3ZDR | pdb_00003zdr

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.240 (Depositor), 0.242 (DCC)
R-Value Work:
0.174 (Depositor), 0.181 (DCC)
R-Value Observed:
0.177 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 2.1 of the entry. See complete history.

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 Search on PubMed
DOI: https://doi.org/10.1107/S0907444913020349
Primary Citation 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.

Organizational Affiliation

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

Macromolecule Content

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

Macromolecules

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| 3D Structure

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	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSO Query on 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 (Depositor), 0.242 (DCC)
R-Value Work: 0.174 (Depositor), 0.181 (DCC)
R-Value Observed: 0.177 (Depositor)

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

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Entry History

Deposition Data

Released Date: 2013-10-02

Deposition Author(s):

Revision History (Full details and data files)

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
Version 2.1: 2024-11-20
Changes: Structure summary