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P00175

- CYB2_YEAST

UniProt

P00175 - CYB2_YEAST

Protein

Cytochrome b2, mitochondrial

Gene

CYB2

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 162 (01 Oct 2014)
      Sequence version 1 (01 Apr 1988)
      Previous versions | rss
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    Functioni

    Catalytic activityi

    (S)-lactate + 2 ferricytochrome c = pyruvate + 2 ferrocytochrome c + 2 H+.

    Cofactori

    FMN.1 Publication
    Binds 1 heme B (iron-protoporphyrin IX) group non-covalently per subunit.1 Publication

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Metal bindingi123 – 1231Iron (heme axial ligand)
    Metal bindingi146 – 1461Iron (heme axial ligand)
    Binding sitei177 – 1771Heme b
    Binding sitei219 – 2191Heme b
    Binding sitei223 – 2231Heme b
    Binding sitei376 – 3761Heme b
    Active sitei453 – 4531Proton acceptor
    Binding sitei456 – 4561Substrate

    GO - Molecular functioni

    1. FMN binding Source: InterPro
    2. heme binding Source: InterPro
    3. L-lactate dehydrogenase (cytochrome) activity Source: SGD
    4. metal ion binding Source: UniProtKB-KW

    GO - Biological processi

    1. lactate metabolic process Source: SGD

    Keywords - Molecular functioni

    Oxidoreductase

    Keywords - Biological processi

    Electron transport, Respiratory chain, Transport

    Keywords - Ligandi

    Flavoprotein, FMN, Heme, Iron, Metal-binding

    Enzyme and pathway databases

    BioCyciMetaCyc:MONOMER-12911.
    YEAST:YML054C-MONOMER.
    ReactomeiREACT_189012. Mitochondrial protein import.
    SABIO-RKP00175.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Cytochrome b2, mitochondrial (EC:1.1.2.3)
    Alternative name(s):
    L-lactate dehydrogenase [Cytochrome]
    L-lactate ferricytochrome C oxidoreductase
    Short name:
    L-LCR
    Gene namesi
    Name:CYB2
    Ordered Locus Names:YML054C
    ORF Names:YM9958.08C
    OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
    Taxonomic identifieri559292 [NCBI]
    Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
    ProteomesiUP000002311: Chromosome XIII

    Organism-specific databases

    CYGDiYML054c.
    SGDiS000004518. CYB2.

    Subcellular locationi

    Mitochondrion intermembrane space 1 Publication

    GO - Cellular componenti

    1. cytosol Source: Reactome
    2. mitochondrial inner membrane Source: Reactome
    3. mitochondrial intermembrane space Source: SGD
    4. mitochondrion Source: SGD
    5. respiratory chain Source: UniProtKB-KW

    Keywords - Cellular componenti

    Mitochondrion

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Transit peptidei1 – 8080Mitochondrion2 PublicationsAdd
    BLAST
    Chaini81 – 591511Cytochrome b2, mitochondrialPRO_0000006480Add
    BLAST

    Proteomic databases

    PaxDbiP00175.
    PeptideAtlasiP00175.

    Expressioni

    Inductioni

    By L-lactate. Induced during respiratory adaptation.

    Gene expression databases

    GenevestigatoriP00175.

    Interactioni

    Subunit structurei

    Homotetramer.

    Protein-protein interaction databases

    BioGridi35113. 29 interactions.
    DIPiDIP-5810N.
    IntActiP00175. 9 interactions.
    MINTiMINT-605329.
    STRINGi4932.YML054C.

    Structurei

    Secondary structure

    1
    591
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi95 – 984
    Beta strandi104 – 1096
    Beta strandi112 – 1154
    Turni117 – 1193
    Helixi120 – 1223
    Helixi127 – 1315
    Turni132 – 1354
    Helixi139 – 1424
    Helixi143 – 1453
    Helixi150 – 1545
    Helixi157 – 1593
    Beta strandi160 – 1645
    Beta strandi170 – 1734
    Helixi183 – 19412
    Helixi199 – 2013
    Helixi205 – 21511
    Helixi218 – 2258
    Beta strandi228 – 2303
    Helixi232 – 2398
    Helixi240 – 2434
    Beta strandi261 – 2633
    Beta strandi266 – 2749
    Helixi280 – 2823
    Turni285 – 2884
    Helixi289 – 2979
    Beta strandi298 – 3014
    Beta strandi305 – 3073
    Helixi315 – 3206
    Beta strandi325 – 3273
    Beta strandi329 – 3335
    Helixi339 – 35214
    Beta strandi357 – 3604
    Helixi370 – 3778
    Helixi398 – 4014
    Beta strandi404 – 4063
    Helixi412 – 42110
    Beta strandi426 – 4316
    Helixi434 – 4429
    Beta strandi446 – 4505
    Turni453 – 4564
    Helixi464 – 47613
    Turni477 – 4793
    Helixi481 – 4833
    Beta strandi484 – 4918
    Helixi495 – 50410
    Beta strandi507 – 5115
    Helixi513 – 54533
    Helixi550 – 5523
    Helixi555 – 5573
    Turni561 – 5644
    Helixi574 – 5796

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1FCBX-ray2.40A/B81-591[»]
    1KBIX-ray2.30A/B81-591[»]
    1KBJX-ray2.50A/B180-591[»]
    1LCOX-ray2.90A/B81-591[»]
    1LDCX-ray2.90A/B81-591[»]
    1LTDX-ray2.60A/B86-591[»]
    1QCWX-ray2.75A/B182-591[»]
    1SZEX-ray3.00A/B81-591[»]
    1SZFX-ray2.70A/B81-591[»]
    1SZGX-ray2.70A/B81-591[»]
    2OZ0X-ray2.80A/B81-591[»]
    3KS0X-ray2.70A/B86-180[»]
    ProteinModelPortaliP00175.
    SMRiP00175. Positions 81-591.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP00175.

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini88 – 16578Cytochrome b5 heme-bindingPROSITE-ProRule annotationAdd
    BLAST
    Domaini197 – 563367FMN hydroxy acid dehydrogenasePROSITE-ProRule annotationAdd
    BLAST

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni177 – 19014HingeAdd
    BLAST
    Regioni567 – 59125Tail (wraps around the molecular 4-fold axis)Add
    BLAST

    Sequence similaritiesi

    Contains 1 cytochrome b5 heme-binding domain.PROSITE-ProRule annotation
    Contains 1 FMN hydroxy acid dehydrogenase domain.PROSITE-ProRule annotation

    Keywords - Domaini

    Transit peptide

    Phylogenomic databases

    eggNOGiCOG1304.
    GeneTreeiENSGT00390000018717.
    HOGENOMiHOG000217463.
    KOiK00101.
    OMAiAWFQSIT.
    OrthoDBiEOG7N63X3.

    Family and domain databases

    Gene3Di3.10.120.10. 1 hit.
    3.20.20.70. 1 hit.
    InterProiIPR013785. Aldolase_TIM.
    IPR012133. Alpha-hydoxy_acid_DH_FMN.
    IPR001199. Cyt_B5-like_heme/steroid-bd.
    IPR018506. Cyt_B5_heme-BS.
    IPR000262. FMN-dep_DH.
    IPR008259. FMN_hydac_DH_AS.
    [Graphical view]
    PfamiPF00173. Cyt-b5. 1 hit.
    PF01070. FMN_dh. 1 hit.
    [Graphical view]
    PRINTSiPR00363. CYTOCHROMEB5.
    SUPFAMiSSF55856. SSF55856. 1 hit.
    PROSITEiPS00191. CYTOCHROME_B5_1. 1 hit.
    PS50255. CYTOCHROME_B5_2. 1 hit.
    PS00557. FMN_HYDROXY_ACID_DH_1. 1 hit.
    PS51349. FMN_HYDROXY_ACID_DH_2. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

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

    P00175-1 [UniParc]FASTAAdd to Basket

    « Hide

    MLKYKPLLKI SKNCEAAILR ASKTRLNTIR AYGSTVPKSK SFEQDSRKRT    50
    QSWTALRVGA ILAATSSVAY LNWHNGQIDN EPKLDMNKQK ISPAEVAKHN 100
    KPDDCWVVIN GYVYDLTRFL PNHPGGQDVI KFNAGKDVTA IFEPLHAPNV 150
    IDKYIAPEKK LGPLQGSMPP ELVCPPYAPG ETKEDIARKE QLKSLLPPLD 200
    NIINLYDFEY LASQTLTKQA WAYYSSGAND EVTHRENHNA YHRIFFKPKI 250
    LVDVRKVDIS TDMLGSHVDV PFYVSATALC KLGNPLEGEK DVARGCGQGV 300
    TKVPQMISTL ASCSPEEIIE AAPSDKQIQW YQLYVNSDRK ITDDLVKNVE 350
    KLGVKALFVT VDAPSLGQRE KDMKLKFSNT KAGPKAMKKT NVEESQGASR 400
    ALSKFIDPSL TWKDIEELKK KTKLPIVIKG VQRTEDVIKA AEIGVSGVVL 450
    SNHGGRQLDF SRAPIEVLAE TMPILEQRNL KDKLEVFVDG GVRRGTDVLK 500
    ALCLGAKGVG LGRPFLYANS CYGRNGVEKA IEILRDEIEM SMRLLGVTSI 550
    AELKPDLLDL STLKARTVGV PNDVLYNEVY EGPTLTEFED A 591
    Length:591
    Mass (Da):65,539
    Last modified:April 1, 1988 - v1
    Checksum:iDBADA0751B3C5B83
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti165 – 1651Q → E AA sequence (PubMed:6365548)Curated
    Sequence conflicti165 – 1651Q → E AA sequence (PubMed:776230)Curated
    Sequence conflicti466 – 4661E → Q AA sequence (PubMed:3902473)Curated
    Sequence conflicti513 – 5131R → E AA sequence (PubMed:3902473)Curated
    Sequence conflicti570 – 5701V → P AA sequence (PubMed:11502169)Curated

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    X03215 Genomic DNA. Translation: CAA26959.1.
    Z46729 Genomic DNA. Translation: CAA86721.1.
    BK006946 Genomic DNA. Translation: DAA09844.1.
    PIRiA24583. CBBY2.
    RefSeqiNP_013658.1. NM_001182412.1.

    Genome annotation databases

    EnsemblFungiiYML054C; YML054C; YML054C.
    GeneIDi854950.
    KEGGisce:YML054C.

    Cross-referencesi

    Web resourcesi

    Worthington enzyme manual

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    X03215 Genomic DNA. Translation: CAA26959.1 .
    Z46729 Genomic DNA. Translation: CAA86721.1 .
    BK006946 Genomic DNA. Translation: DAA09844.1 .
    PIRi A24583. CBBY2.
    RefSeqi NP_013658.1. NM_001182412.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1FCB X-ray 2.40 A/B 81-591 [» ]
    1KBI X-ray 2.30 A/B 81-591 [» ]
    1KBJ X-ray 2.50 A/B 180-591 [» ]
    1LCO X-ray 2.90 A/B 81-591 [» ]
    1LDC X-ray 2.90 A/B 81-591 [» ]
    1LTD X-ray 2.60 A/B 86-591 [» ]
    1QCW X-ray 2.75 A/B 182-591 [» ]
    1SZE X-ray 3.00 A/B 81-591 [» ]
    1SZF X-ray 2.70 A/B 81-591 [» ]
    1SZG X-ray 2.70 A/B 81-591 [» ]
    2OZ0 X-ray 2.80 A/B 81-591 [» ]
    3KS0 X-ray 2.70 A/B 86-180 [» ]
    ProteinModelPortali P00175.
    SMRi P00175. Positions 81-591.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 35113. 29 interactions.
    DIPi DIP-5810N.
    IntActi P00175. 9 interactions.
    MINTi MINT-605329.
    STRINGi 4932.YML054C.

    Proteomic databases

    PaxDbi P00175.
    PeptideAtlasi P00175.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblFungii YML054C ; YML054C ; YML054C .
    GeneIDi 854950.
    KEGGi sce:YML054C.

    Organism-specific databases

    CYGDi YML054c.
    SGDi S000004518. CYB2.

    Phylogenomic databases

    eggNOGi COG1304.
    GeneTreei ENSGT00390000018717.
    HOGENOMi HOG000217463.
    KOi K00101.
    OMAi AWFQSIT.
    OrthoDBi EOG7N63X3.

    Enzyme and pathway databases

    BioCyci MetaCyc:MONOMER-12911.
    YEAST:YML054C-MONOMER.
    Reactomei REACT_189012. Mitochondrial protein import.
    SABIO-RK P00175.

    Miscellaneous databases

    EvolutionaryTracei P00175.
    NextBioi 978016.

    Gene expression databases

    Genevestigatori P00175.

    Family and domain databases

    Gene3Di 3.10.120.10. 1 hit.
    3.20.20.70. 1 hit.
    InterProi IPR013785. Aldolase_TIM.
    IPR012133. Alpha-hydoxy_acid_DH_FMN.
    IPR001199. Cyt_B5-like_heme/steroid-bd.
    IPR018506. Cyt_B5_heme-BS.
    IPR000262. FMN-dep_DH.
    IPR008259. FMN_hydac_DH_AS.
    [Graphical view ]
    Pfami PF00173. Cyt-b5. 1 hit.
    PF01070. FMN_dh. 1 hit.
    [Graphical view ]
    PRINTSi PR00363. CYTOCHROMEB5.
    SUPFAMi SSF55856. SSF55856. 1 hit.
    PROSITEi PS00191. CYTOCHROME_B5_1. 1 hit.
    PS50255. CYTOCHROME_B5_2. 1 hit.
    PS00557. FMN_HYDROXY_ACID_DH_1. 1 hit.
    PS51349. FMN_HYDROXY_ACID_DH_2. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "Structure, expression and regulation of a nuclear gene encoding a mitochondrial protein: the yeast L(+)-lactate cytochrome c oxidoreductase (cytochrome b2)."
      Guiard B.
      EMBO J. 4:3265-3272(1985) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: ATCC 204508 / S288c.
    3. Cited for: GENOME REANNOTATION.
      Strain: ATCC 204508 / S288c.
    4. "Primary structure of flavocytochrome b2 from baker's yeast. Purification by reverse-phase high-pressure liquid chromatography and sequencing of fragment alpha cyanogen bromide peptides."
      Ghrir R., Becam A.-M., Lederer F.
      Eur. J. Biochem. 139:59-74(1984) [PubMed] [Europe PMC] [Abstract]
      Cited for: PROTEIN SEQUENCE OF 81-394.
    5. "Complete amino acid sequence of flavocytochrome b2 from baker's yeast."
      Lederer F., Cortial S., Becam A.-M., Haumont P.-Y., Perez L.
      Eur. J. Biochem. 152:419-428(1985) [PubMed] [Europe PMC] [Abstract]
      Cited for: PROTEIN SEQUENCE OF 395-591.
    6. "More similarity between bakers'yeast L-(+)-lactate dehydrogenase and liver microsomal sytochrome B5."
      Guiard B., Lederer F., Jacq C.
      Nature 255:422-423(1975) [PubMed] [Europe PMC] [Abstract]
      Cited for: PROTEIN SEQUENCE OF 81-94.
    7. "Yeast mitochondrial dehydrogenases are associated in a supramolecular complex."
      Grandier-Vazeille X., Bathany K., Chaignepain S., Camougrand N., Manon S., Schmitter J.-M.
      Biochemistry 40:9758-9769(2001) [PubMed] [Europe PMC] [Abstract]
      Cited for: PROTEIN SEQUENCE OF 83-88 AND 564-570, SUBCELLULAR LOCATION.
      Strain: ATCC 201238 / W303-1B.
    8. "Complete amino acid sequence of the heme-binding core in bakers' yeast cytochrome b2 (L-(+)-lactate dehydrogenase)."
      Guiard B., Lederer F.
      Biochimie 58:305-316(1976) [PubMed] [Europe PMC] [Abstract]
      Cited for: PROTEIN SEQUENCE OF 88-183.
    9. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
    10. "Molecular structure of flavocytochrome b2 at 2.4-A resolution."
      Xia Z.-X., Mathews F.S.
      J. Mol. Biol. 212:837-863(1990) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS).
    11. "Crystallographic study of the recombinant flavin-binding domain of Baker's yeast flavocytochrome b(2): comparison with the intact wild-type enzyme."
      Cunane L.M., Barton J.D., Chen Z.-W., Welsh F.E., Chapman S.K., Reid G.A., Mathews F.S.
      Biochemistry 41:4264-4272(2002) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS) OF 81-591 IN COMPLEXES WITH HEME AND FMN.

    Entry informationi

    Entry nameiCYB2_YEAST
    AccessioniPrimary (citable) accession number: P00175
    Secondary accession number(s): D6VZC0
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: July 21, 1986
    Last sequence update: April 1, 1988
    Last modified: October 1, 2014
    This is version 162 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programFungal Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    Present with 4590 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. SIMILARITY comments
      Index of protein domains and families
    3. Yeast
      Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
    4. Yeast chromosome XIII
      Yeast (Saccharomyces cerevisiae) chromosome XIII: entries and gene names

    External Data

    Dasty 3