Apo histidine-tagged saccharopine dehydrogenase (L-Glu forming) from Saccharomyces cerevisiae

Experimental Data Snapshot

  • Resolution: 1.70 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.200 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


Crystal structure of the his-tagged saccharopine reductase from Saccharomyces cerevisiae at 1.7-A resolution.

Andi, B.Cook, P.F.West, A.H.

(2006) Cell Biochem Biophys 46: 17-26

  • DOI: https://doi.org/10.1385/CBB:46:1:17
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The three-dimensional structure of the saccharopine reductase enzyme from the budding yeast Saccharomyces cerevisiae was determined to 1.7-A resolution in the apo form by using molecular replacement. The enzyme monomer consists of three domains: domain I is a variant of the Rossmann fold, domain II folds into a alpha/beta structure containing a mixed seven-stranded beta-sheet as the central core, and domain III has an all-helical fold. Comparative fold alignment with the enzyme from Magnaporthe grisea suggests that domain I binds to NADPH, and domain II binds to saccharopine and is involved in dimer formation. Domain III is involved in closing the active site of the enzyme once substrates are bound. Structural comparison of the saccharopine reductase enzymes from S. cerevisiae and M. grisea indicates that domain II has the highest number of conserved residues, suggesting that it plays an important role in substrate binding and in spatially orienting domains I and III.

  • Organizational Affiliation

    Department of Chemistry and Biochemistry, University of Oklahoma, 620 Parrington Oval, Norman, OK 73019, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Saccharopine dehydrogenase467Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: LYS9LYS13
Find proteins for P38999 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P38999 
Go to UniProtKB:  P38999
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP38999
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.70 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.200 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.279α = 90
b = 85.279β = 90
c = 141.977γ = 120
Software Package:
Software NamePurpose
d*TREKdata scaling
PDB_EXTRACTdata extraction
CrystalCleardata reduction
CCP4data scaling
ARP/wARPmodel building

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-08-15
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-08-23
    Changes: Data collection, Database references, Derived calculations, Refinement description