6SCZ | pdb_00006scz

Mycobacterium tuberculosis alanine racemase inhibited by DCS

PDB DOI: https://doi.org/10.2210/pdb6SCZ/pdb

Classification: ISOMERASE
Organism(s): Mycobacterium tuberculosis H37Rv
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2019-07-26 Released: 2020-04-01
Deposition Author(s): de Chiara, C., Purkiss, A., Prosser, G., Homsak, M., de Carvalho, L.P.S.
Funding Organization(s): The Francis Crick Institute, Cancer Research UK, Medical Research Council (MRC, United Kingdom), Wellcome Trust

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.57 Å
R-Value Free:
0.190 (Depositor), 0.190 (DCC)
R-Value Work:
0.150 (Depositor), 0.151 (DCC)
R-Value Observed:
0.152 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

D-Cycloserine destruction by alanine racemase and the limit of irreversible inhibition.

de Chiara, C., Homsak, M., Prosser, G.A., Douglas, H.L., Garza-Garcia, A., Kelly, G., Purkiss, A.G., Tate, E.W., de Carvalho, L.P.S.

(2020) Nat Chem Biol 16: 686-694

PubMed: 32203411 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41589-020-0498-9
Primary Citation Related Structures:
6SCZ

PubMed Abstract:
The broad-spectrum antibiotic D-cycloserine (DCS) is a key component of regimens used to treat multi- and extensively drug-resistant tuberculosis. DCS, a structural analog of D-alanine, binds to and inactivates two essential enzymes involved in peptidoglycan biosynthesis, alanine racemase (Alr) and D-Ala:D-Ala ligase. Inactivation of Alr is thought to proceed via a mechanism-based irreversible route, forming an adduct with the pyridoxal 5'-phosphate cofactor, leading to bacterial death. Inconsistent with this hypothesis, Mycobacterium tuberculosis Alr activity can be detected after exposure to clinically relevant DCS concentrations. To address this paradox, we investigated the chemical mechanism of Alr inhibition by DCS. Inhibition of M. tuberculosis Alr and other Alrs is reversible, mechanistically revealed by a previously unidentified DCS-adduct hydrolysis. Dissociation and subsequent rearrangement to a stable substituted oxime explains Alr reactivation in the cellular milieu. This knowledge provides a novel route for discovery of improved Alr inhibitors against M. tuberculosis and other bacteria.

Organizational Affiliation

Mycobacterial Metabolism and Antibiotic Research Laboratory, The Francis Crick Institute, London, UK.

Macromolecule Content

Total Structure Weight: 89.56 kDa
Atom Count: 6,525
Modeled Residue Count: 744
Deposited Residue Count: 774
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alanine racemase	A, B	387	Mycobacterium tuberculosis H37Rv	Mutation(s): 0 Gene Names: alr, Rv3423c, MTCY78.06 EC: 5.1.1.1
UniProt
Find proteins for P9WQA9 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WQA9 Go to UniProtKB: P9WQA9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P9WQA9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 9 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
P4K Query on P4K Download:Ideal Coordinates CCD File SDF format, chain Z [auth A] SDF format, chain Y [auth A] SDF format, chain XA [auth B] SDF format, chain WA [auth B] SDF format, chain VA [auth B] MOL2 format, chain Z [auth A] MOL2 format, chain Y [auth A] MOL2 format, chain XA [auth B] MOL2 format, chain WA [auth B] MOL2 format, chain VA [auth B] mmCIF format, chain Z [auth A] mmCIF format, chain Y [auth A] mmCIF format, chain XA [auth B] mmCIF format, chain WA [auth B] mmCIF format, chain VA [auth B]	VA [auth B], WA [auth B], XA [auth B], Y [auth A], Z [auth A]	polyethylene glycol C₃₀ H₆₂ O₁₅ WWPGFZAAWXFBTF-UHFFFAOYSA-N		Interactions Focus chain VA [auth B] Focus chain WA [auth B] Focus chain XA [auth B] Focus chain Y [auth A] Focus chain Z [auth A] Interactions & Density Focus chain VA [auth B] Focus chain WA [auth B] Focus chain XA [auth B] Focus chain Y [auth A] Focus chain Z [auth A]
L7N (Subject of Investigation/LOI) Query on L7N Download:Ideal Coordinates CCD File SDF format, chain AA [auth A] MOL2 format, chain AA [auth A] mmCIF format, chain AA [auth A]	AA [auth A]	(~{E})-[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylidene-[(4~{R})-3-oxidanylidene-1,2-oxazolidin-4-yl]azanium C₁₁ H₁₅ N₃ O₇ P PWALIMMCDFLLIJ-RZTFRGLUSA-O		Interactions Focus chain AA [auth A] Interactions & Density Focus chain AA [auth A]
OJQ Query on OJQ Download:Ideal Coordinates CCD File SDF format, chain YA [auth B] SDF format, chain BA [auth A] MOL2 format, chain YA [auth B] MOL2 format, chain BA [auth A] mmCIF format, chain YA [auth B] mmCIF format, chain BA [auth A]	BA [auth A], YA [auth B]	[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methyl-(3-oxidanyl-1,2-oxazol-4-yl)azanium C₁₁ H₁₅ N₃ O₇ P PXWFNGNWQUPGPJ-UHFFFAOYSA-O		Interactions Focus chain BA [auth A] Focus chain YA [auth B] Interactions & Density Focus chain BA [auth A] Focus chain YA [auth B]
TRS Query on TRS Download:Ideal Coordinates CCD File SDF format, chain ZA [auth B] SDF format, chain CA [auth A] MOL2 format, chain ZA [auth B] MOL2 format, chain CA [auth A] mmCIF format, chain ZA [auth B] mmCIF format, chain CA [auth A]	CA [auth A], ZA [auth B]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain CA [auth A] Focus chain ZA [auth B] Interactions & Density Focus chain CA [auth A] Focus chain ZA [auth B]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain X [auth A] SDF format, chain W [auth A] SDF format, chain V [auth A] SDF format, chain UA [auth B] SDF format, chain U [auth A] SDF format, chain TA [auth B] SDF format, chain SA [auth B] MOL2 format, chain X [auth A] MOL2 format, chain W [auth A] MOL2 format, chain V [auth A] MOL2 format, chain UA [auth B] MOL2 format, chain U [auth A] MOL2 format, chain TA [auth B] MOL2 format, chain SA [auth B] mmCIF format, chain X [auth A] mmCIF format, chain W [auth A] mmCIF format, chain V [auth A] mmCIF format, chain UA [auth B] mmCIF format, chain U [auth A] mmCIF format, chain TA [auth B] mmCIF format, chain SA [auth B]	SA [auth B] TA [auth B] U [auth A] UA [auth B] V [auth A] SA [auth B], TA [auth B], U [auth A], UA [auth B], V [auth A], W [auth A], X [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain SA [auth B] Focus chain TA [auth B] Focus chain U [auth A] Focus chain UA [auth B] Focus chain V [auth A] Focus chain W [auth A] Focus chain X [auth A] Interactions & Density Focus chain SA [auth B] Focus chain TA [auth B] Focus chain U [auth A] Focus chain UA [auth B] Focus chain V [auth A] Focus chain W [auth A] Focus chain X [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain FA [auth B] SDF format, chain F [auth A] SDF format, chain EA [auth B] SDF format, chain E [auth A] SDF format, chain DA [auth B] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain FA [auth B] MOL2 format, chain F [auth A] MOL2 format, chain EA [auth B] MOL2 format, chain E [auth A] MOL2 format, chain DA [auth B] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain FA [auth B] mmCIF format, chain F [auth A] mmCIF format, chain EA [auth B] mmCIF format, chain E [auth A] mmCIF format, chain DA [auth B] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A] D [auth A] DA [auth B] E [auth A] EA [auth B] C [auth A], D [auth A], DA [auth B], E [auth A], EA [auth B], F [auth A], FA [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain DA [auth B] Focus chain E [auth A] Focus chain EA [auth B] Focus chain F [auth A] Focus chain FA [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain DA [auth B] Focus chain E [auth A] Focus chain EA [auth B] Focus chain F [auth A] Focus chain FA [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain T [auth A] SDF format, chain S [auth A] SDF format, chain RA [auth B] SDF format, chain R [auth A] SDF format, chain QA [auth B] SDF format, chain Q [auth A] SDF format, chain PA [auth B] SDF format, chain P [auth A] SDF format, chain OA [auth B] SDF format, chain O [auth A] SDF format, chain NA [auth B] SDF format, chain N [auth A] SDF format, chain MA [auth B] SDF format, chain M [auth A] SDF format, chain LA [auth B] SDF format, chain L [auth A] SDF format, chain KA [auth B] SDF format, chain K [auth A] SDF format, chain JA [auth B] SDF format, chain J [auth A] SDF format, chain IA [auth B] SDF format, chain HA [auth B] MOL2 format, chain T [auth A] MOL2 format, chain S [auth A] MOL2 format, chain RA [auth B] MOL2 format, chain R [auth A] MOL2 format, chain QA [auth B] MOL2 format, chain Q [auth A] MOL2 format, chain PA [auth B] MOL2 format, chain P [auth A] MOL2 format, chain OA [auth B] MOL2 format, chain O [auth A] MOL2 format, chain NA [auth B] MOL2 format, chain N [auth A] MOL2 format, chain MA [auth B] MOL2 format, chain M [auth A] MOL2 format, chain LA [auth B] MOL2 format, chain L [auth A] MOL2 format, chain KA [auth B] MOL2 format, chain K [auth A] MOL2 format, chain JA [auth B] MOL2 format, chain J [auth A] MOL2 format, chain IA [auth B] MOL2 format, chain HA [auth B] mmCIF format, chain T [auth A] mmCIF format, chain S [auth A] mmCIF format, chain RA [auth B] mmCIF format, chain R [auth A] mmCIF format, chain QA [auth B] mmCIF format, chain Q [auth A] mmCIF format, chain PA [auth B] mmCIF format, chain P [auth A] mmCIF format, chain OA [auth B] mmCIF format, chain O [auth A] mmCIF format, chain NA [auth B] mmCIF format, chain N [auth A] mmCIF format, chain MA [auth B] mmCIF format, chain M [auth A] mmCIF format, chain LA [auth B] mmCIF format, chain L [auth A] mmCIF format, chain KA [auth B] mmCIF format, chain K [auth A] mmCIF format, chain JA [auth B] mmCIF format, chain J [auth A] mmCIF format, chain IA [auth B] mmCIF format, chain HA [auth B]	HA [auth B] IA [auth B] J [auth A] JA [auth B] K [auth A] HA [auth B], IA [auth B], J [auth A], JA [auth B], K [auth A], KA [auth B], L [auth A], LA [auth B], M [auth A], MA [auth B], N [auth A], NA [auth B], O [auth A], OA [auth B], P [auth A], PA [auth B], Q [auth A], QA [auth B], R [auth A], RA [auth B], S [auth A], T [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain HA [auth B] Focus chain IA [auth B] Focus chain J [auth A] Focus chain JA [auth B] Focus chain K [auth A] Focus chain KA [auth B] Focus chain L [auth A] Focus chain LA [auth B] Focus chain M [auth A] Focus chain MA [auth B] Focus chain N [auth A] Focus chain NA [auth B] Focus chain O [auth A] Focus chain OA [auth B] Focus chain P [auth A] Focus chain PA [auth B] Focus chain Q [auth A] Focus chain QA [auth B] Focus chain R [auth A] Focus chain RA [auth B] Focus chain S [auth A] Focus chain T [auth A] Interactions & Density Focus chain HA [auth B] Focus chain IA [auth B] Focus chain J [auth A] Focus chain JA [auth B] Focus chain K [auth A] Focus chain KA [auth B] Focus chain L [auth A] Focus chain LA [auth B] Focus chain M [auth A] Focus chain MA [auth B] Focus chain N [auth A] Focus chain NA [auth B] Focus chain O [auth A] Focus chain OA [auth B] Focus chain P [auth A] Focus chain PA [auth B] Focus chain Q [auth A] Focus chain QA [auth B] Focus chain R [auth A] Focus chain RA [auth B] Focus chain S [auth A] Focus chain T [auth A]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain GA [auth B] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain GA [auth B] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain GA [auth B]	GA [auth B], H [auth A], I [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain GA [auth B] Focus chain H [auth A] Focus chain I [auth A] Interactions & Density Focus chain GA [auth B] Focus chain H [auth A] Focus chain I [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.57 Å
R-Value Free: 0.190 (Depositor), 0.190 (DCC)
R-Value Work: 0.150 (Depositor), 0.151 (DCC)
R-Value Observed: 0.152 (Depositor)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 164.178	α = 90
b = 164.178	β = 90
c = 57.742	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
DIALS	data reduction
DIALS	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2020-04-01

Deposition Author(s):

Funding Organization	Location	Grant Number
The Francis Crick Institute	United Kingdom	See list below
Cancer Research UK	United Kingdom	FC001060
Medical Research Council (MRC, United Kingdom)	United Kingdom	FC001060
Wellcome Trust	United Kingdom	FC001060
Wellcome Trust	United Kingdom	104785/B/14/Z

Revision History (Full details and data files)

Version 1.0: 2020-04-01
Type: Initial release
Version 1.1: 2020-06-03
Changes: Database references
Version 1.2: 2024-01-24
Changes: Data collection, Database references, Derived calculations, Refinement description