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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

Manual assertion based on experiment ini

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)DescriptionActionsGraphical viewLength
    Metal bindingi46Zinc 11 Publication1
    Metal bindingi67Zinc 1; via tele nitrogen1 Publication1
    Metal bindingi97Zinc 21 Publication1
    Metal bindingi100Zinc 21 Publication1
    Metal bindingi103Zinc 21 Publication1
    Metal bindingi111Zinc 21 Publication1
    Metal bindingi170Zinc 11 Publication1
    Binding sitei174NAD1 Publication1
    Metal bindingi177Zinc 1; catalyticBy similarity1
    Binding sitei223NAD1 Publication1
    Binding sitei263NAD; via carbonyl oxygen1 Publication1
    Binding sitei268NAD; via amide nitrogen and carbonyl oxygen1 Publication1
    Binding sitei299NAD; via carbonyl oxygen1 Publication1

    Regions

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Nucleotide bindingi47 – 51NAD1 Publication5
    Nucleotide bindingi197 – 198NAD1 Publication2
    Nucleotide bindingi218 – 219NAD1 Publication2
    Nucleotide bindingi299 – 301NAD1 Publication3
    Nucleotide bindingi336 – 338NAD1 Publication3

    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)DescriptionActionsGraphical viewLength
    Initiator methionineiRemoved1 Publication
    ChainiPRO_00004135822 – 399Formaldehyde dismutase1 PublicationAdd BLAST398

    Interactioni

    Subunit structurei

    Homotetramer.1 Publication

    Structurei

    Secondary structure

    1399
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Beta strandi4 – 11Combined sources8
    Beta strandi14 – 20Combined sources7
    Beta strandi25 – 27Combined sources3
    Beta strandi36 – 44Combined sources9
    Helixi47 – 53Combined sources7
    Beta strandi69 – 76Combined sources8
    Beta strandi88 – 90Combined sources3
    Helixi101 – 104Combined sources4
    Helixi108 – 110Combined sources3
    Turni114 – 116Combined sources3
    Beta strandi118 – 121Combined sources4
    Turni125 – 128Combined sources4
    Beta strandi129 – 131Combined sources3
    Beta strandi135 – 144Combined sources10
    Helixi145 – 148Combined sources4
    Helixi155 – 160Combined sources6
    Helixi162 – 165Combined sources4
    Turni166 – 170Combined sources5
    Helixi171 – 181Combined sources11
    Beta strandi189 – 193Combined sources5
    Helixi197 – 209Combined sources13
    Beta strandi212 – 219Combined sources8
    Helixi221 – 228Combined sources8
    Turni229 – 231Combined sources3
    Beta strandi233 – 236Combined sources4
    Beta strandi239 – 241Combined sources3
    Helixi243 – 251Combined sources9
    Beta strandi252 – 254Combined sources3
    Beta strandi256 – 261Combined sources6
    Helixi271 – 273Combined sources3
    Helixi281 – 289Combined sources9
    Beta strandi290 – 297Combined sources8
    Helixi312 – 315Combined sources4
    Beta strandi319 – 321Combined sources3
    Helixi323 – 328Combined sources6
    Beta strandi332 – 334Combined sources3
    Helixi340 – 342Combined sources3
    Helixi344 – 352Combined sources9
    Helixi358 – 363Combined sources6
    Beta strandi365 – 368Combined sources4
    Helixi373 – 381Combined sources9
    Beta strandi387 – 390Combined sources4

    3D structure databases

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

    Miscellaneous databases

    EvolutionaryTraceiQ52078.

    Family & Domainsi

    Sequence similaritiesi

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

    Phylogenomic databases

    KOiK17068.

    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_MCBJ01000007.1.

    Genome annotation databases

    KEGGiag:AAA25818.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    L25862 Genomic DNA. Translation: AAA25818.1.
    PIRiJC2516.
    RefSeqiWP_016974636.1. NZ_MCBJ01000007.1.

    3D structure databases

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

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    KEGGiag:AAA25818.

    Phylogenomic databases

    KOiK17068.

    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: November 2, 2016
    This is version 95 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.