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Protein

Formate dehydrogenase

Gene
N/A
Organism
Pseudomonas sp. (strain 101) (Achromobacter parvulus T1)
Status
Reviewed-Annotation score: Annotation score: 5 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. Has a role in the detoxification of exogenous formate in non-methylotrophic organisms.UniRule annotation1 Publication

Catalytic activityi

Formate + NAD+ = CO2 + NADH.UniRule annotation2 Publications

Kineticsi

kcat is 10 sec(-1) with formate as substrate.2 Publications

  1. KM=7.5 mM for formate1 Publication
  2. KM=7.0 mM for formate1 Publication
  3. KM=0.11 mM for NAD+1 Publication
  4. KM=60 µM for NAD+1 Publication

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei123 – 1231Substrate; via amide nitrogenUniRule annotation1 Publication
    Binding sitei147 – 1471SubstrateUniRule annotation1 Publication
    Binding sitei148 – 1481NADUniRule annotation1 Publication
    Binding sitei222 – 2221NADUniRule annotation1 Publication
    Binding sitei283 – 2831NAD; via carbonyl oxygenUniRule annotation1 Publication
    Sitei285 – 2851Important for catalytic activityUniRule annotation1 Publication
    Binding sitei309 – 3091NADUniRule annotation1 Publication
    Sitei333 – 3331Important for catalytic activityUniRule annotation1 Publication
    Binding sitei381 – 3811NADUniRule annotation1 Publication

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Nucleotide bindingi202 – 2032NADUniRule annotation1 Publication
    Nucleotide bindingi257 – 2615NADUniRule annotation1 Publication
    Nucleotide bindingi333 – 3364NADUniRule annotation1 Publication

    GO - Molecular functioni

    Complete GO annotation...

    Keywords - Molecular functioni

    Oxidoreductase

    Keywords - Ligandi

    NAD

    Enzyme and pathway databases

    BRENDAi1.2.1.2. 5085.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Formate dehydrogenase1 PublicationUniRule annotation (EC:1.2.1.2UniRule annotation2 Publications)
    Short name:
    FDHUniRule annotation
    Alternative name(s):
    NAD-dependent formate dehydrogenase1 PublicationUniRule annotation
    OrganismiPseudomonas sp. (strain 101) (Achromobacter parvulus T1)
    Taxonomic identifieri33067 [NCBI]
    Taxonomic lineageiBacteriaProteobacteria

    Subcellular locationi

    • Cytoplasm UniRule annotation

    Keywords - Cellular componenti

    Cytoplasm

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi256 – 2561C → S or M: High resistance to inactivation by Hg(2+), Increased stability at 25 degree Celsius and decreased thermostability at 45 degree Celsius. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Initiator methionineiRemoved1 Publication
    Chaini2 – 401400Formate dehydrogenasePRO_0000076027Add
    BLAST

    Interactioni

    Subunit structurei

    Homodimer.UniRule annotation1 Publication

    Structurei

    Secondary structure

    1
    401
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi3 – 75Combined sources
    Beta strandi21 – 233Combined sources
    Turni54 – 563Combined sources
    Helixi57 – 593Combined sources
    Helixi61 – 666Combined sources
    Beta strandi70 – 756Combined sources
    Helixi83 – 886Combined sources
    Beta strandi92 – 976Combined sources
    Helixi106 – 1116Combined sources
    Beta strandi117 – 1237Combined sources
    Helixi130 – 1356Combined sources
    Beta strandi139 – 1424Combined sources
    Turni144 – 1474Combined sources
    Helixi148 – 16316Combined sources
    Helixi166 – 1749Combined sources
    Helixi180 – 1845Combined sources
    Beta strandi194 – 1985Combined sources
    Helixi202 – 21110Combined sources
    Helixi212 – 2143Combined sources
    Beta strandi217 – 2215Combined sources
    Helixi228 – 2347Combined sources
    Beta strandi237 – 2415Combined sources
    Helixi242 – 2454Combined sources
    Helixi246 – 2483Combined sources
    Beta strandi250 – 2545Combined sources
    Turni260 – 2645Combined sources
    Helixi268 – 2714Combined sources
    Beta strandi278 – 2825Combined sources
    Helixi286 – 2883Combined sources
    Helixi291 – 2999Combined sources
    Beta strandi302 – 3098Combined sources
    Beta strandi312 – 3154Combined sources
    Helixi321 – 3233Combined sources
    Helixi335 – 3373Combined sources
    Helixi339 – 35820Combined sources
    Helixi364 – 3663Combined sources
    Beta strandi367 – 3704Combined sources
    Beta strandi371 – 3733Combined sources
    Helixi377 – 3815Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    2GO1X-ray2.10A1-401[»]
    2GUGX-ray2.28A/B/C/D1-401[»]
    2NACX-ray1.80A/B2-394[»]
    2NADX-ray2.05A/B2-394[»]
    ProteinModelPortaliP33160.
    SMRiP33160. Positions 2-392.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP33160.

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni3 – 147145CatalyticUniRule annotation1 PublicationAdd
    BLAST
    Regioni148 – 334187Coenzyme-bindingUniRule annotation1 PublicationAdd
    BLAST
    Regioni335 – 38248CatalyticUniRule annotation1 PublicationAdd
    BLAST

    Sequence similaritiesi

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

    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.
    IPR029752. D-isomer_DH_CS1.
    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.
    PROSITEiPS00065. D_2_HYDROXYACID_DH_1. 1 hit.
    PS00670. D_2_HYDROXYACID_DH_2. 1 hit.
    PS00671. D_2_HYDROXYACID_DH_3. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

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

    P33160-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MAKVLCVLYD DPVDGYPKTY ARDDLPKIDH YPGGQTLPTP KAIDFTPGQL
    60 70 80 90 100
    LGSVSGELGL RKYLESNGHT LVVTSDKDGP DSVFERELVD ADVVISQPFW
    110 120 130 140 150
    PAYLTPERIA KAKNLKLALT AGIGSDHVDL QSAIDRNVTV AEVTYCNSIS
    160 170 180 190 200
    VAEHVVMMIL SLVRNYLPSH EWARKGGWNI ADCVSHAYDL EAMHVGTVAA
    210 220 230 240 250
    GRIGLAVLRR LAPFDVHLHY TDRHRLPESV EKELNLTWHA TREDMYPVCD
    260 270 280 290 300
    VVTLNCPLHP ETEHMINDET LKLFKRGAYI VNTARGKLCD RDAVARALES
    310 320 330 340 350
    GRLAGYAGDV WFPQPAPKDH PWRTMPYNGM TPHISGTTLT AQARYAAGTR
    360 370 380 390 400
    EILECFFEGR PIRDEYLIVQ GGALAGTGAH SYSKGNATGG SEEAAKFKKA

    V
    Length:401
    Mass (Da):44,136
    Last modified:January 23, 2007 - v3
    Checksum:i6B3EBA21F03A89A2
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti78 – 781D → S (PubMed:1954846).Curated
    Sequence conflicti139 – 1402TV → VT (PubMed:1954846).Curated
    Sequence conflicti146 – 1461C → V (PubMed:1954846).Curated
    Sequence conflicti216 – 2172VH → HV (PubMed:1954846).Curated
    Sequence conflicti328 – 3281N → D (PubMed:1954846).Curated

    Sequence databases

    PIRiJU0334.

    Cross-referencesi

    Sequence databases

    PIRiJU0334.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    2GO1X-ray2.10A1-401[»]
    2GUGX-ray2.28A/B/C/D1-401[»]
    2NACX-ray1.80A/B2-394[»]
    2NADX-ray2.05A/B2-394[»]
    ProteinModelPortaliP33160.
    SMRiP33160. Positions 2-392.
    ModBaseiSearch...
    MobiDBiSearch...

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Enzyme and pathway databases

    BRENDAi1.2.1.2. 5085.

    Miscellaneous databases

    EvolutionaryTraceiP33160.

    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.
    IPR029752. D-isomer_DH_CS1.
    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.
    PROSITEiPS00065. D_2_HYDROXYACID_DH_1. 1 hit.
    PS00670. D_2_HYDROXYACID_DH_2. 1 hit.
    PS00671. D_2_HYDROXYACID_DH_3. 1 hit.
    [Graphical view]
    ProtoNetiSearch...

    Publicationsi

    1. "NAD-dependent formate dehydrogenase of methylotrophic bacteria Pseudomonas sp. 101: cloning, expression, and study of the genetic structure."
      Tishkov V.I., Galkin A.G., Egorov A.M.
      Dokl. Akad. Nauk SSSR 317:745-748(1991) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    2. "NAD-dependent formate dehydrogenase from methylotrophic bacteria Pseudomonas sp. 101. I. Amino acid sequence."
      Popov V.O., Shumilin I.A., Ustinnikova T.B., Lamzin V.S., Egorov T.A.
      Bioorg. Khim. 16:324-335(1990) [PubMed] [Europe PMC] [Abstract]
      Cited for: PROTEIN SEQUENCE OF 2-394.
    3. Cited for: X-RAY CRYSTALLOGRAPHY (3.0 ANGSTROMS).
    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: CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES.
    5. "Catalytic properties and stability of a Pseudomonas sp.101 formate dehydrogenase mutants containing Cys-255-Ser and Cys-255-Met replacements."
      Tishkov V.I., Galkin A.G., Marchenko G.N., Egorova O.A., Sheluho D.V., Kulakova L.B., Dementieva L.A., Egorov A.M.
      Biochem. Biophys. Res. Commun. 192:976-981(1993) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, MUTAGENESIS OF CYS-256.
    6. "High resolution structures of holo and apo formate dehydrogenase."
      Lamzin V.S., Dauter Z., Popov V.O., Harutyunyan E.H., Wilson K.S.
      J. Mol. Biol. 236:759-785(1994) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.80 ANGSTROMS) OF 2-394 IN COMPLEX WITH NAD.
    7. "Structure of a new crystal modification of the bacterial NAD-dependent formate dehydrogenase with a resolution of 2.1 A."
      Filippova E.V., Polyakov K.M., Tikhonova T.V., Stekhanova T.N., Boiko K.M., Popov V.O.
      Crystallogr. Rep. 50:796-800(2005)
      Cited for: X-RAY CRYSTALLOGRAPHY (2.10 ANGSTROMS), SUBUNIT.
    8. "Crystal structure of the complex of NAD-dependent formate dehydrogenase from metylotrophic bacterium Pseudomonas sp.101 with formate."
      Filippova E.V., Polyakov K.M., Tikhonova T.V., Stekhanova T.N., Boiko K.M., Sadihov I.G., Tishkov V.I., Labrou N., Popov V.O.
      Crystallogr. Rep. 51:627-631(2006)
      Cited for: X-RAY CRYSTALLOGRAPHY (2.28 ANGSTROMS) IN COMPLEX WITH NAD AND FORMATE.

    Entry informationi

    Entry nameiFDH_PSESR
    AccessioniPrimary (citable) accession number: P33160
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: October 1, 1993
    Last sequence update: January 23, 2007
    Last modified: January 20, 2016
    This is version 98 of the entry and version 3 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Direct protein sequencing

    Documents

    1. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    2. SIMILARITY comments
      Index of protein domains and families

    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.