3DXV

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

• PDB DOI: https://doi.org/10.2210/pdb3DXV/pdb

• Classification: ISOMERASE
• Organism(s): Achromobacter obae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-07-25 Released: 2009-02-17 
• Deposition Author(s): Okazaki, S., Suzuki, A., Komeda, H., Asano, Y., Yamane, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.21 Å
• R-Value Free: 0.245 
• R-Value Work: 0.197 
• R-Value Observed: 0.200 

Starting Model: experimental

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

• PubMed: 19146406 
• DOI: https://doi.org/10.1021/bi801574p
• Primary Citation of Related Structures:  
  2ZUK, 3DXV, 3DXW


• 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 2.21 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 92.56 kDa 
• Atom Count: 6,486 
• Modelled Residue Count: 856 
• Deposited Residue Count: 878 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha-amino-epsilon-caprolactam racemase	A, B	439	Achromobacter obae	Mutation(s): 0  EC: 5.1.1.15
UniProt
Find proteins for Q7M181 (Achromobacter obae) Explore Q7M181  Go to UniProtKB:  Q7M181

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PLP	C [auth A], D [auth B]	PYRIDOXAL-5'-PHOSPHATE C8 H10 N O6 P NGVDGCNFYWLIFO-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.21 Å
• R-Value Free: 0.245 
• R-Value Work: 0.197 
• R-Value Observed: 0.200 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.547	α = 90
b = 61.063	β = 103.22
c = 105.227	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
ADSC	data collection
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-02-17 
Deposition Author(s): Okazaki, S., Suzuki, A., Komeda, H., Asano, Y., Yamane, T.

Revision History  

• Version 1.0: 2009-02-17
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description