1EBF

HOMOSERINE DEHYDROGENASE FROM S. CEREVISIAE COMPLEX WITH NAD+

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.218 

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Ligand Structure Quality Assessment 


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 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 a dimer, with each monomer composed of three regions, the nucleotide-binding region, the dimerization region and the catalytic region ...

    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 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)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HOMOSERINE DEHYDROGENASEA, B358Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: HOM6P
EC: 1.1.1.3
UniProt
Find proteins for P31116 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P31116 
Go to UniProtKB:  P31116
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP31116
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAD
Query on NAD
Download Ideal Coordinates CCD File 
D [auth A]NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N		 Ligand Interaction
NA
Query on NA
Download Ideal Coordinates CCD File 
C [auth A],
E [auth B]		SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.218 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.396α = 90
b = 80.396β = 90
c = 250.165γ = 90
Software Package:
Software NamePurpose
SOLVEphasing
SHARPphasing
GLRFphasing
CCP4model building
DMmodel building
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CCP4phasing
DMphasing
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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
  • Version 1.3: 2017-10-04
    Changes: Refinement description