3DXW

The crystal structure of alpha-amino-epsilon-caprolactam racemase from Achromobacter obae complexed with epsilon caprolactam


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.41 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.194 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

The novel structure of a pyridoxal 5'-phosphate-dependent fold-type I racemase, alpha-amino-epsilon-caprolactam racemase from Achromobacter obae

Okazaki, S.Suzuki, A.Mizushima, T.Kawano, T.Komeda, H.Asano, Y.Yamane, T.

(2009) Biochemistry 48: 941-950

  • DOI: 10.1021/bi801574p
  • Primary Citation of Related Structures:  
    3DXW, 3DXV, 2ZUK

  • PubMed Abstract: 
  • Alpha-amino-epsilon-caprolactam (ACL) racemase (ACLR) from Achromobacter obae catalyzes the interconversion of l- and d-ACL. ACLR belongs to the fold-type I group of pyridoxal 5'-phosphate (PLP) dependent enzymes. In this study, the first crystal structures of a fold-type I racemase are solved for the native form and epsilon-caprolactam-complexed form of ACLR at 2 ...

    Alpha-amino-epsilon-caprolactam (ACL) racemase (ACLR) from Achromobacter obae catalyzes the interconversion of l- and d-ACL. ACLR belongs to the fold-type I group of pyridoxal 5'-phosphate (PLP) dependent enzymes. In this study, the first crystal structures of a fold-type I racemase are solved for the native form and epsilon-caprolactam-complexed form of ACLR at 2.21 and 2.40 A resolution, respectively. Based on the location of epsilon-caprolactam in the complex structure, the substrate-binding site is assigned between Trp49 and Tyr137. The carboxyl group of Asp210 is a reasonable candidate that recognizes the nitrogen atom of a lactam or amide in the substrate. Based on a structural comparison with fold-type III alanine racemase, Tyr137 is potentially the acid/base catalytic residue that is essential for the two-base racemization mechanism. The overall structure of ACLR is similar to that of fold-type I enzymes. A structural comparison with these enzymes explains the different reaction specificities.


    Organizational Affiliation

    Department of Biotechnology, Graduate School of Engineering, Nagoya University, Chikusa, Nagoya 464-8603, Japan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Alpha-amino-epsilon-caprolactam racemaseA, B452Achromobacter obaeMutation(s): 0 
EC: 5.1 (PDB Primary Data), 5.1.1.15 (UniProt)
Find proteins for Q7M181 (Achromobacter obae)
Explore Q7M181 
Go to UniProtKB:  Q7M181
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PLP
Query on PLP

Download Ideal Coordinates CCD File 
C [auth A], E [auth B]PYRIDOXAL-5'-PHOSPHATE
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
 Ligand Interaction
ICC
Query on ICC

Download Ideal Coordinates CCD File 
D [auth A], F [auth B]azepan-2-one
C6 H11 N O
JBKVHLHDHHXQEQ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.41 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.194 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.581α = 90
b = 60.653β = 103.07
c = 105.315γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-07-28
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Non-polymer description, Version format compliance