Biological Assembly 1  

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

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

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

Macromolecule Content

• Total Structure Weight: 77.43 kDa 
• Atom Count: 5462 
• Modelled Residue Count: 716 
• Deposited Residue Count: 716 
• Unique protein chains: 1

1TVE

Homoserine Dehydrogenase in complex with 4-(4-hydroxy-3-isopropylphenylthio)-2-isopropylphenol

• PDB DOI: 10.2210/pdb1TVE/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Saccharomyces cerevisiae
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2004-06-29 Released: 2004-07-13 
• Deposition Author(s): Ejim, L., Mirza, I.A., Capone, C., Nazi, I., Jenkins, S., Chee, G.L., Berghuis, A.M., Wright, G.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.363 
• R-Value Work: 0.289 
• R-Value Observed: 0.289 

Literature

New phenolic inhibitors of yeast homoserine dehydrogenase

Ejim, L., Mirza, I.A., Capone, C., Nazi, I., Jenkins, S., Chee, G.L., Berghuis, A.M., Wright, G.D.

(2004) Bioorg Med Chem 12: 3825-3830

• PubMed: 15210149 
• DOI: 10.1016/j.bmc.2004.05.009
• Primary Citation of Related Structures:  
  1TVE


• PubMed Abstract: 
  

A relatively unexploited potential target for antimicrobial agents is the biosynthesis of essential amino acids. Homoserine dehydrogenase, which reduces aspartate semi-aldehyde to homoserine in a NAD(P)H-dependent reaction, is one such target that is required for the biosynthesis of Met, Thr, and Ile from Asp. We report a small molecule screen of yeast homoserine dehydrogenase that has identified a new class of phenolic inhibitors of this class of enzyme. X-ray crystal structural analysis of one of the inhibitors in complex with homoserine dehydrogenase reveals that these molecules bind in the amino acid binding region of the active site and that the phenolic hydroxyl group interacts specifically with the backbone amide of Gly175. These results provide the first nonamino acid inhibitors of this class of enzyme and have the potential to be exploited as leads in antifungal compound design.

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Organizational Affiliation: 

Antimicrobial Research Centre, Department of Biochemistry, McMaster University, 1200 Main Street West, Hamilton, ON, Canada L8N 3Z5.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Homoserine dehydrogenase	A, B	358	Saccharomyces cerevisiae	Mutation(s): 0  Gene Names: HOM6 EC: 1.1.1.3
UniProt
Find proteins for P31116 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P31116  Go to UniProtKB:  P31116

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
178	C [auth A], D [auth B]	4-(4-HYDROXY-3-ISOPROPYLPHENYLTHIO)-2-ISOPROPYLPHENOL C18 H22 O2 S NEMLLZAROZVCCE-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
178	PDBBind:  1TVE	IC50: 2100 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.363 
• R-Value Work: 0.289 
• R-Value Observed: 0.289 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.456	α = 90
b = 54.379	β = 98.97
c = 92.497	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-06-29 
• Released Date: 2004-07-13 
Deposition Author(s): Ejim, L., Mirza, I.A., Capone, C., Nazi, I., Jenkins, S., Chee, G.L., Berghuis, A.M., Wright, G.D.

Revision History  

• Version 1.0: 2004-07-13
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance