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Protein

4-hydroxybutyryl-CoA dehydratase/vinylacetyl-CoA-Delta-isomerase

Gene

abfD

Organism
Clostridium aminobutyricum
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the reversible conversion of 4-hydroxybutyryl-CoA to crotonyl-CoA. The mechanism of the reaction seems to go through three steps: (1) the FAD-dependent oxidation of 4-hydroxybutyryl-CoA to 4-hydroxycrotonyl-CoA; (2) the hydroxyl group is substituted by a hydride derived from the now reduced FAD in an SN2' reaction leading to vinylacetyl-CoA; (3) isomerization to yield crotonyl-CoA.

Catalytic activityi

4-hydroxybutanoyl-CoA = but-3-enoyl-CoA + H2O.1 Publication
Vinylacetyl-CoA = (E)-but-2-enoyl-CoA.1 Publication

Cofactori

Protein has several cofactor binding sites:

Kineticsi

  1. KM=50 µM for 4-hydroxybutanoyl-CoA1 Publication

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Metal bindingi99 – 991Iron-sulfur (4Fe-4S)1 Publication
    Metal bindingi103 – 1031Iron-sulfur (4Fe-4S)1 Publication
    Metal bindingi292 – 2921Iron-sulfur (4Fe-4S)1 Publication
    Metal bindingi299 – 2991Iron-sulfur (4Fe-4S)1 Publication
    Binding sitei325 – 3251FAD1 Publication

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Nucleotide bindingi149 – 1568FAD1 Publication
    Nucleotide bindingi188 – 1903FAD1 Publication
    Nucleotide bindingi386 – 3905FAD1 Publication

    GO - Molecular functioni

    Complete GO annotation...

    Keywords - Molecular functioni

    Isomerase, Lyase, Oxidoreductase

    Keywords - Ligandi

    4Fe-4S, FAD, Flavoprotein, Iron, Iron-sulfur, Metal-binding

    Enzyme and pathway databases

    BioCyciMetaCyc:MONOMER-13485.
    BRENDAi4.2.1.120. 1455.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    4-hydroxybutyryl-CoA dehydratase/vinylacetyl-CoA-Delta-isomerase (EC:4.2.1.120, EC:5.3.3.3)
    Short name:
    4-BUDH
    Alternative name(s):
    Gamma-aminobutyrate metabolism dehydratase/isomerase
    Gene namesi
    Name:abfD
    OrganismiClostridium aminobutyricum
    Taxonomic identifieri33953 [NCBI]
    Taxonomic lineageiBacteriaFirmicutesClostridiaClostridialesClostridiaceaeClostridium

    Pathology & Biotechi

    Chemistry

    DrugBankiDB03147. Flavin adenine dinucleotide.

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 4904904-hydroxybutyryl-CoA dehydratase/vinylacetyl-CoA-Delta-isomerasePRO_0000083940Add
    BLAST

    Interactioni

    Subunit structurei

    Homotetramer.2 Publications

    Structurei

    Secondary structure

    1
    490
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi5 – 128Combined sources
    Beta strandi19 – 213Combined sources
    Helixi29 – 313Combined sources
    Turni33 – 353Combined sources
    Helixi36 – 5015Combined sources
    Turni52 – 543Combined sources
    Helixi55 – 584Combined sources
    Beta strandi59 – 613Combined sources
    Turni63 – 653Combined sources
    Beta strandi66 – 705Combined sources
    Helixi71 – 733Combined sources
    Helixi79 – 9618Combined sources
    Helixi103 – 12321Combined sources
    Helixi127 – 14115Combined sources
    Beta strandi145 – 1484Combined sources
    Helixi160 – 1623Combined sources
    Beta strandi171 – 1755Combined sources
    Beta strandi177 – 18610Combined sources
    Beta strandi196 – 2005Combined sources
    Helixi208 – 2136Combined sources
    Beta strandi215 – 2206Combined sources
    Beta strandi226 – 2305Combined sources
    Helixi236 – 2405Combined sources
    Helixi246 – 2483Combined sources
    Beta strandi249 – 2524Combined sources
    Beta strandi258 – 26811Combined sources
    Helixi269 – 2713Combined sources
    Beta strandi272 – 2765Combined sources
    Helixi278 – 2803Combined sources
    Helixi281 – 31838Combined sources
    Helixi324 – 34926Combined sources
    Helixi363 – 37311Combined sources
    Helixi376 – 38813Combined sources
    Helixi391 – 3944Combined sources
    Helixi398 – 4014Combined sources
    Helixi414 – 4218Combined sources
    Helixi430 – 44415Combined sources
    Helixi449 – 4524Combined sources
    Helixi454 – 4585Combined sources
    Helixi463 – 47311Combined sources
    Helixi476 – 48712Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1U8VX-ray1.60A/B/C/D1-490[»]
    ProteinModelPortaliP55792.
    SMRiP55792. Positions 1-490.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP55792.

    Family & Domainsi

    Family and domain databases

    Gene3Di2.40.110.10. 1 hit.
    InterProiIPR006091. Acyl-CoA_Oxase/DH_cen-dom.
    IPR009075. AcylCo_DH/oxidase_C.
    IPR009100. AcylCoA_DH/oxidase_NM_dom.
    IPR004925. HpaB/PvcC/4-BUDH.
    IPR024719. HpaB/PvcC/4-BUDH_C.
    IPR024674. HpaB/PvcC/4-BUDH_N.
    [Graphical view]
    PfamiPF03241. HpaB. 1 hit.
    PF11794. HpaB_N. 1 hit.
    [Graphical view]
    PIRSFiPIRSF000331. HpaA_HpaB. 1 hit.
    SUPFAMiSSF47203. SSF47203. 1 hit.
    SSF56645. SSF56645. 1 hit.

    Sequencei

    Sequence statusi: Complete.

    P55792-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MLMTAEQYIE SLRKLNTRVY MFGEKIENWV DHPMIRPSIN CVAMTYELAQ
    60 70 80 90 100
    DPQYADLMTT KSNLIGKTIN RFANLHQSTD DLRKKVKMQR LLGQKTASCF
    110 120 130 140 150
    QRCVGMDAFN AVFSTTYEID QKYGTNYHKN FTEYLKYIQE NDLIVDGAMT
    160 170 180 190 200
    DPKGDRGLAP SAQKDPDLFL RIVEKREDGI VVRGAKAHQT GSINSHEHII
    210 220 230 240 250
    MPTIAMTEAD KDYAVSFACP SDADGLFMIY GRQSCDTRKM EEGADIDLGN
    260 270 280 290 300
    KQFGGQEALV VFDNVFIPND RIFLCQEYDF AGMMVERFAG YHRQSYGGCK
    310 320 330 340 350
    VGVGDVVIGA AALAADYNGA QKASHVKDKL IEMTHLNETL YCCGIACSAE
    360 370 380 390 400
    GYPTAAGNYQ IDLLLANVCK QNITRFPYEI VRLAEDIAGG LMVTMPSEAD
    410 420 430 440 450
    FKSETVVGRD GETIGDFCNK FFAAAPTCTT EERMRVLRFL ENICLGASAV
    460 470 480 490
    GYRTESMHGA GSPQAQRIMI ARQGNINAKK ELAKAIAGIK
    Length:490
    Mass (Da):54,422
    Last modified:December 20, 2005 - v3
    Checksum:iEDC1E40336806E38
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AJ250267 Genomic DNA. Translation: CAB60035.2.
    PIRiS34765.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AJ250267 Genomic DNA. Translation: CAB60035.2.
    PIRiS34765.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1U8VX-ray1.60A/B/C/D1-490[»]
    ProteinModelPortaliP55792.
    SMRiP55792. Positions 1-490.
    ModBaseiSearch...
    MobiDBiSearch...

    Chemistry

    DrugBankiDB03147. Flavin adenine dinucleotide.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Enzyme and pathway databases

    BioCyciMetaCyc:MONOMER-13485.
    BRENDAi4.2.1.120. 1455.

    Miscellaneous databases

    EvolutionaryTraceiP55792.

    Family and domain databases

    Gene3Di2.40.110.10. 1 hit.
    InterProiIPR006091. Acyl-CoA_Oxase/DH_cen-dom.
    IPR009075. AcylCo_DH/oxidase_C.
    IPR009100. AcylCoA_DH/oxidase_NM_dom.
    IPR004925. HpaB/PvcC/4-BUDH.
    IPR024719. HpaB/PvcC/4-BUDH_C.
    IPR024674. HpaB/PvcC/4-BUDH_N.
    [Graphical view]
    PfamiPF03241. HpaB. 1 hit.
    PF11794. HpaB_N. 1 hit.
    [Graphical view]
    PIRSFiPIRSF000331. HpaA_HpaB. 1 hit.
    SUPFAMiSSF47203. SSF47203. 1 hit.
    SSF56645. SSF56645. 1 hit.
    ProtoNetiSearch...

    Publicationsi

    1. "Fermentation of 4-aminobutyrate by Clostridium aminobutyricum: cloning of two genes involved in the formation and dehydration of 4-hydroxybutyryl-CoA."
      Gerhardt A., Cinkaya I., Linder D., Huisman G., Buckel W.
      Arch. Microbiol. 174:189-199(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: ATCC 13726 / DSM 2634.
    2. Zhang J.
      Submitted (JUL-2005) to the EMBL/GenBank/DDBJ databases
      Cited for: SEQUENCE REVISION TO 43; 167 AND 357.
    3. "Purification and properties of an iron-sulfur and FAD-containing 4-hydroxybutyryl-CoA dehydratase/vinylacetyl-CoA delta 3-delta 2-isomerase from Clostridium aminobutyricum."
      Scherf U., Buckel W.
      Eur. J. Biochem. 215:421-429(1993) [PubMed] [Europe PMC] [Abstract]
      Cited for: PROTEIN SEQUENCE OF 1-30, CATALYTIC ACTIVITY, SUBUNIT, COFACTOR, BIOPHYSICOCHEMICAL PROPERTIES, REACTION MECHANISM.
      Strain: ATCC 13726 / DSM 2634.
    4. "Crystal structure of 4-hydroxybutyryl-CoA dehydratase: radical catalysis involving a [4Fe-4S] cluster and flavin."
      Martins B.M., Dobbek H., Cinkaya I., Buckel W., Messerschmidt A.
      Proc. Natl. Acad. Sci. U.S.A. 101:15645-15649(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.6 ANGSTROMS) IN COMPLEX WITH IRON-SULFUR AND FAD, COFACTOR, REACTION MECHANISM.

    Entry informationi

    Entry nameiHDVD_CLOAM
    AccessioniPrimary (citable) accession number: P55792
    Secondary accession number(s): Q9RM87
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: November 1, 1997
    Last sequence update: December 20, 2005
    Last modified: April 1, 2015
    This is version 79 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, Multifunctional enzyme

    Documents

    1. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references

    External Data

    Dasty 3

    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 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.