3DXW | pdb_00003dxw

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

PDB DOI: https://doi.org/10.2210/pdb3DXW/pdb

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

Deposited: 2008-07-25 Released: 2009-07-28
Deposition Author(s): Okazaki, S., Suzuki, A., Komeda, H., Asano, Y., Yamane, T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.41 Å
R-Value Free:
0.252 (Depositor), 0.249 (DCC)
R-Value Work:
0.191 (Depositor), 0.191 (DCC)
R-Value Observed:
0.194 (Depositor)

Starting Model: experimental
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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 Search on PubMed
DOI: https://doi.org/10.1021/bi801574p
Primary Citation 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.

Organizational Affiliation

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

Macromolecule Content

Total Structure Weight: 95.84 kDa
Atom Count: 6,374
Modeled Residue Count: 848
Deposited Residue Count: 904
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha-amino-epsilon-caprolactam racemase	A, B	452	Achromobacter obae	Mutation(s): 0 EC: 5.1 (PDB Primary Data), 5.1.1.15 (UniProt)
UniProt
Find proteins for Q7M181 (Achromobacter obae) Explore Q7M181 Go to UniProtKB: Q7M181
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q7M181
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PLP Query on PLP Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain E [auth B] MOL2 format, chain C [auth A] MOL2 format, chain E [auth B] mmCIF format, chain C [auth A] mmCIF format, chain E [auth B]	C [auth A], E [auth B]	PYRIDOXAL-5'-PHOSPHATE C₈ H₁₀ N O₆ P NGVDGCNFYWLIFO-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]
ICC Query on ICC Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain F [auth B] MOL2 format, chain D [auth A] MOL2 format, chain F [auth B] mmCIF format, chain D [auth A] mmCIF format, chain F [auth B]	D [auth A], F [auth B]	azepan-2-one C₆ H₁₁ N O JBKVHLHDHHXQEQ-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain F [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.41 Å
R-Value Free: 0.252 (Depositor), 0.249 (DCC)
R-Value Work: 0.191 (Depositor), 0.191 (DCC)
R-Value Observed: 0.194 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.581	α = 90
b = 60.653	β = 103.07
c = 105.315	γ = 90

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2009-07-28

Deposition Author(s):

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
Version 1.2: 2023-11-01
Changes: Data collection, Database references, Derived calculations, Refinement description