6QK4 | pdb_00006qk4

Lytic transglycosylase, LtgG, of Burkholderia pseudomallei.

• PDB DOI: https://doi.org/10.2210/pdb6QK4/pdb

• Classification: LYASE
• Organism(s): Burkholderia pseudomallei
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-01-28 Released: 2019-08-14 
• Deposition Author(s): Jenkins, C.H., Wallis, R., Allcock, N., Barnes, K.B., Richards, M.I., Auty, J.M., Galyov, E.E., Harding, S.V., Mukamolova, G.V.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.73 Å
• R-Value Free: 
  0.209 (Depositor), 0.214 (DCC) 
• R-Value Work: 
  0.176 (Depositor), 0.184 (DCC) 
• R-Value Observed: 
  0.178 (Depositor) 

Starting Models: experimental

Literature

The lytic transglycosylase, LtgG, controls cell morphology and virulence in Burkholderia pseudomallei.

Jenkins, C.H., Wallis, R., Allcock, N., Barnes, K.B., Richards, M.I., Auty, J.M., Galyov, E.E., Harding, S.V., Mukamolova, G.V.

(2019) Sci Rep 9: 11060-11060

• PubMed: 31363151 
• DOI: https://doi.org/10.1038/s41598-019-47483-z
• Primary Citation Related Structures: 
  6QK4


• PubMed Abstract: 
  

  Burkholderia pseudomallei is the causative agent of the tropical disease melioidosis. Its genome encodes an arsenal of virulence factors that allow it, when required, to switch from a soil dwelling bacterium to a deadly intracellular pathogen. With a high intrinsic resistance to antibiotics and the ability to overcome challenges from the host immune system, there is an increasing requirement for new antibiotics and a greater understanding into the molecular mechanisms of B. pseudomallei virulence and dormancy. The peptidoglycan remodeling enzymes, lytic transglycosylases (Ltgs) are potential targets for such new antibiotics. Ltgs cleave the glycosidic bonds within bacterial peptidoglycan allowing for the insertion of peptidoglycan precursors during cell growth and division, and cell membrane spanning structures such as flagella and secretion systems. Using bioinformatic analysis we have identified 8 putative Ltgs in B. pseudomallei K96243. We aimed to investigate one of these Ltgs, LtgG (BPSL3046) through the generation of deletion mutants and biochemical analysis. We have shown that LtgG is a key contributor to cellular morphology, division, motility and virulence in BALB/c mice. We have determined the crystal structure of LtgG and have identified various amino acids likely to be important in peptidoglycan binding and catalytic activity. Recombinant protein assays and complementation studies using LtgG containing a site directed mutation in aspartate 343, confirmed the essentiality of this amino acid in the function of LtgG.

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Organizational Affiliation: 
• Department of Infection, Immunity and Inflammation, University of Leicester, Leicester, UK. [e-mail].
Defence Science and Technology Laboratory, Chemical, Biological and Radiological Division, Porton Down, Salisbury, Wiltshire, UK. [e-mail].
Department of Infection, Immunity and Inflammation, University of Leicester, Leicester, UK.
The Leicester Institute of Structural and Chemical Biology, Henry Wellcome Building, University of Leicester, Leicester, UK.
Electron Microscopy Facility, Core Biotechnology Services, University of Leicester, Leicester, UK.
Defence Science and Technology Laboratory, Chemical, Biological and Radiological Division, Porton Down, Salisbury, Wiltshire, UK.
Department of Respiratory Sciences, University of Leicester, Leicester, UK.
Department of Genetics and Genome Biology, University of Leicester, Leicester, UK.
Department of Infection, Immunity and Inflammation, University of Leicester, Leicester, UK. [e-mail].
Department of Respiratory Sciences, University of Leicester, Leicester, UK. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 37.68 kDa 
• Atom Count: 2,771 
• Modeled Residue Count: 331 
• Deposited Residue Count: 348 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Membrane-bound lytic murein transglycosylase A	A [auth B]	348	Burkholderia pseudomallei	Mutation(s): 0  Gene Names: mltA, CXQ84_03095, DP49_5753, ERS013345_03240 EC: 4.2.2
UniProt
Find proteins for Q63QH7 (Burkholderia pseudomallei (strain K96243)) Explore Q63QH7  Go to UniProtKB:  Q63QH7

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.73 Å
• R-Value Free:  0.209 (Depositor), 0.214 (DCC) 
• R-Value Work:  0.176 (Depositor), 0.184 (DCC) 
• R-Value Observed: 0.178 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.57	α = 90
b = 59.57	β = 90
c = 168.28	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-08-14 
Deposition Author(s): Jenkins, C.H., Wallis, R., Allcock, N., Barnes, K.B., Richards, M.I., Auty, J.M., Galyov, E.E., Harding, S.V., Mukamolova, G.V.

Revision History  

• Version 1.0: 2019-08-14
  Type: Initial release
  
• Version 1.1: 2024-01-24
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-11-20
  Changes: Structure summary