1EBF

HOMOSERINE DEHYDROGENASE FROM S. CEREVISIAE COMPLEX WITH NAD+


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.218 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal structures of homoserine dehydrogenase suggest a novel catalytic mechanism for oxidoreductases.

DeLaBarre, B.Thompson, P.R.Wright, G.D.Berghuis, A.M.

(2000) Nat.Struct.Mol.Biol. 7: 238-244

  • DOI: 10.1038/73359
  • Primary Citation of Related Structures:  1EBU

  • PubMed Abstract: 
  • The structure of the antifungal drug target homoserine dehydrogenase (HSD) was determined from Saccharomyces cerevisiae in apo and holo forms, and as a ternary complex with bound products, by X-ray diffraction. The three forms show that the enzyme is ...

    The structure of the antifungal drug target homoserine dehydrogenase (HSD) was determined from Saccharomyces cerevisiae in apo and holo forms, and as a ternary complex with bound products, by X-ray diffraction. The three forms show that the enzyme is a dimer, with each monomer composed of three regions, the nucleotide-binding region, the dimerization region and the catalytic region. The dimerization and catalytic regions have novel folds, whereas the fold of the nucleotide-binding region is a variation on the Rossmann fold. The novel folds impose a novel composition and arrangement of active site residues when compared to all other currently known oxidoreductases. This observation, in conjunction with site-directed mutagenesis of active site residues and steady-state kinetic measurements, suggest that HSD exhibits a new variation on dehydrogenase chemistry.


    Related Citations: 
    • Crystallization and Preliminary X-ray Siffraction Studies of Homoserine Dehydrogenase from Saccharomyces Cerevisiae
      DeLaBarre, B.,Jacques, S.L.,Pratt, C.E.,Wright, G.D.,Berghuis, A.M.
      (1998) Acta Crystallogr.,Sect.D 54: 413


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HOMOSERINE DEHYDROGENASE
A, B
358Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: HOM6
EC: 1.1.1.3
Find proteins for P31116 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P31116
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A, B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
NAD
Query on NAD

Download SDF File 
Download CCD File 
A
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.218 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 80.396α = 90.00
b = 80.396β = 90.00
c = 250.165γ = 90.00
Software Package:
Software NamePurpose
GLRFphasing
SCALEPACKdata scaling
CCP4model building
CNSrefinement
DMphasing
DENZOdata reduction
SOLVEphasing
SHARPphasing
CCP4phasing
CNSphasing
DMmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-03-08
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-04
    Type: Refinement description