Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  (To be retired June 1st  )
Protein Workshop | Ligand Explorer

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: 77.95 kDa 
• Atom Count: 5571 
• Residue Count: 716 
• Unique protein chains: 1

1Q7G

Homoserine Dehydrogenase in complex with suicide inhibitor complex NAD-5-hydroxy-4-Oxonorvaline

• DOI: 10.2210/pdb1Q7G/pdb

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


• Deposited: 2003-08-18 Released: 2003-10-21 
• Deposition Author(s): Jacques, S.L., Mirza, I.A., Ejim, L., Koteva, K., Hughes, D.W., Green, K., Kinach, R., Honek, J.F., Lai, H.K., Berghuis, A.M., Wright, G.D.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.306 
• R-Value Work: 0.247 
• R-Value Observed: 0.247 

Literature

Enzyme assisted suicide: Molecular basis for the antifungal activity of 5-hydroxy-4-oxonorvaline by potent inhibition of homoserine dehydrogenase

Jacques, S.L., Mirza, I.A., Ejim, L., Koteva, K., Hughes, D.W., Green, K., Kinach, R., Honek, J.F., Lai, H.K., Berghuis, A.M., Wright, G.D.

(2003) Chem Biol 10: 989-995

• PubMed: 14583265 
• DOI: 10.1016/j.chembiol.2003.09.015
• Structures With Same Primary Citation


• PubMed Abstract: 
  

The structure of the antifungal drug 5-hydroxy-4-oxonorvaline (HON) in complex with its target homoserine dehydrogenase (HSD) has been determined by X-ray diffraction to 2.6 A resolution. HON shows potent in vitro and in vivo activity against various fungal pathogens despite its weak (2 mM) affinity for HSD in the steady state. The structure together with structure-activity relationship studies, mass spectrometry experiments, and spectroscopic data reveals that the molecular mechanism of antifungal action conferred by HON involves enzyme-dependent formation of a covalent adduct between C4 of the nicotinamide ring of NAD(+) and C5 of HON. Furthermore, novel interactions are involved in stabilizing the (HON*NAD)-adduct, which are not observed in the enzyme's ternary complex structure. These findings clarify the apparent paradox of the potent antifungal actions of HON given its weak steady-state inhibition characteristics.

---

Organizational Affiliation: 

Antimicrobial Research Centre and Department of Biochemistry, McMaster University, Hamilton L8N 3Z5, Canada.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Homoserine dehydrogenase	A, B	359	Saccharomyces cerevisiae	Mutation(s): 0  Gene Names: HOM6, YJR139C OR J2132 EC: 1.1.1.3
Find proteins for P31116 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  P31116

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NHO	A	NICOTINAMIDE-ADENINE-DINUCLEOTIDE-5-HYDROXY-4-OXONORVALINE C26 H35 N8 O18 P2 RSVNLFPFYXGAGU-GIBQRGJUSA-O
NA	A, B	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.306 
• R-Value Work: 0.247 
• R-Value Observed: 0.247 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.863	α = 90
b = 80.863	β = 90
c = 248.986	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-08-18 
• Released Date: 2003-10-21 
Deposition Author(s): Jacques, S.L., Mirza, I.A., Ejim, L., Koteva, K., Hughes, D.W., Green, K., Kinach, R., Honek, J.F., Lai, H.K., Berghuis, A.M., Wright, G.D.

Revision History 

• Version 1.0: 2003-10-21
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance