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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 = (E)-but-2-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)DescriptionActionsGraphical viewLength
    Metal bindingi99Iron-sulfur (4Fe-4S)1 Publication1
    Metal bindingi103Iron-sulfur (4Fe-4S)1 Publication1
    Metal bindingi292Iron-sulfur (4Fe-4S)1 Publication1
    Metal bindingi299Iron-sulfur (4Fe-4S)1 Publication1
    Binding sitei325FAD1 Publication1

    Regions

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Nucleotide bindingi149 – 156FAD1 Publication8
    Nucleotide bindingi188 – 190FAD1 Publication3
    Nucleotide bindingi386 – 390FAD1 Publication5

    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 databases

    DrugBankiDB03147. Flavin adenine dinucleotide.

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    ChainiPRO_00000839401 – 4904-hydroxybutyryl-CoA dehydratase/vinylacetyl-CoA-Delta-isomeraseAdd BLAST490

    Interactioni

    Subunit structurei

    Homotetramer.2 Publications

    Structurei

    Secondary structure

    1490
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Helixi5 – 12Combined sources8
    Beta strandi19 – 21Combined sources3
    Helixi29 – 31Combined sources3
    Turni33 – 35Combined sources3
    Helixi36 – 50Combined sources15
    Turni52 – 54Combined sources3
    Helixi55 – 58Combined sources4
    Beta strandi59 – 61Combined sources3
    Turni63 – 65Combined sources3
    Beta strandi66 – 70Combined sources5
    Helixi71 – 73Combined sources3
    Helixi79 – 96Combined sources18
    Helixi103 – 123Combined sources21
    Helixi127 – 141Combined sources15
    Beta strandi145 – 148Combined sources4
    Helixi160 – 162Combined sources3
    Beta strandi171 – 175Combined sources5
    Beta strandi177 – 186Combined sources10
    Beta strandi196 – 200Combined sources5
    Helixi208 – 213Combined sources6
    Beta strandi215 – 220Combined sources6
    Beta strandi226 – 230Combined sources5
    Helixi236 – 240Combined sources5
    Helixi246 – 248Combined sources3
    Beta strandi249 – 252Combined sources4
    Beta strandi258 – 268Combined sources11
    Helixi269 – 271Combined sources3
    Beta strandi272 – 276Combined sources5
    Helixi278 – 280Combined sources3
    Helixi281 – 318Combined sources38
    Helixi324 – 349Combined sources26
    Helixi363 – 373Combined sources11
    Helixi376 – 388Combined sources13
    Helixi391 – 394Combined sources4
    Helixi398 – 401Combined sources4
    Helixi414 – 421Combined sources8
    Helixi430 – 444Combined sources15
    Helixi449 – 452Combined sources4
    Helixi454 – 458Combined sources5
    Helixi463 – 473Combined sources11
    Helixi476 – 487Combined sources12

    3D structure databases

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

    Miscellaneous databases

    EvolutionaryTraceiP55792.

    Family & Domainsi

    Phylogenomic databases

    KOiK14534.

    Family and domain databases

    InterProiIPR009075. 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.

    Genome annotation databases

    KEGGiag:CAB60035.

    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
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    1U8VX-ray1.60A/B/C/D1-490[»]
    ProteinModelPortaliP55792.
    SMRiP55792.
    ModBaseiSearch...
    MobiDBiSearch...

    Chemistry databases

    DrugBankiDB03147. Flavin adenine dinucleotide.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    KEGGiag:CAB60035.

    Phylogenomic databases

    KOiK14534.

    Enzyme and pathway databases

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

    Miscellaneous databases

    EvolutionaryTraceiP55792.

    Family and domain databases

    InterProiIPR009075. 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...

    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: November 2, 2016
    This is version 86 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

    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.