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P55792

- HDVD_CLOAM

UniProt

P55792 - HDVD_CLOAM

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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

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.2 Publications
Binds 1 4Fe-4S cluster per subunit.2 Publications

Kineticsi

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

Sites

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

Regions

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

GO - Molecular functioni

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

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-isomerase
PRO_0000083940Add
BLAST

Interactioni

Subunit structurei

Homotetramer.1 Publication

Structurei

Secondary structure

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.

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 16, 2013
This is version 75 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

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