3QDQ

Complex between 4-hydroxybutyrate CoA-transferase from Clostridium aminobutyricum and CoA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.218 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of the complex between 4-hydroxybutyrate CoA-transferase from Clostridium aminobutyricum and CoA.

Macieira, S.Zhang, J.Buckel, W.Messerschmidt, A.

(2012) Arch.Microbiol. 194: 157-166

  • DOI: 10.1007/s00203-011-0737-2

  • PubMed Abstract: 
  • Clostridium aminobutyricum ferments 4-aminobutyrate (γ-aminobutyrate, GABA) to ammonia, acetate and butyrate via 4-hydroxybutyrate that is activated to the CoA-thioester catalyzed by 4-hydroxybutyrate CoA-transferase. Then, 4-hydroxybutyryl-CoA is de ...

    Clostridium aminobutyricum ferments 4-aminobutyrate (γ-aminobutyrate, GABA) to ammonia, acetate and butyrate via 4-hydroxybutyrate that is activated to the CoA-thioester catalyzed by 4-hydroxybutyrate CoA-transferase. Then, 4-hydroxybutyryl-CoA is dehydrated to crotonyl-CoA, which disproportionates to butyryl-CoA and acetyl-CoA. Cocrystallization of the CoA-transferase with the alternate substrate butyryl-CoA yielded crystals with non-covalently bound CoA and two water molecules at the active site. Most likely, butyryl-CoA reacted with the active site Glu238 to CoA and the mixed anhydride, which slowly hydrolyzed during crystallization. The structure of the CoA is similar but less stretched than that of the CoA-moiety of the covalent enzyme-CoA-thioester in 4-hydroxybutyrate CoA-transferase from Shewanella oneidensis. In contrast to the structures of the apo-enzyme and enzyme-CoA-thioester, the structure described here has a closed conformation, probably caused by a flip of the active site loop (residues 215-219). During turnover, the closed conformation may protect the anhydride intermediate from hydrolysis and CoA from dissociation from the enzyme. Hence, one catalytic cycle changes conformation of the enzyme four times: free enzyme-open conformation, CoA+ anhydride 1-closed, enzyme-CoA-thioester-open, CoA + anhydride-2-closed, free enzyme-open.


    Organizational Affiliation

    Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Martinsried, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
4-Hydroxybutyrate CoA-transferase
A
448Clostridium aminobutyricumMutation(s): 0 
Gene Names: abfT
Find proteins for Q9RM86 (Clostridium aminobutyricum)
Go to UniProtKB:  Q9RM86
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
COA
Query on COA

Download SDF File 
Download CCD File 
A
COENZYME A
C21 H36 N7 O16 P3 S
RGJOEKWQDUBAIZ-IBOSZNHHSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.218 
  • Space Group: P 42 2 2
Unit Cell:
Length (Å)Angle (°)
a = 118.215α = 90.00
b = 118.215β = 90.00
c = 87.392γ = 90.00
Software Package:
Software NamePurpose
MAR345data collection
SCALEPACKdata scaling
REFMACrefinement
HKL-2000data reduction
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-08-24
    Type: Initial release
  • Version 1.1: 2012-02-29
    Type: Database references
  • Version 1.2: 2017-11-08
    Type: Refinement description