Crystal structure of G52A-P55G mutant of L-serine-O-acetyltransferase found in D-cycloserine biosynthetic pathway

Experimental Data Snapshot

  • Resolution: 1.70 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.192 

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Crystallographic study to determine the substrate specificity of an L-serine-acetylating enzyme found in the D-cycloserine biosynthetic pathway

Oda, K.Matoba, Y.Kumagai, T.Noda, M.Sugiyama, M.

(2013) J Bacteriol 195: 1741-1749

  • DOI: https://doi.org/10.1128/JB.02085-12
  • Primary Citation of Related Structures:  
    3VVL, 3VVM

  • PubMed Abstract: 

    DcsE, one of the enzymes found in the d-cycloserine biosynthetic pathway, displays a high sequence homology to l-homoserine O-acetyltransferase (HAT), but it prefers l-serine over l-homoserine as the substrate. To clarify the substrate specificity, in the present study we determined the crystal structure of DcsE at a 1.81-Å resolution, showing that the overall structure of DcsE is similar to that of HAT, whereas a turn region to form an oxyanion hole is obviously different between DcsE and HAT: in detail, the first and last residues in the turn of DcsE are Gly(52) and Pro(55), respectively, but those of HAT are Ala and Gly, respectively. In addition, more water molecules were laid on one side of the turn region of DcsE than on that of HAT, and a robust hydrogen-bonding network was formed only in DcsE. We created a HAT-like mutant of DcsE in which Gly(52) and Pro(55) were replaced by Ala and Gly, respectively, showing that the mutant acetylates l-homoserine but scarcely acetylates l-serine. The crystal structure of the mutant DcsE shows that the active site, including the turn and its surrounding waters, is similar to that of HAT. These findings suggest that a methyl group of the first residue in the turn of HAT plays a role in excluding the binding of l-serine to the substrate-binding pocket. In contrast, the side chain of the last residue in the turn of DcsE may need to form an extensive hydrogen-bonding network on the turn, which interferes with the binding of l-homoserine.

  • Organizational Affiliation

    Department of Molecular Microbiology and Biotechnology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Homoserine O-acetyltransferase
A, B
394Streptomyces lavendulae subsp. lavendulaeMutation(s): 2 
Gene Names: dcsEmetX
EC: (PDB Primary Data), (UniProt)
Find proteins for D2Z028 (Streptomyces lavendulae)
Explore D2Z028 
Go to UniProtKB:  D2Z028
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD2Z028
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.70 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.192 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.56α = 90
b = 102.33β = 90
c = 147.3γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-03-20
    Type: Initial release
  • Version 1.1: 2013-06-05
    Changes: Database references
  • Version 1.2: 2023-11-08
    Changes: Data collection, Database references, Refinement description