Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

Global Symmetry: Dihedral - D2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

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

Biological Assembly 2  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

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

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

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

Biological assembly 3 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 123.60 kDa 
• Atom Count: 8515 
• Modelled Residue Count: 1129 
• Deposited Residue Count: 1204 
• Unique protein chains: 1

3CKY

Structural and Kinetic Properties of a beta-hydroxyacid dehydrogenase involved in nicotinate fermentation

• PDB DOI: 10.2210/pdb3CKY/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Eubacterium barkeri
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-03-18 Released: 2008-08-26 
• Deposition Author(s): Reitz, S., Alhapel, A., Pierik, A.J., Essen, L.-O.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.222 
• R-Value Work: 0.194 
• R-Value Observed: 0.195 

Literature

Structural and Kinetic Properties of a beta-Hydroxyacid Dehydrogenase Involved in Nicotinate Fermentation.

Reitz, S., Alhapel, A., Essen, L.O., Pierik, A.J.

(2008) J Mol Biol 382: 802-811

• PubMed: 18680749 
• DOI: 10.1016/j.jmb.2008.07.050
• Primary Citation of Related Structures:  
  3CKY


• PubMed Abstract: 
  

2-(Hydroxymethyl)glutarate dehydrogenase, the fourth enzyme of the anaerobic nicotinate fermentation pathway of Eubacterium barkeri, catalyzes the NADH-dependent conversion between (S)-2-formylglutarate and (S)-2-(hydroxymethyl)glutarate. As shown by its 2.3-A crystal structure, this enzyme is a novel member of the beta-hydroxyacid dehydrogenase family and adopts a tetrameric architecture with monomers interacting via their C-terminal catalytic domains. The NAD-binding domains protrude heterogeneously from the central, tetrameric core with domain rotation angles differing up to 12 degrees. Kinetic properties of the enzyme, including NADH inhibition constants, were determined. A strong NADH binding in contrast to weaker NAD(+) binding of the protein was inferred from fluorometrically determined binding constants for the dinucleotide cofactor. The data support either an Iso Ordered Bi Bi mechanism or a more common Ordered Bi Bi mechanism as found in other dehydrogenases.

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Organizational Affiliation: 

Philipps-Universität Marburg, Fachbereich Chemie, Hans-Meerwein-Strasse, D-35032 Marburg, Germany.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2-hydroxymethyl glutarate dehydrogenase	A, B, C, D	301	Eubacterium barkeri	Mutation(s): 0  Gene Names: Hgd EC: 1.1.1.291
UniProt
Find proteins for Q0QLF5 (Eubacterium barkeri) Explore Q0QLF5  Go to UniProtKB:  Q0QLF5

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.222 
• R-Value Work: 0.194 
• R-Value Observed: 0.195 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.978	α = 90
b = 175.779	β = 90
c = 83.709	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2008-03-18 
• Released Date: 2008-08-26 
Deposition Author(s): Reitz, S., Alhapel, A., Pierik, A.J., Essen, L.-O.

Revision History  

• Version 1.0: 2008-08-26
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance