3WO1

Crystal structure of Trp332Ala mutant YwfE, an L-amino acid ligase, with bound ADP-Mg-Ala


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.224 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

Single Mutation Alters the Substrate Specificity of l-Amino Acid Ligase

Tsuda, T.Asami, M.Koguchi, Y.Kojima, S.

(2014) Biochemistry 53: 2650-2660

  • DOI: https://doi.org/10.1021/bi500292b
  • Primary Citation of Related Structures:  
    3WNZ, 3WO0, 3WO1

  • PubMed Abstract: 

    L-Amino acid ligase (Lal) catalyzes the formation of a dipeptide from two L-amino acids in an ATP-dependent manner and belongs to the ATP-grasp superfamily. Bacillus subtilis YwfE, the first identified Lal, produces the dipeptide antibiotic bacilysin, which consists of L-Ala and L-anticapsin. Its substrate specificity is restricted to smaller amino acids such as L-Ala for the N-terminal end of the dipeptide, whereas a wide range of hydrophobic amino acids including L-Phe and L-Met are recognized for the C-terminal end in vitro. We determined the crystal structures of YwfE with bound ADP-Mg(2+)-Pi and ADP-Mg(2+)-L-Ala at 1.9 and 2.0 Å resolutions, respectively. On the basis of these structures, we generated point mutants of residues that are considered to participate in the recognition of L-Ala and measured their ATPase activity. The conserved Arg328 is suggested to be a crucial residue for L-Ala recognition and catalysis. The mutation of Trp332 to Ala caused the enzyme to hydrolyze ATP, even in the absence of l-Ala, and the structure of this mutant protein appeared to show a cavity in the N-terminal substrate-binding pocket. These results suggest that Trp332 plays a key role in restricting the substrate specificity to smaller amino acids such as L-Ala. Moreover, Trp332 mutants can alter the substrate specificity and activity depending on the size and shape of substituted amino acids. These observations provide sufficient scope for the rational design of Lal to produce desirable dipeptides. We propose that the positioning of the conserved Arg residue in Lal is important for enantioselective recognition of L-amino acids.


  • Organizational Affiliation

    Department of Life Science, Faculty of Science, Gakushuin University , 1-5-1 Mejiro, Toshima-ku, Tokyo 171-8588, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Alanine-anticapsin ligase BacD470Bacillus subtilis subsp. subtilis str. 168Mutation(s): 1 
Gene Names: ywfe
EC: 6.3.2.28
UniProt
Find proteins for P39641 (Bacillus subtilis (strain 168))
Explore P39641 
Go to UniProtKB:  P39641
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP39641
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.224 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.129α = 90
b = 91.129β = 90
c = 258.757γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
CRANKphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-05-14
    Type: Initial release