1JQ5

Bacillus Stearothermophilus Glycerol dehydrogenase complex with NAD+

• PDB DOI:  https://doi.org/10.2210/pdb1JQ5/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Geobacillus stearothermophilus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2001-08-03 Released: 2001-10-01 
• Deposition Author(s): Ruzheinikov, S.N., Burke, J., Sedelnikova, S., Baker, P.J., Taylor, R., Bullough, P.A., Muir, N.M., Gore, M.G., Rice, D.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.190 
• R-Value Work: 0.151 

Literature

Glycerol dehydrogenase. structure, specificity, and mechanism of a family III polyol dehydrogenase.

Ruzheinikov, S.N., Burke, J., Sedelnikova, S., Baker, P.J., Taylor, R., Bullough, P.A., Muir, N.M., Gore, M.G., Rice, D.W.

(2001) Structure 9: 789-802

• PubMed: 11566129 
• DOI: https://doi.org/10.1016/s0969-2126(01)00645-1
• Primary Citation of Related Structures:  
  1JPU, 1JQ5, 1JQA


• PubMed Abstract: 
  

Bacillus stearothermophilus glycerol dehydrogenase (GlyDH) (glycerol:NAD(+) 2-oxidoreductase, EC 1.1.1.6) catalyzes the oxidation of glycerol to dihydroxyacetone (1,3-dihydroxypropanone) with concomitant reduction of NAD(+) to NADH. Analysis of the sequence of this enzyme indicates that it is a member of the so-called iron-containing alcohol dehydrogenase family. Despite this sequence similarity, GlyDH shows a strict dependence on zinc for activity. On the basis of this, we propose to rename this group the family III metal-dependent polyol dehydrogenases. To date, no structural data have been reported for any enzyme in this group.

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Related Citations: 

• Purification, crystallization and quaternary structure analysis of a glycerol dehydrogenase S305C mutant from Bacillus stearothemophilus
  Burke, J., Ruzheinikov, S.N., Sedelnikova, S., Baker, P.J., Holmes, D., Muir, N.M., Gore, M.G., Rice, D.W.
  (2001) Acta Crystallogr D Biol Crystallogr 57: 165

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Organizational Affiliation: 

Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, United Kingdom.

Biological Assembly 1  

Global Symmetry: Dihedral - D4  (3D View)
Global Stoichiometry: Homo 8-mer - A8 

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

Macromolecule Content

• Total Structure Weight: 40.36 kDa 
• Atom Count: 3,144 
• Modelled Residue Count: 366 
• Deposited Residue Count: 370 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycerol dehydrogenase	A	370	Geobacillus stearothermophilus	Mutation(s): 1  Gene Names: GLDA or GLD, gldA, gld EC: 1.1.1.6
UniProt
Find proteins for P32816 (Geobacillus stearothermophilus) Explore P32816  Go to UniProtKB:  P32816

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	D [auth A]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
ZN	B [auth A], C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.190 
• R-Value Work: 0.151 
• Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.66	α = 90
b = 104.66	β = 90
c = 148.51	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2001-10-01 
Deposition Author(s): Ruzheinikov, S.N., Burke, J., Sedelnikova, S., Baker, P.J., Taylor, R., Bullough, P.A., Muir, N.M., Gore, M.G., Rice, D.W.

Revision History  

• Version 1.0: 2001-10-01
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Atomic model, Derived calculations, Version format compliance
• Version 1.3: 2011-11-16
  Changes: Atomic model
• Version 1.4: 2021-10-27
  Changes: Database references, Derived calculations
• Version 1.5: 2023-08-16
  Changes: Data collection, Refinement description