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Protein

Formate dehydrogenase 1

Gene

FDH1

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the NAD+-dependent oxidation of formate to carbon dioxide. Formate oxidation is the final step in the methanol oxidation pathway in methylotrophic microorganisms (PubMed:9178506, PubMed:12144528, PubMed:11921099). Has a role in the detoxification of exogenous formate in non-methylotrophic organisms (PubMed:11921099).UniRule annotation3 Publications

Catalytic activityi

Formate + NAD+ = CO2 + NADH.UniRule annotation1 Publication

Kineticsi

kcat is 6.5 sec(-1) with NAD+ as substrate.1 Publication

  1. KM=5.5 mM for formate1 Publication
  2. KM=36 µM for NAD+1 Publication

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei97 – 971Substrate; via amide nitrogenUniRule annotation
    Binding sitei121 – 1211SubstrateUniRule annotation
    Binding sitei197 – 1971NADUniRule annotation
    Binding sitei270 – 2701NAD; via carbonyl oxygenUniRule annotation
    Sitei272 – 2721Important for catalytic activityUniRule annotation
    Binding sitei296 – 2961NADUniRule annotation
    Sitei325 – 3251Important for catalytic activityUniRule annotation

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Nucleotide bindingi176 – 1772NADUniRule annotation
    Nucleotide bindingi244 – 2485NADUniRule annotation
    Nucleotide bindingi325 – 3284NADUniRule annotation

    GO - Molecular functioni

    GO - Biological processi

    • formate catabolic process Source: SGD
    Complete GO annotation...

    Keywords - Molecular functioni

    Oxidoreductase

    Keywords - Ligandi

    NAD

    Enzyme and pathway databases

    BioCyciYEAST:YOR388C-MONOMER.
    BRENDAi1.2.1.2. 984.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Formate dehydrogenase 11 PublicationUniRule annotation (EC:1.2.1.2UniRule annotation1 Publication)
    Short name:
    FDHUniRule annotation
    Alternative name(s):
    NAD-dependent formate dehydrogenase1 PublicationUniRule annotation
    Gene namesi
    Name:FDH11 Publication
    Ordered Locus Names:YOR388CImported
    OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
    Taxonomic identifieri559292 [NCBI]
    Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
    Proteomesi
    • UP000002311 Componenti: Chromosome XV

    Organism-specific databases

    EuPathDBiFungiDB:YOR388C.
    SGDiS000005915. FDH1.

    Subcellular locationi

    GO - Cellular componenti

    • cytosol Source: SGD
    Complete GO annotation...

    Keywords - Cellular componenti

    Cytoplasm

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi197 – 1982DY → AR: Shifts the coenzyme preference of the enzyme from NAD(+) to NADP(+). 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 376376Formate dehydrogenase 1PRO_0000223647Add
    BLAST

    Expressioni

    Inductioni

    Induced by formate.1 Publication

    Interactioni

    Subunit structurei

    Homodimer.UniRule annotation

    Protein-protein interaction databases

    BioGridi34769. 35 interactions.
    DIPiDIP-5327N.
    IntActiQ08911. 4 interactions.
    MINTiMINT-530466.

    Structurei

    3D structure databases

    ProteinModelPortaliQ08911.
    SMRiQ08911. Positions 4-367.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni5 – 121117CatalyticUniRule annotationAdd
    BLAST
    Regioni122 – 326205Coenzyme-bindingUniRule annotationAdd
    BLAST
    Regioni327 – 37246CatalyticUniRule annotationAdd
    BLAST

    Sequence similaritiesi

    Belongs to the D-isomer specific 2-hydroxyacid dehydrogenase family. FDH subfamily.UniRule annotation

    Phylogenomic databases

    HOGENOMiHOG000136703.
    InParanoidiQ08911.
    KOiK00122.
    OMAiCIENELG.
    OrthoDBiEOG769ZV3.

    Family and domain databases

    Gene3Di3.40.50.720. 2 hits.
    HAMAPiMF_03210. Formate_dehydrogenase.
    InterProiIPR006139. D-isomer_2_OHA_DH_cat_dom.
    IPR029753. D-isomer_DH_CS.
    IPR006140. D-isomer_DH_NAD-bd.
    IPR016040. NAD(P)-bd_dom.
    [Graphical view]
    PfamiPF00389. 2-Hacid_dh. 1 hit.
    PF02826. 2-Hacid_dh_C. 1 hit.
    [Graphical view]
    SUPFAMiSSF51735. SSF51735. 1 hit.
    PROSITEiPS00670. D_2_HYDROXYACID_DH_2. 1 hit.
    PS00671. D_2_HYDROXYACID_DH_3. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    Q08911-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MSKGKVLLVL YEGGKHAEEQ EKLLGCIENE LGIRNFIEEQ GYELVTTIDK
    60 70 80 90 100
    DPEPTSTVDR ELKDAEIVIT TPFFPAYISR NRIAEAPNLK LCVTAGVGSD
    110 120 130 140 150
    HVDLEAANER KITVTEVTGS NVVSVAEHVM ATILVLIRNY NGGHQQAING
    160 170 180 190 200
    EWDIAGVAKN EYDLEDKIIS TVGAGRIGYR VLERLVAFNP KKLLYYDYQE
    210 220 230 240 250
    LPAEAINRLN EASKLFNGRG DIVQRVEKLE DMVAQSDVVT INCPLHKDSR
    260 270 280 290 300
    GLFNKKLISH MKDGAYLVNT ARGAICVAED VAEAVKSGKL AGYGGDVWDK
    310 320 330 340 350
    QPAPKDHPWR TMDNKDHVGN AMTVHISGTS LDAQKRYAQG VKNILNSYFS
    360 370
    KKFDYRPQDI IVQNGSYATR AYGQKK
    Length:376
    Mass (Da):41,714
    Last modified:November 1, 1996 - v1
    Checksum:i67ECDA6F9DDC2A02
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    Z75296 Genomic DNA. Translation: CAA99720.1.
    BK006948 Genomic DNA. Translation: DAA11147.1.
    PIRiS67300.
    RefSeqiNP_015033.1. NM_001183808.1.

    Genome annotation databases

    EnsemblFungiiYOR388C; YOR388C; YOR388C.
    GeneIDi854570.
    KEGGisce:YOR388C.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    Z75296 Genomic DNA. Translation: CAA99720.1.
    BK006948 Genomic DNA. Translation: DAA11147.1.
    PIRiS67300.
    RefSeqiNP_015033.1. NM_001183808.1.

    3D structure databases

    ProteinModelPortaliQ08911.
    SMRiQ08911. Positions 4-367.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    BioGridi34769. 35 interactions.
    DIPiDIP-5327N.
    IntActiQ08911. 4 interactions.
    MINTiMINT-530466.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblFungiiYOR388C; YOR388C; YOR388C.
    GeneIDi854570.
    KEGGisce:YOR388C.

    Organism-specific databases

    EuPathDBiFungiDB:YOR388C.
    SGDiS000005915. FDH1.

    Phylogenomic databases

    HOGENOMiHOG000136703.
    InParanoidiQ08911.
    KOiK00122.
    OMAiCIENELG.
    OrthoDBiEOG769ZV3.

    Enzyme and pathway databases

    BioCyciYEAST:YOR388C-MONOMER.
    BRENDAi1.2.1.2. 984.

    Miscellaneous databases

    NextBioi977021.
    PROiQ08911.

    Family and domain databases

    Gene3Di3.40.50.720. 2 hits.
    HAMAPiMF_03210. Formate_dehydrogenase.
    InterProiIPR006139. D-isomer_2_OHA_DH_cat_dom.
    IPR029753. D-isomer_DH_CS.
    IPR006140. D-isomer_DH_NAD-bd.
    IPR016040. NAD(P)-bd_dom.
    [Graphical view]
    PfamiPF00389. 2-Hacid_dh. 1 hit.
    PF02826. 2-Hacid_dh_C. 1 hit.
    [Graphical view]
    SUPFAMiSSF51735. SSF51735. 1 hit.
    PROSITEiPS00670. D_2_HYDROXYACID_DH_2. 1 hit.
    PS00671. D_2_HYDROXYACID_DH_3. 1 hit.
    [Graphical view]
    ProtoNetiSearch...

    Publicationsi

    « Hide 'large scale' publications
    1. "The nucleotide sequence of Saccharomyces cerevisiae chromosome XV."
      Dujon B., Albermann K., Aldea M., Alexandraki D., Ansorge W., Arino J., Benes V., Bohn C., Bolotin-Fukuhara M., Bordonne R., Boyer J., Camasses A., Casamayor A., Casas C., Cheret G., Cziepluch C., Daignan-Fornier B., Dang V.-D.
      , de Haan M., Delius H., Durand P., Fairhead C., Feldmann H., Gaillon L., Galisson F., Gamo F.-J., Gancedo C., Goffeau A., Goulding S.E., Grivell L.A., Habbig B., Hand N.J., Hani J., Hattenhorst U., Hebling U., Hernando Y., Herrero E., Heumann K., Hiesel R., Hilger F., Hofmann B., Hollenberg C.P., Hughes B., Jauniaux J.-C., Kalogeropoulos A., Katsoulou C., Kordes E., Lafuente M.J., Landt O., Louis E.J., Maarse A.C., Madania A., Mannhaupt G., Marck C., Martin R.P., Mewes H.-W., Michaux G., Paces V., Parle-McDermott A.G., Pearson B.M., Perrin A., Pettersson B., Poch O., Pohl T.M., Poirey R., Portetelle D., Pujol A., Purnelle B., Ramezani Rad M., Rechmann S., Schwager C., Schweizer M., Sor F., Sterky F., Tarassov I.A., Teodoru C., Tettelin H., Thierry A., Tobiasch E., Tzermia M., Uhlen M., Unseld M., Valens M., Vandenbol M., Vetter I., Vlcek C., Voet M., Volckaert G., Voss H., Wambutt R., Wedler H., Wiemann S., Winsor B., Wolfe K.H., Zollner A., Zumstein E., Kleine K.
      Nature 387:98-102(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: ATCC 204508 / S288c.
    2. Cited for: GENOME REANNOTATION.
      Strain: ATCC 204508 / S288c.
    3. "Expression cassettes for formaldehyde and fluoroacetate resistance, two dominant markers in Saccharomyces cerevisiae."
      van den Berg M.A., Steensma H.Y.
      Yeast 13:551-559(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION.
    4. "Engineering of coenzyme specificity of formate dehydrogenase from Saccharomyces cerevisiae."
      Serov A.E., Popova A.S., Fedorchuk V.V., Tishkov V.I.
      Biochem. J. 367:841-847(2002) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, MUTAGENESIS OF 197-ASP-TYR-198.
    5. "Functional analysis of structural genes for NAD(+)-dependent formate dehydrogenase in Saccharomyces cerevisiae."
      Overkamp K.M., Koetter P., van der Hoek R., Schoondermark-Stolk S., Luttik M.A.H., van Dijken J.P., Pronk J.T.
      Yeast 19:509-520(2002) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, SUBCELLULAR LOCATION, INDUCTION.

    Entry informationi

    Entry nameiFDH1_YEAST
    AccessioniPrimary (citable) accession number: Q08911
    Secondary accession number(s): D6W381
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: February 21, 2006
    Last sequence update: November 1, 1996
    Last modified: May 11, 2016
    This is version 113 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programFungal Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    Complete proteome, Reference proteome

    Documents

    1. SIMILARITY comments
      Index of protein domains and families
    2. Yeast
      Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
    3. Yeast chromosome XV
      Yeast (Saccharomyces cerevisiae) chromosome XV: entries and gene names

    Similar proteinsi

    Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
    100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
    90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
    50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.