Biological Assembly 1  

 3D View: Structure | Electron Density

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 36631.15 
• Atom Count: 2564 
• Residue Count: 331 
• Unique protein chains: 1

1XDW

NAD+-dependent (R)-2-Hydroxyglutarate Dehydrogenase from Acidaminococcus fermentans

• DOI: 10.2210/pdb1XDW/pdb

• Classification: OXIDOREDUCTASE
• Expression System: Escherichia coli


• Deposited: 2004-09-08 Released: 2005-03-08 
• Deposition Author(s): Martins, B.M., Macedo-Ribeiro, S., Bresser, J., Buckel, W., Messerschmidt, A.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.98 Å
• R-Value Free: 0.225 
• R-Value Work: 0.177 

Literature

Structural basis for stereo-specific catalysis in NAD(+)-dependent (R)-2-hydroxyglutarate dehydrogenase from Acidaminococcus fermentans.

Martins, B.M., Macedo-Ribeiro, S., Bresser, J., Buckel, W., Messerschmidt, A.

(2005) Febs J. 272: 269-281

• PubMed: 15634349 
• DOI: 10.1111/j.1432-1033.2004.04417.x


• PubMed Abstract: 
  

NAD(+)-dependent (R)-2-hydroxyglutarate dehydrogenase (HGDH) catalyses the reduction of 2-oxoglutarate to (R)-2-hydroxyglutarate and belongs to the d-2-hydroxyacid NAD(+)-dependent dehydrogenase (d-2-hydroxyacid dehydrogenase) protein family. Its crystal structure was determined by phase combination to 1.98 A resolution. Structure-function relationships obtained by the comparison of HGDH with other members of the d-2-hydroxyacid dehydrogenase family give a chemically satisfying view of the substrate stereoselectivity and catalytic requirements for the hydride transfer reaction. A model for substrate recognition and turnover is discussed. The HGDH active site architecture is structurally optimized to recognize and bind the negatively charged substrate 2-oxoglutarate. The structural position of the side chain of Arg52, and its counterparts in other family members, strongly correlates with substrate specificity towards substitutions at the C3 atom (linear or branched substrates). Arg235 interacts with the substrate's alpha-carboxylate and carbonyl groups, having a dual role in both substrate binding and activation, and the gamma-carboxylate group can dock at an arginine cluster. The proton-relay system built up by Glu264 and His297 permits His297 to act as acid-base catalyst and the 4Re-hydrogen from NADH is transferred as hydride to the carbonyl group Si-face leading to the formation of the correct enantiomer (R)-2-hydroxyglutarate.

---

Organizational Affiliation: 

MPI Biochemie, Strukturforschung, Martinsried, Germany. [e-mail]

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
NAD+-dependent (R)-2-Hydroxyglutarate Dehydrogenase	A	331	N/A	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.98 Å
• R-Value Free: 0.225 
• R-Value Work: 0.177 
• Space Group: P 6₁ 2 2

Unit Cell:

Length (Å)	Angle (°)
a = 67.490	α = 90.00
b = 67.490	β = 90.00
c = 312.785	γ = 120.00

Software Package:

Software Name	Purpose
DENZO	data reduction
XDS	data scaling
REFMAC	refinement
SHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-09-08 
• Released Date: 2005-03-08 
• Deposition Author(s): Martins, B.M., Macedo-Ribeiro, S., Bresser, J., Buckel, W., Messerschmidt, A.

Revision History 

• Version 1.0: 2005-03-08
  Type: Initial release
• Version 1.1: 2008-04-30
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance