1EBU

HOMOSERINE DEHYDROGENASE COMPLEX WITH NAD ANALOGUE AND L-HOMOSERINE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.215 

wwPDB Validation 3D Report Full Report


This is version 1.2 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 Biol 7: 238-244

  • DOI: 10.1038/73359
  • Primary Citation of Related Structures:  
    1EBF, 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 diffraction studies of homoserine dehydrogenase from Saccharomyces cerevisiae
      DeLaBarre, B., Jacques, S.L., Pratt, C.E., Wright, G.D., Berghuis, A.M.
      (1998) Acta Crystallogr D Biol Crystallogr 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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HOMOSERINE DEHYDROGENASEABCD358Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: HOM6P
EC: 1.1.1.3
Find proteins for P31116 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P31116 
Go to UniProtKB:  P31116
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NDA
Query on NDA

Download CCD File 
D
3-AMINOMETHYL-PYRIDINIUM-ADENINE-DINUCLEOTIDE
C21 H29 N7 O13 P2
HMCRLFVYYFBZEZ-PLEFRAQWSA-N
 Ligand Interaction
HSE
Query on HSE

Download CCD File 
D
L-HOMOSERINE
C4 H9 N O3
UKAUYVFTDYCKQA-VKHMYHEASA-N
 Ligand Interaction
NA
Query on NA

Download CCD File 
A, B, C, D
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.215 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.78α = 90
b = 104.09β = 91.93
c = 120.64γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-03-08
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance