4A6G | pdb_00004a6g

N-acyl amino acid racemase from Amycalotopsis sp. Ts-1-60: G291D- F323Y mutant in complex with N-acetyl methionine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.71 Å
  • R-Value Free: 
    0.210 (Depositor), 0.207 (DCC) 
  • R-Value Work: 
    0.155 (Depositor), 0.153 (DCC) 
  • R-Value Observed: 
    0.158 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 4A6G

Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

An Improved Racemase/Acylase Biotransformation for the Preparation of Enantiomerically Pure Amino Acids.

Baxter, S.Royer, S.Grogan, G.Brown, F.Holt-Tiffin, K.E.Taylor, I.N.Fotheringham, I.G.Campopiano, D.J.

(2012) J Am Chem Soc 134: 19310

  • DOI: https://doi.org/10.1021/ja305438y
  • Primary Citation Related Structures: 
    4A6G

  • PubMed Abstract: 

    Using directed evolution, a variant N-acetyl amino acid racemase (NAAAR G291D/F323Y) has been developed with up to 6-fold higher activity than the wild-type on a range of N-acetylated amino acids. The variant has been coupled with an enantiospecific acylase to give a preparative scale dynamic kinetic resolution which allows 98% conversion of N-acetyl-DL-allylglycine into D-allylglycine in 18 h at high substrate concentrations (50 g L(-1)). This is the first example of NAAAR operating under conditions which would allow it to be successfully used on an industrial scale for the production of enantiomerically pure α-amino acids. X-ray crystal analysis of the improved NAAAR variant allowed a comparison with the wild-type enzyme. We postulate that a network of novel interactions that result from the introduction of the two side chains is the source of improved catalytic performance.


  • Organizational Affiliation
    • The EastChem School of Chemistry, Joseph Black Building, The University of Edinburgh, Edinburgh, EH9 3JJ, UK.

Macromolecule Content 

  • Total Structure Weight: 158.95 kDa 
  • Atom Count: 11,214 
  • Modeled Residue Count: 1,469 
  • Deposited Residue Count: 1,472 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
N-ACYLAMINO ACID RACEMASE
A, B, C, D
368Amycolatopsis sp.Mutation(s): 2 
EC: 4.2.1.113 (PDB Primary Data), 5.1.1 (UniProt)
UniProt
Find proteins for Q44244 (Amycolatopsis sp)
Explore Q44244 
Go to UniProtKB:  Q44244
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ44244
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AME

Query on AME



Download:Ideal Coordinates CCD File
E [auth A],
G [auth B],
I [auth C],
K [auth D]
N-ACETYLMETHIONINE
C7 H13 N O3 S
XUYPXLNMDZIRQH-LURJTMIESA-N
MG

Query on MG



Download:Ideal Coordinates CCD File
F [auth A],
H [auth B],
J [auth C],
L [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.71 Å
  • R-Value Free:  0.210 (Depositor), 0.207 (DCC) 
  • R-Value Work:  0.155 (Depositor), 0.153 (DCC) 
  • R-Value Observed: 0.158 (Depositor) 
Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 216.71α = 90
b = 216.71β = 90
c = 261.1γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-11-14
    Type: Initial release
  • Version 1.1: 2012-11-21
    Changes: Database references
  • Version 1.2: 2012-12-19
    Changes: Database references
  • Version 1.3: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description