2WTZ | pdb_00002wtz

MurE ligase of Mycobacterium Tuberculosis

PDB DOI: https://doi.org/10.2210/pdb2WTZ/pdb

Classification: LIGASE
Organism(s): Mycobacterium tuberculosis H37Rv
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2009-09-25 Released: 2009-12-15
Deposition Author(s): Basavannacharya, C., Robertson, G., Munshi, T., Keep, N.H., Bhakta, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free:
0.251 (Depositor), 0.248 (DCC)
R-Value Work:
0.193 (Depositor), 0.196 (DCC)
R-Value Observed:
0.195 (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

ATP-Dependent Mure Ligase in Mycobacterium Tuberculosis: Biochemical and Structural Characterisation.

Basavannacharya, C., Robertson, G., Munshi, T., Keep, N.H., Bhakta, S.

(2010) Tuberculosis (Edinb) 90: 16

PubMed: 19945347 Search on PubMed
DOI: https://doi.org/10.1016/j.tube.2009.10.007
Primary Citation Related Structures:
2WTZ

PubMed Abstract:
New therapies are required against Mycobacterium tuberculosis and its cell wall peptidoglycan biosynthesis is a potential therapeutic target. UDP-MurNAc-tripeptide ligase (MurE) is a member of the ATP-dependent ligase family, which incorporate amino acids including meso-diaminopimelic acid (m-DAP) into peptidoglycan during synthesis in a species-specific manner. In the present study, we have cloned, over-expressed, and characterised MurE from M. tuberculosis (Mtb-MurE). The crystal structure has been determined at 3.0A resolution in the presence of the substrate UDP-MurNAc-l-Ala-d-Glu (UAG). The activity of the enzyme was measured through estimating inorganic phosphate released in a non-radioactive high-throughput colourimetric assay. UDP-MurNAc-l-Ala-d-Glu-m-DAP (UMT) formation coupled to inorganic phosphate release was confirmed by HPLC and mass spectrometric analyses. Kinetic constants were determined for a range of natural substrates using optimised conditions. From our findings, it is evident that Mtb-MurE is highly specific in adding m-DAP to UDP-MurNAc-dipeptide and ATP-hydrolysis is an absolute requirement for its activity.

Organizational Affiliation

Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London, Malet Street, London WC1E 7HX, UK.

Macromolecule Content

Total Structure Weight: 225.43 kDa
Atom Count: 14,008
Modeled Residue Count: 1,919
Deposited Residue Count: 2,140
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UDP-N-ACETYLMURAMOYL-L-ALANYL-D-GLUTAMATE--2,6-DIAMINOPIMELATE LIGASE	A, B, C, D	535	Mycobacterium tuberculosis H37Rv	Mutation(s): 0 EC: 6.3.2.13
UniProt
Find proteins for P9WJL3 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WJL3 Go to UniProtKB: P9WJL3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P9WJL3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
UAG Query on UAG Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth B] SDF format, chain I [auth C] SDF format, chain K [auth D] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain I [auth C] MOL2 format, chain K [auth D] mmCIF format, chain E [auth A] mmCIF format, chain G [auth B] mmCIF format, chain I [auth C] mmCIF format, chain K [auth D]	E [auth A], G [auth B], I [auth C], K [auth D]	URIDINE-5'-DIPHOSPHATE-N-ACETYLMURAMOYL-L-ALANINE-D-GLUTAMATE C₂₈ H₄₃ N₅ O₂₃ P₂ OJZCATPXPWFLHF-HPUCEMLMSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain J [auth C] SDF format, chain L [auth D] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain J [auth C] MOL2 format, chain L [auth D] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain J [auth C] mmCIF format, chain L [auth D]	F [auth A], H [auth B], J [auth C], L [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
KCX Query on KCX	A, B, C, D	L-PEPTIDE LINKING	C₇ H₁₄ N₂ O₄		LYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free: 0.251 (Depositor), 0.248 (DCC)
R-Value Work: 0.193 (Depositor), 0.196 (DCC)
R-Value Observed: 0.195 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.92	α = 111.09
b = 79.8	β = 92.16
c = 82.92	γ = 93.98

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
MrBUMP	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2009-12-15

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2009-12-15
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2023-12-20
Changes: Data collection, Database references, Derived calculations, Other, Refinement description