3WWX

Crystal structure of D-stereospecific amidohydrolase from Streptomyces sp. 82F2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.49 Å
  • R-Value Free: 0.162 
  • R-Value Work: 0.141 
  • R-Value Observed: 0.142 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Crystal structure of D-stereospecific amidohydrolase from Streptomyces sp. 82F2 - insight into the structural factors for substrate specificity.

Arima, J.Shimone, K.Miyatani, K.Tsunehara, Y.Isoda, Y.Hino, T.Nagano, S.

(2016) FEBS J 283: 337-349

  • DOI: https://doi.org/10.1111/febs.13579
  • Primary Citation of Related Structures:  
    3WWX

  • PubMed Abstract: 

    D-Stereospecific amidohydrolase (DAH) from Streptomyces sp. 82F2, which catalyzes amide bond formation from d-aminoacyl esters and l-amino acids (aminolysis), can be used to synthesize short peptides with a dl-configuration. We found that DAH can use 1,8-diaminooctane and other amino compounds as acyl acceptors in the aminolysis reaction. Low concentrations of 1,8-diaminooctane inhibited acyl-DAH intermediate formation. By contrast, excess 1,8-diaminooctane promoted aminolysis by DAH, producing d-Phe-1,8-diaminooctane via nucleophilic attack of the diamine on enzyme-bound d-Phe. To clarify the mechanism of substrate specificity and amide bond formation by DAH, the crystal structure of the enzyme that binds 1,8-diaminooctane was determined at a resolution of 1.49 Å. Comparison of the DAH crystal structure with those of other members of the S12 peptidase family indicated that the substrate specificity of DAH arises from its active site structure. The 1,8-diaminooctane molecule binds at the entrance of the active site pocket. The electrkon density map showed that another potential 1,8-diaminooctane binding site, probably with lower affinity, is present close to the active site. The enzyme kinetics and structural comparisons suggest that the location of enzyme-bound diamine can explain the inhibition of the acyl-enzyme intermediate formation, although the bound diamine is too far from the active site for aminolysis. Despite difficulty in locating the diamine binding site for aminolysis definitively, we propose that the excess diamine also binds at or near the second binding site to attack the acyl-enzyme intermediate during aminolysis.


  • Organizational Affiliation

    Department of Agricultural, Biological, and Environmental Sciences, Faculty of Agriculture, Tottori University, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
S12 family peptidase349Streptomyces sp. 82F2Mutation(s): 0 
Gene Names: s12ap
UniProt
Find proteins for E2RVJ1 (Streptomyces sp. 82F2)
Explore E2RVJ1 
Go to UniProtKB:  E2RVJ1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupE2RVJ1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DIA
Query on DIA

Download Ideal Coordinates CCD File 
B [auth A]OCTANE 1,8-DIAMINE
C8 H20 N2
PWGJDPKCLMLPJW-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.49 Å
  • R-Value Free: 0.162 
  • R-Value Work: 0.141 
  • R-Value Observed: 0.142 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.29α = 90
b = 74.681β = 90
c = 76.447γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
BSSdata collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-07-08
    Type: Initial release
  • Version 1.1: 2015-11-25
    Changes: Database references
  • Version 1.2: 2017-11-22
    Changes: Refinement description
  • Version 1.3: 2022-08-24
    Changes: Database references, Derived calculations
  • Version 1.4: 2023-11-08
    Changes: Data collection, Refinement description