287.
    STRINGi4932.YJR048W.

    Structurei

    Secondary structure

    1
    109
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi9 – 1911
    Turni20 – 234
    Beta strandi27 – 293
    Beta strandi33 – 353
    Turni39 – 435
    Beta strandi45 – 473
    Beta strandi50 – 523
    Helixi56 – 616
    Helixi67 – 759
    Helixi77 – 804
    Beta strandi81 – 833
    Helixi94 – 10714

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1CHHX-ray1.97A2-107[»]
    1CHIX-ray2.00A2-107[»]
    1CHJX-ray1.90A2-107[»]
    1CIEX-ray1.80A2-107[»]
    1CIFX-ray1.90A2-107[»]
    1CIGX-ray1.80A2-107[»]
    1CIHX-ray1.80A2-107[»]
    1CRGX-ray2.00A2-107[»]
    1CRHX-ray1.90A2-109[»]
    1CRIX-ray2.00A2-107[»]
    1CRJX-ray2.05A2-107[»]
    1CSUX-ray1.81A2-107[»]
    1CSVX-ray1.90A2-107[»]
    1CSWX-ray1.90A2-107[»]
    1CSXX-ray1.90A2-107[»]
    1CTYX-ray2.20A2-107[»]
    1CTZX-ray1.90A2-107[»]
    1FHBNMR-A2-107[»]
    1IRVX-ray1.90A2-107[»]
    1IRWX-ray2.00A2-107[»]
    1KYOX-ray2.97W2-109[»]
    1LMSNMR-A2-107[»]
    1NMINMR-A2-107[»]
    1RAPX-ray2.25A2-109[»]
    1RAQX-ray1.90A2-109[»]
    1S6VX-ray1.88B/D2-107[»]
    1U74X-ray2.40B/D2-107[»]
    1YCCX-ray1.23A2-109[»]
    1YFCNMR-A2-107[»]
    1YICNMR-A2-107[»]
    2B0ZX-ray2.70B2-109[»]
    2B10X-ray2.80B/D2-109[»]
    2B11X-ray2.30B/D2-109[»]
    2B12X-ray3.02B2-109[»]
    2BCNX-ray1.70B2-107[»]
    2GB8NMR-B2-109[»]
    2HV4NMR-A2-107[»]
    2JQRNMR-A2-107[»]
    2JTINMR-B2-109[»]
    2LIRNMR-A2-107[»]
    2LITNMR-A2-107[»]
    2ORLNMR-A2-107[»]
    2PCCX-ray2.30B/D2-109[»]
    2YCCX-ray1.90A2-107[»]
    3CX5X-ray1.90W2-109[»]
    3TYIX-ray1.40A/B2-107[»]
    4MU8X-ray1.45A/B2-107[»]
    ProteinModelPortaliP00044.
    SMRiP00044. Positions 2-109.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP00044.

    Family & Domainsi

    Sequence similaritiesi

    Belongs to the cytochrome c family.Curated

    Phylogenomic databases

    eggNOGiCOG3474.
    GeneTreeiENSGT00390000009405.
    HOGENOMiHOG000009762.
    KOiK08738.
    OMAiCHNLKEG.
    OrthoDBiEOG71RXXT.

    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.

    P00044-1 [UniParc]FASTAAdd to Basket

    « Hide

    MTEFKAGSAK KGATLFKTRC LQCHTVEKGG PHKVGPNLHG IFGRHSGQAE    50
    GYSYTDANIK KNVLWDENNM SEYLTNPKKY IPGTKMAFGG LKKEKDRNDL 100
    ITYLKKACE 109
    Length:109
    Mass (Da):12,182
    Last modified:January 23, 2007 - v2
    Checksum:i1F8B6CB3B60C0BE8
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    M37696 Genomic DNA. Translation: AAB59344.1.
    V01298 Genomic DNA. Translation: CAA24605.1.
    L26347 Genomic DNA. Translation: AAA62856.1.
    L36344 Genomic DNA. Translation: AAA88751.1.
    Z49548 Genomic DNA. Translation: CAA89576.1.
    X03472 Genomic DNA. Translation: CAA27189.1.
    BK006943 Genomic DNA. Translation: DAA08835.1.
    PIRiA00037. CCBY.
    RefSeqiNP_012582.1. NM_001181706.1.

    Genome annotation databases

    EnsemblFungiiYJR048W; YJR048W; YJR048W.
    GeneIDi853507.
    KEGGisce:YJR048W.

    Cross-referencesi

    Web resourcesi

    Protein Spotlight

    Life shuttle - Issue 76 of November 2006

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    M37696 Genomic DNA. Translation: AAB59344.1 .
    V01298 Genomic DNA. Translation: CAA24605.1 .
    L26347 Genomic DNA. Translation: AAA62856.1 .
    L36344 Genomic DNA. Translation: AAA88751.1 .
    Z49548 Genomic DNA. Translation: CAA89576.1 .
    X03472 Genomic DNA. Translation: CAA27189.1 .
    BK006943 Genomic DNA. Translation: DAA08835.1 .
    PIRi A00037. CCBY.
    RefSeqi NP_012582.1. NM_001181706.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1CHH X-ray 1.97 A 2-107 [» ]
    1CHI X-ray 2.00 A 2-107 [» ]
    1CHJ X-ray 1.90 A 2-107 [» ]
    1CIE X-ray 1.80 A 2-107 [» ]
    1CIF X-ray 1.90 A 2-107 [» ]
    1CIG X-ray 1.80 A 2-107 [» ]
    1CIH X-ray 1.80 A 2-107 [» ]
    1CRG X-ray 2.00 A 2-107 [» ]
    1CRH X-ray 1.90 A 2-109 [» ]
    1CRI X-ray 2.00 A 2-107 [» ]
    1CRJ X-ray 2.05 A 2-107 [» ]
    1CSU X-ray 1.81 A 2-107 [» ]
    1CSV X-ray 1.90 A 2-107 [» ]
    1CSW X-ray 1.90 A 2-107 [» ]
    1CSX X-ray 1.90 A 2-107 [» ]
    1CTY X-ray 2.20 A 2-107 [» ]
    1CTZ X-ray 1.90 A 2-107 [» ]
    1FHB NMR - A 2-107 [» ]
    1IRV X-ray 1.90 A 2-107 [» ]
    1IRW X-ray 2.00 A 2-107 [» ]
    1KYO X-ray 2.97 W 2-109 [» ]
    1LMS NMR - A 2-107 [» ]
    1NMI NMR - A 2-107 [» ]
    1RAP X-ray 2.25 A 2-109 [» ]
    1RAQ X-ray 1.90 A 2-109 [» ]
    1S6V X-ray 1.88 B/D 2-107 [» ]
    1U74 X-ray 2.40 B/D 2-107 [» ]
    1YCC X-ray 1.23 A 2-109 [» ]
    1YFC NMR - A 2-107 [» ]
    1YIC NMR - A 2-107 [» ]
    2B0Z X-ray 2.70 B 2-109 [» ]
    2B10 X-ray 2.80 B/D 2-109 [» ]
    2B11 X-ray 2.30 B/D 2-109 [» ]
    2B12 X-ray 3.02 B 2-109 [» ]
    2BCN X-ray 1.70 B 2-107 [» ]
    2GB8 NMR - B 2-109 [» ]
    2HV4 NMR - A 2-107 [» ]
    2JQR NMR - A 2-107 [» ]
    2JTI NMR - B 2-109 [» ]
    2LIR NMR - A 2-107 [» ]
    2LIT NMR - A 2-107 [» ]
    2ORL NMR - A 2-107 [» ]
    2PCC X-ray 2.30 B/D 2-109 [» ]
    2YCC X-ray 1.90 A 2-107 [» ]
    3CX5 X-ray 1.90 W 2-109 [» ]
    3TYI X-ray 1.40 A/B 2-107 [» ]
    4MU8 X-ray 1.45 A/B 2-107 [» ]
    ProteinModelPortali P00044.
    SMRi P00044. Positions 2-109.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 33801. 72 interactions.
    DIPi DIP-4265N.
    IntActi P00044. 5 interactions.
    MINTi MINT-8285287.
    STRINGi 4932.YJR048W.

    Proteomic databases

    MaxQBi P00044.
    PaxDbi P00044.
    PeptideAtlasi P00044.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblFungii YJR048W ; YJR048W ; YJR048W .
    GeneIDi 853507.
    KEGGi sce:YJR048W.

    Organism-specific databases

    SGDi S000003809. CYC1.

    Phylogenomic databases

    eggNOGi COG3474.
    GeneTreei ENSGT00390000009405.
    HOGENOMi HOG000009762.
    KOi K08738.
    OMAi CHNLKEG.
    OrthoDBi EOG71RXXT.

    Enzyme and pathway databases

    BioCyci YEAST:G3O-31683-MONOMER.
    Reactomei REACT_188673. Release of apoptotic factors from the mitochondria.
    REACT_191152. Detoxification of Reactive Oxygen Species.

    Miscellaneous databases

    EvolutionaryTracei P00044.
    NextBioi 974162.

    Gene expression databases

    Genevestigatori P00044.

    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. "Sequence of the gene for iso-1-cytochrome c in Saccharomyces cerevisiae."
      Smith M., Leung D.W., Gillam S., Astell C.R., Montgomery D.L., Hall B.D.
      Cell 16:753-761(1979) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    2. "Sequence of the yeast iso-1-cytochrome c mRNA."
      Boss J.M., Gillam S., Ziotmer R.S., Smith M.
      J. Biol. Chem. 256:12958-12961(1981) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [MRNA].
    3. "Nucleotide sequence of the COR region: a cluster of six genes in the yeast Saccharomyces cerevisiae."
      Melnick L., Sherman F.
      Gene 87:157-166(1990) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    4. "Revised nucleotide sequence of the COR region of yeast Saccharomyces cerevisiae chromosome X."
      Huang M.-E., Manus V., Chuat J.-C., Galibert F.
      Yeast 10:811-818(1994) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: ATCC 204508 / S288c.
    5. "Complete nucleotide sequence of Saccharomyces cerevisiae chromosome X."
      Galibert F., Alexandraki D., Baur A., Boles E., Chalwatzis N., Chuat J.-C., Coster F., Cziepluch C., de Haan M., Domdey H., Durand P., Entian K.-D., Gatius M., Goffeau A., Grivell L.A., Hennemann A., Herbert C.J., Heumann K.
      , Hilger F., Hollenberg C.P., Huang M.-E., Jacq C., Jauniaux J.-C., Katsoulou C., Kirchrath L., Kleine K., Kordes E., Koetter P., Liebl S., Louis E.J., Manus V., Mewes H.-W., Miosga T., Obermaier B., Perea J., Pohl T.M., Portetelle D., Pujol A., Purnelle B., Ramezani Rad M., Rasmussen S.W., Rose M., Rossau R., Schaaff-Gerstenschlaeger I., Smits P.H.M., Scarcez T., Soriano N., To Van D., Tzermia M., Van Broekhoven A., Vandenbol M., Wedler H., von Wettstein D., Wambutt R., Zagulski M., Zollner A., Karpfinger-Hartl L.
      EMBO J. 15:2031-2049(1996) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: ATCC 204508 / S288c.
    6. Cited for: GENOME REANNOTATION.
      Strain: ATCC 204508 / S288c.
    7. "The complete amino acid sequence in baker's yeast cytochrome c."
      Narita K., Titani K.
      J. Biochem. 65:259-267(1969) [PubMed] [Europe PMC] [Abstract]
      Cited for: PROTEIN SEQUENCE OF 2-109.
      Strain: Oviformis.
    8. "Transcription initiation of the Saccharomyces cerevisiae iso-1-cytochrome c gene. Multiple, independent T-A-T-A sequences."
      McNeil J.B., Smith M.
      J. Mol. Biol. 187:363-378(1986) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-22.
    9. "Studies on cytochrome c. 8. Synthesis of the protected hexadecapeptide (sequence 93-108) of Baker's yeast iso-1-cytochrome c."
      Moroder L., Marchiori F., Borin G., Scoffone E.
      Biopolymers 12:729-750(1973) [PubMed] [Europe PMC] [Abstract]
      Cited for: SYNTHESIS.
    10. "Enzymatic methylation of in vitro synthesized apocytochrome c enhances its transport into mitochondria."
      Park K.S., Frost B., Tuck M., Ho L.L., Kim S., Paik W.K.
      J. Biol. Chem. 262:14702-14708(1987) [PubMed] [Europe PMC] [Abstract]
      Cited for: METHYLATION.
    11. "Determinants of cytochrome c pro-apoptotic activity. The role of lysine 72 trimethylation."
      Kluck R.M., Ellerby L.M., Ellerby H.M., Naiem S., Yaffe M.P., Margoliash E., Bredesen D., Mauk A.G., Sherman F., Newmeyer D.D.
      J. Biol. Chem. 275:16127-16133(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: METHYLATION AT LYS-79.
    12. Cited for: METHYLATION AT LYS-78, MUTAGENESIS OF LYS-78.
    13. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
    14. Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    15. "Yeast iso-1-cytochrome c. A 2.8-A resolution three-dimensional structure determination."
      Louie G.V., Hutcheon W.L., Brayer G.D.
      J. Mol. Biol. 199:295-314(1988) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS).
    16. "High-resolution refinement of yeast iso-1-cytochrome c and comparisons with other eukaryotic cytochromes c."
      Louie G.V., Brayer G.D.
      J. Mol. Biol. 214:527-555(1990) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.23 ANGSTROMS).
    17. "Crystal structure of the yeast cytochrome bc1 complex with its bound substrate cytochrome c."
      Lange C., Hunte C.
      Proc. Natl. Acad. Sci. U.S.A. 99:2800-2805(2002) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.97 ANGSTROMS).
    18. "Three-dimensional solution structure of Saccharomyces cerevisiae reduced iso-1-cytochrome c."
      Baistrocchi P., Banci L., Bertini I., Turano P., Bren K.L., Gray H.B.
      Biochemistry 35:13788-13796(1996) [PubMed] [Europe PMC] [Abstract]
      Cited for: STRUCTURE BY NMR.
    19. "Solution structure of oxidized Saccharomyces cerevisiae iso-1-cytochrome c."
      Banci L., Bertini I., Bren K.L., Gray H.B., Sompornpisut P., Turano P.
      Biochemistry 36:8992-9001(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: STRUCTURE BY NMR.
    20. "Structure of complex III with bound cytochrome c in reduced state and definition of a minimal core interface for electron transfer."
      Solmaz S.R., Hunte C.
      J. Biol. Chem. 283:17542-17549(2008) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS) OF 2-109 IN THE BC1 COMPLEX, METHYLATION AT LYS-79.

    Entry informationi

    Entry nameiCYC1_YEAST
    AccessioniPrimary (citable) accession number: P00044
    Secondary accession number(s): D6VWL9
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: July 21, 1986
    Last sequence update: January 23, 2007
    Last modified: October 1, 2014
    This is version 168 of the entry and version 2 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programFungal Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    Present with 7330 molecules/cell in log phase SD medium.1 Publication

    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. SIMILARITY comments
      Index of protein domains and families
    4. Yeast
      Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
    5. Yeast chromosome X
      Yeast (Saccharomyces cerevisiae) chromosome X: entries and gene names

    External Data

    Dasty 3