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Protein

Formaldehyde dismutase

Gene

fdm

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

Functioni

Active against a range of primary alcohols as well as some secondary alcohols. Exhibits higher activity against alcohols with longer carbon chains.1 Publication

Catalytic activityi

2 formaldehyde + H2O = formate + methanol.1 Publication

Cofactori

Protein has several cofactor binding sites:

Enzyme regulationi

Inhibited by the substrate analog pyrazole but not by NAD analogs such as AMP, ADP, ATP or N-methylnicotinamide chloride.1 Publication

Absorptioni

Abs(max)=275 nm1 Publication

Exhibits a small and broad shoulder at 320 nm as the characteristic absorption spectrum of the reduced form of the coenzyme.1 Publication

Kineticsi

Does not catalyze oxidation of methanol at pH 7.0.

  1. KM=40 mM for ethanol (at 30 degrees Celsius and pH 7.0)1 Publication
  2. KM=20 mM for 1-propanol (at 30 degrees Celsius and pH 7.0)1 Publication
  3. KM=3.2 mM for 1-butanol (at 30 degrees Celsius and pH 7.0)1 Publication
  4. KM=1.4 mM for 1-pentanol (at 30 degrees Celsius and pH 7.0)1 Publication
  5. KM=330 mM for cyclohexanol (at 30 degrees Celsius and pH 7.0)1 Publication

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Metal bindingi46 – 461Zinc 11 Publication
    Metal bindingi67 – 671Zinc 1; via tele nitrogen1 Publication
    Metal bindingi97 – 971Zinc 21 Publication
    Metal bindingi100 – 1001Zinc 21 Publication
    Metal bindingi103 – 1031Zinc 21 Publication
    Metal bindingi111 – 1111Zinc 21 Publication
    Metal bindingi170 – 1701Zinc 11 Publication
    Binding sitei174 – 1741NAD1 Publication
    Metal bindingi177 – 1771Zinc 1; catalyticBy similarity
    Binding sitei223 – 2231NAD1 Publication
    Binding sitei263 – 2631NAD; via carbonyl oxygen1 Publication
    Binding sitei268 – 2681NAD; via amide nitrogen and carbonyl oxygen1 Publication
    Binding sitei299 – 2991NAD; via carbonyl oxygen1 Publication

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Nucleotide bindingi47 – 515NAD1 Publication
    Nucleotide bindingi197 – 1982NAD1 Publication
    Nucleotide bindingi218 – 2192NAD1 Publication
    Nucleotide bindingi299 – 3013NAD1 Publication
    Nucleotide bindingi336 – 3383NAD1 Publication

    GO - Molecular functioni

    Complete GO annotation...

    Keywords - Molecular functioni

    Oxidoreductase

    Keywords - Ligandi

    Metal-binding, NAD, Nucleotide-binding, Zinc

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Formaldehyde dismutase1 Publication (EC:1.2.98.11 Publication)
    Gene namesi
    Name:fdmImported
    OrganismiPseudomonas putida (Arthrobacter siderocapsulatus)
    Taxonomic identifieri303 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaPseudomonadalesPseudomonadaceaePseudomonas

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Initiator methionineiRemoved1 Publication
    Chaini2 – 399398Formaldehyde dismutase1 PublicationPRO_0000413582Add
    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 strandi25 – 273Combined sources
    Beta strandi36 – 449Combined sources
    Helixi47 – 537Combined sources
    Beta strandi69 – 768Combined sources
    Beta strandi88 – 903Combined sources
    Helixi101 – 1044Combined sources
    Helixi108 – 1103Combined sources
    Turni114 – 1163Combined sources
    Beta strandi118 – 1214Combined sources
    Turni125 – 1284Combined sources
    Beta strandi129 – 1313Combined sources
    Beta strandi135 – 14410Combined sources
    Helixi145 – 1484Combined sources
    Helixi155 – 1606Combined sources
    Helixi162 – 1654Combined sources
    Turni166 – 1705Combined sources
    Helixi171 – 18111Combined sources
    Beta strandi189 – 1935Combined sources
    Helixi197 – 20913Combined sources
    Beta strandi212 – 2198Combined sources
    Helixi221 – 2288Combined sources
    Turni229 – 2313Combined sources
    Beta strandi233 – 2364Combined sources
    Beta strandi239 – 2413Combined sources
    Helixi243 – 2519Combined sources
    Beta strandi252 – 2543Combined sources
    Beta strandi256 – 2616Combined sources
    Helixi271 – 2733Combined sources
    Helixi281 – 2899Combined sources
    Beta strandi290 – 2978Combined sources
    Helixi312 – 3154Combined sources
    Beta strandi319 – 3213Combined sources
    Helixi323 – 3286Combined sources
    Beta strandi332 – 3343Combined sources
    Helixi340 – 3423Combined sources
    Helixi344 – 3529Combined sources
    Helixi358 – 3636Combined sources
    Beta strandi365 – 3684Combined sources
    Helixi373 – 3819Combined sources
    Beta strandi387 – 3904Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    2DPHX-ray2.27A/B2-399[»]
    ProteinModelPortaliQ52078.
    SMRiQ52078. Positions 2-399.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ52078.

    Family & Domainsi

    Sequence similaritiesi

    Belongs to the zinc-containing alcohol dehydrogenase family.Sequence analysis

    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.
    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.
    PROSITEiPS00059. ADH_ZINC. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

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

    Q52078-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MAGNKSVVYH GTRDLRVETV PYPKLEHNNR KLEHAVILKV VSTNICGSDQ
    60 70 80 90 100
    HIYRGRFIVP KGHVLGHEIT GEVVEKGSDV ELMDIGDLVS VPFNVACGRC
    110 120 130 140 150
    RNCKEARSDV CENNLVNPDA DLGAFGFDLK GWSGGQAEYV LVPYADYMLL
    160 170 180 190 200
    KFGDKEQAME KIKDLTLISD ILPTGFHGCV SAGVKPGSHV YIAGAGPVGR
    210 220 230 240 250
    CAAAGARLLG AACVIVGDQN PERLKLLSDA GFETIDLRNS APLRDQIDQI
    260 270 280 290 300
    LGKPEVDCGV DAVGFEAHGL GDEANTETPN GALNSLFDVV RAGGAIGIPG
    310 320 330 340 350
    IYVGSDPDPV NKDAGSGRLH LDFGKMWTKS IRIMTGMAPV TNYNRHLTEA
    360 370 380 390
    ILWDQMPYLS KVMNIEVITL DQAPDGYAKF DKGSPAKFVI DPHGMLKNK
    Length:399
    Mass (Da):42,981
    Last modified:November 1, 1996 - v1
    Checksum:iE953AA05A1404EFB
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    L25862 Genomic DNA. Translation: AAA25818.1.
    PIRiJC2516.
    RefSeqiWP_016974636.1. NZ_LGRH01000007.1.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    L25862 Genomic DNA. Translation: AAA25818.1.
    PIRiJC2516.
    RefSeqiWP_016974636.1. NZ_LGRH01000007.1.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    2DPHX-ray2.27A/B2-399[»]
    ProteinModelPortaliQ52078.
    SMRiQ52078. Positions 2-399.
    ModBaseiSearch...
    MobiDBiSearch...

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ52078.

    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.
    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.
    PROSITEiPS00059. ADH_ZINC. 1 hit.
    [Graphical view]
    ProtoNetiSearch...

    Entry informationi

    Entry nameiFDM_PSEPU
    AccessioniPrimary (citable) accession number: Q52078
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: October 19, 2011
    Last sequence update: November 1, 1996
    Last modified: January 20, 2016
    This is version 93 of the entry and version 1 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.