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P55792

- HDVD_CLOAM

UniProt

P55792 - HDVD_CLOAM

Protein

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

Gene

abfD

Organism
Clostridium aminobutyricum
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 76 (01 Oct 2014)
      Sequence version 3 (20 Dec 2005)
      Previous versions | rss
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    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

    Binds 1 FAD per subunit.
    Binds 1 4Fe-4S cluster per subunit.

    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

    1. 4-hydroxybutanoyl-CoA dehydratase activity Source: UniProtKB-EC
    2. 4 iron, 4 sulfur cluster binding Source: UniProtKB-KW
    3. acyl-CoA dehydrogenase activity Source: InterPro
    4. metal ion binding Source: UniProtKB-KW
    5. vinylacetyl-CoA delta-isomerase activity Source: UniProtKB-EC

    Keywords - Molecular functioni

    Isomerase, Lyase, Oxidoreductase

    Keywords - Ligandi

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

    Enzyme and pathway databases

    BioCyciMetaCyc:MONOMER-13485.

    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

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

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    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

    MLMTAEQYIE SLRKLNTRVY MFGEKIENWV DHPMIRPSIN CVAMTYELAQ    50
    DPQYADLMTT KSNLIGKTIN RFANLHQSTD DLRKKVKMQR LLGQKTASCF 100
    QRCVGMDAFN AVFSTTYEID QKYGTNYHKN FTEYLKYIQE NDLIVDGAMT 150
    DPKGDRGLAP SAQKDPDLFL RIVEKREDGI VVRGAKAHQT GSINSHEHII 200
    MPTIAMTEAD KDYAVSFACP SDADGLFMIY GRQSCDTRKM EEGADIDLGN 250
    KQFGGQEALV VFDNVFIPND RIFLCQEYDF AGMMVERFAG YHRQSYGGCK 300
    VGVGDVVIGA AALAADYNGA QKASHVKDKL IEMTHLNETL YCCGIACSAE 350
    GYPTAAGNYQ IDLLLANVCK QNITRFPYEI VRLAEDIAGG LMVTMPSEAD 400
    FKSETVVGRD GETIGDFCNK FFAAAPTCTT EERMRVLRFL ENICLGASAV 450
    GYRTESMHGA GSPQAQRIMI ARQGNINAKK ELAKAIAGIK 490
    Length:490
    Mass (Da):54,422
    Last modified:December 20, 2005 - v3
    Checksum:iEDC1E40336806E38
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AJ250267 Genomic DNA. Translation: CAB60035.2.
    PIRiS34765.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AJ250267 Genomic DNA. Translation: CAB60035.2 .
    PIRi S34765.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1U8V X-ray 1.60 A/B/C/D 1-490 [» ]
    ProteinModelPortali P55792.
    SMRi P55792. Positions 1-490.
    ModBasei Search...
    MobiDBi Search...

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Enzyme and pathway databases

    BioCyci MetaCyc:MONOMER-13485.

    Miscellaneous databases

    EvolutionaryTracei P55792.

    Family and domain databases

    Gene3Di 2.40.110.10. 1 hit.
    InterProi IPR006091. 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 ]
    Pfami PF03241. HpaB. 1 hit.
    PF11794. HpaB_N. 1 hit.
    [Graphical view ]
    PIRSFi PIRSF000331. HpaA_HpaB. 1 hit.
    SUPFAMi SSF47203. SSF47203. 1 hit.
    SSF56645. SSF56645. 1 hit.
    ProtoNeti Search...

    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 MECHANIMSM.

    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: October 1, 2014
    This is version 76 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