4Y2W

Crystal structure of a thermostable alanine racemase from Thermoanaerobacter tengcongensis MB4

PDB DOI: https://doi.org/10.2210/pdb4Y2W/pdb

Classification: ISOMERASE
Organism(s): Caldanaerobacter subterraneus subsp. tengcongensis MB4
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2015-02-10 Released: 2015-09-23
Deposition Author(s): Xu, X., Ju, J., Dong, H.
Funding Organization(s): National Natural Science Foundation of China, Zhejiang Provincial Natural Science Foundation of China, Natural Science Foundation of Hebei Province, Hangzhou Normal University

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.252
R-Value Work: 0.214
R-Value Observed: 0.215

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Crystal Structure of a Thermostable Alanine Racemase from Thermoanaerobacter tengcongensis MB4 Reveals the Role of Gln360 in Substrate Selection

Sun, X., He, G., Wang, X., Xu, S., Ju, J., Xu, X.

(2015) PLoS One 10: e0133516-e0133516

PubMed: 26218070 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1371/journal.pone.0133516
Primary Citation of Related Structures:
4Y2W

PubMed Abstract:
Pyridoxal 5'-phosphate (PLP) dependent alanine racemase catalyzes racemization of L-Ala to D-Ala, a key component of the peptidoglycan network in bacterial cell wall. It has been extensively studied as an important antimicrobial drug target due to its restriction in eukaryotes. However, many marketed alanine racemase inhibitors also act on eukaryotic PLP-dependent enzymes and cause side effects. A thermostable alanine racemase (AlrTt) from Thermoanaerobacter tengcongensis MB4 contains an evolutionarily non-conserved residue Gln360 in inner layer of the substrate entryway, which is supposed to be a key determinant in substrate specificity. Here we determined the crystal structure of AlrTt in complex with L-Ala at 2.7 Å resolution, and investigated the role of Gln360 by saturation mutagenesis and kinetic analysis. Compared to typical bacterial alanine racemase, presence of Gln360 and conformational changes of active site residues disrupted the hydrogen bonding interactions necessary for proper PLP immobilization, and decreased both the substrate affinity and turnover number of AlrTt. However, it could be complemented by introduction of hydrophobic amino acids at Gln360, through steric blocking and interactions with a hydrophobic patch near active site pocket. These observations explained the low racemase activity of AlrTt, revealed the essential role of Gln360 in substrate selection, and its preference for hydrophobic amino acids especially Tyr in bacterial alanine racemization. Our work will contribute new insights into the alanine racemization mechanism for antimicrobial drug development.

Organizational Affiliation

Institute of Ageing Research, School of Medicine, Hangzhou Normal University, Hangzhou, China.

Macromolecule Content

Total Structure Weight: 88.69 kDa
Atom Count: 6,234
Modelled Residue Count: 776
Deposited Residue Count: 776
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alanine racemase 1	A, B	388	Caldanaerobacter subterraneus subsp. tengcongensis MB4	Mutation(s): 1 Gene Names: alr1, TTE1207 EC: 5.1.1.1
UniProt
Find proteins for Q8RAK6 (Caldanaerobacter subterraneus subsp. tengcongensis (strain DSM 15242 / JCM 11007 / NBRC 100824 / MB4)) Explore Q8RAK6 Go to UniProtKB: Q8RAK6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8RAK6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 Query on PO4 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]	C [auth A], E [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]
ALA Query on ALA 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]	D [auth A], F [auth B]	ALANINE C₃ H₇ N O₂ QNAYBMKLOCPYGJ-REOHCLBHSA-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: 2.70 Å
R-Value Free: 0.252
R-Value Work: 0.214
R-Value Observed: 0.215
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.843	α = 90
b = 73.077	β = 90
c = 218.746	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2015-09-23

Deposition Author(s):

Xu, X.

Ju, J.

Dong, H.

Funding Organization	Location	Grant Number
National Natural Science Foundation of China	China	31400630
Zhejiang Provincial Natural Science Foundation of China	China	LY14C050002
Natural Science Foundation of Hebei Province	China	C2015205212
Hangzhou Normal University	China	PE13002004007

Revision History (Full details and data files)

Version 1.0: 2015-09-23
Type: Initial release
Version 1.1: 2023-11-08
Changes: Data collection, Database references, Derived calculations, Refinement description