5J78

Crystal structure of an Acetylating Aldehyde Dehydrogenase from Geobacillus thermoglucosidasius


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.143 
  • R-Value Observed: 0.146 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structure of an acetylating aldehyde dehydrogenase from the thermophilic ethanologen Geobacillus thermoglucosidasius.

Extance, J.Danson, M.J.Crennell, S.J.

(2016) Protein Sci 25: 2045-2053

  • DOI: 10.1002/pro.3027
  • Primary Citation of Related Structures:  
    5J78, 5J7I

  • PubMed Abstract: 
  • Acetylating aldehyde dehydrogenases (AcAldDH) catalyse the acetylation of Coenzyme-A (CoA), or in reverse generate acetaldehyde from Acetyl-CoA using NADH as a co-factor. This article reports the expression, purification, enzyme assay, and X-ray crystal structures of an AcAldDH from Geobacillus thermoglucosidasius (GtAcAldDH) to 2 ...

    Acetylating aldehyde dehydrogenases (AcAldDH) catalyse the acetylation of Coenzyme-A (CoA), or in reverse generate acetaldehyde from Acetyl-CoA using NADH as a co-factor. This article reports the expression, purification, enzyme assay, and X-ray crystal structures of an AcAldDH from Geobacillus thermoglucosidasius (GtAcAldDH) to 2.1Å and in complex with CoA and NAD + to 4.0Å. In the structure, the AcAldDH forms a close-knit dimer, similar to that seen in other Alcohol Dehydrogenase (ADH) structures. In GtAcAldDH, these dimers associate via their N-termini to form weakly interacting tetramers. This mode of tetrameric association is also seen in an unpublished AcAldDH deposited in the PDB, but is in contrast to all other ADH structures, (including the one other published AcAldDH found in a bacterial microcompartment), in which the dimers bury a large surface area including the C-termini. This novel mode of association sequesters the active sites and potentially reactive acyl-enzyme intermediates in the center of the tetramer. In other respects, the structure is very similar to the other AcAldDH, binding the cofactors in a corresponding fashion. This similarity enabled the identification of a shortened substrate cavity in G. thermoglucosidasius AcAldDH, explaining the limitations on the length of substrate accepted by the enzyme.


    Organizational Affiliation

    Centre for Extremophile Research, Department of Biology and Biochemistry, University of Bath, Bath, BA2 7AY, England. s.j.crennell@bath.ac.uk.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Acetaldehyde dehydrogenase (Acetylating)A, B, C, D488Parageobacillus thermoglucosidasiusMutation(s): 0 
Gene Names: AcAldDH
EC: 1.2.1.10
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download Ideal Coordinates CCD File 
AA [auth B] , CA [auth C] , DA [auth C] , F [auth A] , G [auth A] , GA [auth C] , HA [auth C] , IA [auth C] , 
AA [auth B],  CA [auth C],  DA [auth C],  F [auth A],  G [auth A],  GA [auth C],  HA [auth C],  IA [auth C],  J [auth A],  JA [auth C],  K [auth A],  KA [auth C],  L [auth A],  LA [auth C],  M [auth A],  MA [auth C],  N [auth A],  NA [auth C],  O [auth A],  OA [auth C],  Q [auth B],  R [auth B],  SA [auth D],  TA [auth D],  U [auth B],  UA [auth D],  V [auth B],  VA [auth D],  W [auth B],  WA [auth D],  X [auth B],  XA [auth D],  Y [auth B],  YA [auth D],  Z [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

Download Ideal Coordinates CCD File 
BA [auth C], E [auth A], FA [auth C], I [auth A], P [auth B], PA [auth D], RA [auth D], T [auth B]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
EA [auth C], H [auth A], QA [auth D], S [auth B]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CSD
Query on CSD
A, B, C, DL-PEPTIDE LINKINGC3 H7 N O4 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.143 
  • R-Value Observed: 0.146 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.579α = 90
b = 109.12β = 90
c = 196.243γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
BALBESphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-09-07
    Type: Initial release
  • Version 1.1: 2016-11-02
    Changes: Database references