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Protein

Glutathione-independent formaldehyde dehydrogenase

Gene

fdhA

Organism
Pseudomonas putida (Arthrobacter siderocapsulatus)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the NAD+-dependent oxidation of formaldehyde and acetoaldehyde as well as long-chain alcohols but is inactive against propionaldehyde, butyraldehyde, methanol and ethanol. Can also catalyze the dismutation of a wide range of aldehydes such as formaldehyde.2 Publications

Catalytic activityi

Formaldehyde + NAD+ + H2O = formate + NADH.2 Publications
An alcohol + NAD+ = an aldehyde or ketone + NADH.2 Publications
2 formaldehyde + H2O = formate + methanol.2 Publications

Cofactori

Protein has several cofactor binding sites:
  • Zn2+Note: Binds 2 Zn2+ ions per subunit.
  • NAD+Note: Contains a tightly but non-covalently bound NAD cofactor required for formaldehyde dismutase activity.

Enzyme regulationi

Inactivated by bipyridine and p-chloromercuribenzoate.1 Publication

Kineticsi

  1. KM=0.25 mM for formaldehyde

    pH dependencei

    Optimum pH is 8.9. Active from pH 5 to 10.

    Temperature dependencei

    Thermostable up to 60 degrees Celsius.

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Metal bindingi47 – 471Zinc 1; catalytic
    Metal bindingi68 – 681Zinc 1; catalytic
    Metal bindingi98 – 981Zinc 2
    Metal bindingi101 – 1011Zinc 2
    Metal bindingi104 – 1041Zinc 2
    Metal bindingi112 – 1121Zinc 2
    Metal bindingi177 – 1771Zinc 1; catalytic

    GO - Molecular functioni

    Complete GO annotation...

    Keywords - Molecular functioni

    Oxidoreductase

    Keywords - Ligandi

    Metal-binding, NAD, Zinc

    Enzyme and pathway databases

    BioCyciRETL1328306-WGS:GSTH-6728-MONOMER.
    BRENDAi1.2.1.46. 5092.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Glutathione-independent formaldehyde dehydrogenase (EC:1.2.1.462 Publications)
    Short name:
    FALDH
    Short name:
    FDH
    Alternative name(s):
    Formaldehyde dismutase (EC:1.2.98.12 Publications)
    Gene namesi
    Name:fdhA
    OrganismiPseudomonas putida (Arthrobacter siderocapsulatus)
    Taxonomic identifieri303 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaPseudomonadalesPseudomonadaceaePseudomonas

    Pathology & Biotechi

    Chemistry

    ChEMBLiCHEMBL1293291.

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Initiator methionineiRemoved
    Chaini2 – 399398Glutathione-independent formaldehyde dehydrogenasePRO_0000160757Add
    BLAST

    Interactioni

    Subunit structurei

    Homotetramer.1 Publication

    Structurei

    Secondary structure

    1
    399
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi4 – 118Combined sources
    Beta strandi14 – 207Combined sources
    Beta strandi37 – 459Combined sources
    Helixi48 – 547Combined sources
    Beta strandi70 – 778Combined sources
    Beta strandi89 – 913Combined sources
    Beta strandi94 – 963Combined sources
    Beta strandi99 – 1013Combined sources
    Helixi102 – 1054Combined sources
    Helixi109 – 1113Combined sources
    Beta strandi113 – 1153Combined sources
    Beta strandi117 – 1204Combined sources
    Beta strandi122 – 1243Combined sources
    Beta strandi136 – 1449Combined sources
    Helixi145 – 1484Combined sources
    Helixi155 – 1606Combined sources
    Helixi162 – 1654Combined sources
    Helixi166 – 1694Combined sources
    Helixi171 – 18111Combined sources
    Beta strandi189 – 1935Combined sources
    Helixi197 – 20812Combined sources
    Beta strandi212 – 2198Combined sources
    Helixi221 – 2299Combined sources
    Beta strandi233 – 2364Combined sources
    Beta strandi239 – 2413Combined sources
    Helixi243 – 2519Combined sources
    Beta strandi252 – 2543Combined sources
    Beta strandi256 – 2616Combined sources
    Helixi274 – 2763Combined sources
    Helixi282 – 2909Combined sources
    Beta strandi296 – 2994Combined sources
    Helixi313 – 3164Combined sources
    Helixi324 – 3296Combined sources
    Beta strandi333 – 3386Combined sources
    Helixi341 – 35313Combined sources
    Helixi359 – 3635Combined sources
    Beta strandi365 – 3684Combined sources
    Helixi370 – 3723Combined sources
    Helixi373 – 38210Combined sources
    Beta strandi387 – 3904Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1KOLX-ray1.65A/B2-399[»]
    ProteinModelPortaliP46154.
    SMRiP46154. Positions 3-398.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP46154.

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni172 – 338167Cofactor-bindingAdd
    BLAST

    Sequence similaritiesi

    Family and domain databases

    Gene3Di3.40.50.720. 1 hit.
    3.90.180.10. 1 hit.
    InterProiIPR013149. ADH_C.
    IPR013154. ADH_N.
    IPR002085. ADH_SF_Zn-type.
    IPR002328. ADH_Zn_CS.
    IPR011032. GroES-like.
    IPR014184. HCHO_DH_non_GSH.
    IPR016040. NAD(P)-bd_dom.
    [Graphical view]
    PANTHERiPTHR11695. PTHR11695. 1 hit.
    PfamiPF08240. ADH_N. 1 hit.
    PF00107. ADH_zinc_N. 1 hit.
    [Graphical view]
    SUPFAMiSSF50129. SSF50129. 1 hit.
    SSF51735. SSF51735. 1 hit.
    TIGRFAMsiTIGR02819. fdhA_non_GSH. 1 hit.
    PROSITEiPS00059. ADH_ZINC. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

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

    P46154-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MSGNRGVVYL GSGKVEVQKI DYPKMQDPRG KKIEHGVILK VVSTNICGSD
    60 70 80 90 100
    QHMVRGRTTA QVGLVLGHEI TGEVIEKGRD VENLQIGDLV SVPFNVACGR
    110 120 130 140 150
    CRSCKEMHTG VCLTVNPARA GGAYGYVDMG DWTGGQAEYL LVPYADFNLL
    160 170 180 190 200
    KLPDRDKAME KIRDLTCLSD ILPTGYHGAV TAGVGPGSTV YVAGAGPVGL
    210 220 230 240 250
    AAAASARLLG AAVVIVGDLN PARLAHAKAQ GFEIADLSLD TPLHEQIAAL
    260 270 280 290 300
    LGEPEVDCAV DAVGFEARGH GHEGAKHEAP ATVLNSLMQV TRVAGKIGIP
    310 320 330 340 350
    GLYVTEDPGA VDAAAKIGSL SIRFGLGWAK SHSFHTGQTP VMKYNRALMQ
    360 370 380 390
    AIMWDRINIA EVVGVQVISL DDAPRGYGEF DAGVPKKFVI DPHKTFSAA
    Length:399
    Mass (Da):42,082
    Last modified:January 23, 2007 - v3
    Checksum:iEBBA418C97E76A9F
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    D21201 Genomic DNA. Translation: BAA04743.1.
    PIRiA55577.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    D21201 Genomic DNA. Translation: BAA04743.1.
    PIRiA55577.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1KOLX-ray1.65A/B2-399[»]
    ProteinModelPortaliP46154.
    SMRiP46154. Positions 3-398.
    ModBaseiSearch...
    MobiDBiSearch...

    Chemistry

    ChEMBLiCHEMBL1293291.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Enzyme and pathway databases

    BioCyciRETL1328306-WGS:GSTH-6728-MONOMER.
    BRENDAi1.2.1.46. 5092.

    Miscellaneous databases

    EvolutionaryTraceiP46154.

    Family and domain databases

    Gene3Di3.40.50.720. 1 hit.
    3.90.180.10. 1 hit.
    InterProiIPR013149. ADH_C.
    IPR013154. ADH_N.
    IPR002085. ADH_SF_Zn-type.
    IPR002328. ADH_Zn_CS.
    IPR011032. GroES-like.
    IPR014184. HCHO_DH_non_GSH.
    IPR016040. NAD(P)-bd_dom.
    [Graphical view]
    PANTHERiPTHR11695. PTHR11695. 1 hit.
    PfamiPF08240. ADH_N. 1 hit.
    PF00107. ADH_zinc_N. 1 hit.
    [Graphical view]
    SUPFAMiSSF50129. SSF50129. 1 hit.
    SSF51735. SSF51735. 1 hit.
    TIGRFAMsiTIGR02819. fdhA_non_GSH. 1 hit.
    PROSITEiPS00059. ADH_ZINC. 1 hit.
    [Graphical view]
    ProtoNetiSearch...

    Publicationsi

    1. "Cloning and high-level expression of the glutathione-independent formaldehyde dehydrogenase gene from Pseudomonas putida."
      Ito K., Takahashi M., Yoshimoto T., Tsuru D.
      J. Bacteriol. 176:2483-2491(1994) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PARTIAL PROTEIN SEQUENCE.
      Strain: C-83.
    2. "Formaldehyde dehydrogenase from Pseudomonas putida: a zinc metalloenzyme."
      Ogushi S., Ando M., Tsuru D.
      J. Biochem. 96:1587-1591(1984) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, CATALYTIC ACTIVITY, COFACTOR, ENZYME REGULATION.
      Strain: C-83.
    3. "P. putida formaldehyde dehydrogenase. An alcohol dehydrogenase masquerading as an aldehyde dehydrogenase."
      Oppenheimer N.J., Henehan G.T., Huete-Perez J.A., Ito K.
      Adv. Exp. Med. Biol. 414:417-423(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, CATALYTIC ACTIVITY.
    4. "Crystal structure of formaldehyde dehydrogenase from Pseudomonas putida: the structural origin of the tightly bound cofactor in nicotinoprotein dehydrogenases."
      Tanaka N., Kusakabe Y., Ito K., Yoshimoto T., Nakamura K.T.
      J. Mol. Biol. 324:519-533(2002) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.65 ANGSTROMS), SUBUNIT, COFACTOR.

    Entry informationi

    Entry nameiFADH_PSEPU
    AccessioniPrimary (citable) accession number: P46154
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: November 1, 1995
    Last sequence update: January 23, 2007
    Last modified: December 9, 2015
    This is version 105 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.