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P55792 (HDVD_CLOAM) Reviewed, UniProtKB/Swiss-Prot

Last modified October 16, 2013. Version 75. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (1) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
4-hydroxybutyryl-CoA dehydratase/vinylacetyl-CoA-Delta-isomerase

Short name=4-BUDH
EC=4.2.1.120
EC=5.3.3.3
Alternative name(s):
Gamma-aminobutyrate metabolism dehydratase/isomerase
Gene names
Name:abfD
OrganismClostridium aminobutyricum
Taxonomic identifier33953 [NCBI]
Taxonomic lineageBacteriaFirmicutesClostridiaClostridialesClostridiaceaeClostridium

Protein attributes

Sequence length490 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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 activity

4-hydroxybutanoyl-CoA = but-3-enoyl-CoA + H2O. Ref.3

Vinylacetyl-CoA = (E)-but-2-enoyl-CoA. Ref.3

Cofactor

Binds 1 FAD per subunit. Ref.3 Ref.4

Binds 1 4Fe-4S cluster per subunit. Ref.3 Ref.4

Subunit structure

Homotetramer. Ref.3

Biophysicochemical properties

Kinetic parameters:

KM=50 µM for 4-hydroxybutanoyl-CoA Ref.3

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 4904904-hydroxybutyryl-CoA dehydratase/vinylacetyl-CoA-Delta-isomerase
PRO_0000083940

Regions

Nucleotide binding149 – 1568FAD
Nucleotide binding188 – 1903FAD
Nucleotide binding386 – 3905FAD

Sites

Metal binding991Iron-sulfur (4Fe-4S)
Metal binding1031Iron-sulfur (4Fe-4S)
Metal binding2921Iron-sulfur (4Fe-4S)
Metal binding2991Iron-sulfur (4Fe-4S)
Binding site3251FAD

Secondary structure

.......................................................................... 490
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P55792 [UniParc].

Last modified December 20, 2005. Version 3.
Checksum: EDC1E40336806E38

FASTA49054,422
        10         20         30         40         50         60 
MLMTAEQYIE SLRKLNTRVY MFGEKIENWV DHPMIRPSIN CVAMTYELAQ DPQYADLMTT 

        70         80         90        100        110        120 
KSNLIGKTIN RFANLHQSTD DLRKKVKMQR LLGQKTASCF QRCVGMDAFN AVFSTTYEID 

       130        140        150        160        170        180 
QKYGTNYHKN FTEYLKYIQE NDLIVDGAMT DPKGDRGLAP SAQKDPDLFL RIVEKREDGI 

       190        200        210        220        230        240 
VVRGAKAHQT GSINSHEHII MPTIAMTEAD KDYAVSFACP SDADGLFMIY GRQSCDTRKM 

       250        260        270        280        290        300 
EEGADIDLGN KQFGGQEALV VFDNVFIPND RIFLCQEYDF AGMMVERFAG YHRQSYGGCK 

       310        320        330        340        350        360 
VGVGDVVIGA AALAADYNGA QKASHVKDKL IEMTHLNETL YCCGIACSAE GYPTAAGNYQ 

       370        380        390        400        410        420 
IDLLLANVCK QNITRFPYEI VRLAEDIAGG LMVTMPSEAD FKSETVVGRD GETIGDFCNK 

       430        440        450        460        470        480 
FFAAAPTCTT EERMRVLRFL ENICLGASAV GYRTESMHGA GSPQAQRIMI ARQGNINAKK 

       490 
ELAKAIAGIK 

« Hide

References

[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.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
AJ250267 Genomic DNA. Translation: CAB60035.2.
PIRS34765.

3D structure databases

PDBe
RCSB-PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1U8VX-ray1.60A/B/C/D1-490[»]
ProteinModelPortalP55792.
SMRP55792. Positions 1-490.
ModBaseSearch...
MobiDBSearch...

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Enzyme and pathway databases

BioCycMetaCyc:MONOMER-13485.

Family and domain databases

Gene3D2.40.110.10. 1 hit.
InterProIPR006091. 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]
PfamPF03241. HpaB. 1 hit.
PF11794. HpaB_N. 1 hit.
[Graphical view]
PIRSFPIRSF000331. HpaA_HpaB. 1 hit.
SUPFAMSSF47203. SSF47203. 1 hit.
SSF56645. SSF56645. 1 hit.
ProtoNetSearch...

Other

EvolutionaryTraceP55792.

Entry information

Entry nameHDVD_CLOAM
AccessionPrimary (citable) accession number: P55792
Secondary accession number(s): Q9RM87
Entry history
Integrated into UniProtKB/Swiss-Prot: November 1, 1997
Last sequence update: December 20, 2005
Last modified: October 16, 2013
This is version 75 of the entry and version 3 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

PDB cross-references

Index of Protein Data Bank (PDB) cross-references