3ZDR

Structure of the Alcohol dehydrogenase (ADH) domain of a bifunctional ADHE dehydrogenase from Geobacillus thermoglucosidasius NCIMB 11955

• PDB DOI: https://doi.org/10.2210/pdb3ZDR/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Parageobacillus thermoglucosidasius
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2012-11-30 Released: 2013-10-02 
• Deposition Author(s): Extance, J., Crennell, S.J., Eley, K., Cripps, R., Hough, D.W., Danson, M.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.240 
• R-Value Work: 0.174 
• R-Value Observed: 0.177 

Literature

Structure of a Bifunctional Alcohol Dehydrogenase Involved in Bioethanol Generation in Geobacillus Thermoglucosidasius

Extance, J., Crennell, S.J., Eley, K., Cripps, R., Hough, D.W., Danson, M.J.

(2013) Acta Crystallogr D Biol Crystallogr 69: 2104

• PubMed: 24100328 
• DOI: https://doi.org/10.1107/S0907444913020349
• Primary Citation of Related Structures:  
  3ZDR


• PubMed Abstract: 
  

  Bifunctional alcohol/aldehyde dehydrogenase (ADHE) enzymes are found within many fermentative microorganisms. They catalyse the conversion of an acyl-coenzyme A to an alcohol via an aldehyde intermediate; this is coupled to the oxidation of two NADH molecules to maintain the NAD(+) pool during fermentative metabolism. The structure of the alcohol dehydrogenase (ADH) domain of an ADHE protein from the ethanol-producing thermophile Geobacillus thermoglucosidasius has been determined to 2.5 Å resolution. This is the first structure to be reported for such a domain. In silico modelling has been carried out to generate a homology model of the aldehyde dehydrogenase domain, and this was subsequently docked with the ADH-domain structure to model the structure of the complete ADHE protein. This model suggests, for the first time, a structural mechanism for the formation of the large multimeric assemblies or `spirosomes' that are observed for this ADHE protein and which have previously been reported for ADHEs from other organisms.

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Organizational Affiliation: 

Centre for Extremophile Research, Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, England.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 48.95 kDa 
• Atom Count: 3,237 
• Modelled Residue Count: 403 
• Deposited Residue Count: 433 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ALCOHOL DEHYDROGENASE DOMAIN OF THE BIFUNCTIONAL ACETALDEHYDE DEHYDROGENASE	A	433	Parageobacillus thermoglucosidasius	Mutation(s): 0  EC: 1.2.1.10 (PDB Primary Data), 1.1.1.1 (PDB Primary Data)

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSO	A	L-PEPTIDE LINKING	C3 H7 N O3 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.240 
• R-Value Work: 0.174 
• R-Value Observed: 0.177 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.721	α = 90
b = 96.588	β = 90
c = 58.2	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
BALBES	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-10-02 
Deposition Author(s): Extance, J., Crennell, S.J., Eley, K., Cripps, R., Hough, D.W., Danson, M.J.

Revision History  

• Version 1.0: 2013-10-02
  Type: Initial release
  
• Version 1.1: 2013-10-16
  Changes: Database references, Structure summary
• Version 2.0: 2023-12-20
  Changes: Atomic model, Data collection, Database references, Derived calculations, Other, Refinement description