4B6G

The Crystal Structure of the Neisserial Esterase D.

• PDB DOI: https://doi.org/10.2210/pdb4B6G/pdb

• Classification: HYDROLASE
• Organism(s): Neisseria meningitidis MC58
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-08-13 Released: 2012-11-14 
• Deposition Author(s): Counago, R.M., Kobe, B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 0.154 
• R-Value Work: 0.143 
• R-Value Observed: 0.143 

Literature

A glutathione-dependent detoxification system is required for formaldehyde resistance and optimal survival of Neisseria meningitidis in biofilms.

Chen, N.H., Counago, R.M., Djoko, K.Y., Jennings, M.P., Apicella, M.A., Kobe, B., McEwan, A.G.

(2013) Antioxid Redox Signal 18: 743-755

• PubMed: 22937752 
• DOI: https://doi.org/10.1089/ars.2012.4749
• Primary Citation of Related Structures:  
  4B6G


• PubMed Abstract: 
  

  The glutathione-dependent AdhC-EstD formaldehyde detoxification system is found in eukaryotes and prokaryotes. It is established that it confers protection against formaldehyde that is produced from environmental sources or methanol metabolism. Thus, its presence in the human host-adapted bacterial pathogen Neisseria meningitidis is intriguing. This work defined the biological function of this system in the meningococcus using phenotypic analyses of mutants linked to biochemical and structural characterization of purified enzymes.

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Organizational Affiliation: 

Australian Centre for Infectious Disease Research, School of Chemistry and Molecular Biosciences, Faculty of Science, The University of Queensland, St. Lucia, Australia.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 64.78 kDa 
• Atom Count: 5,246 
• Modelled Residue Count: 558 
• Deposited Residue Count: 566 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PUTATIVE ESTERASE	A, B	283	Neisseria meningitidis MC58	Mutation(s): 0  EC: 3.1.2.12
UniProt
Find proteins for Q9JZ43 (Neisseria meningitidis serogroup B (strain MC58)) Explore Q9JZ43  Go to UniProtKB:  Q9JZ43

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 0.154 
• R-Value Work: 0.143 
• R-Value Observed: 0.143 
• Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 111.268	α = 90
b = 111.268	β = 90
c = 169.861	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-11-14 
Deposition Author(s): Counago, R.M., Kobe, B.

Revision History  

• Version 1.0: 2012-11-14
  Type: Initial release
  
• Version 1.1: 2013-02-13
  Changes: Database references
• Version 1.2: 2018-03-28
  Changes: Database references
• Version 1.3: 2023-12-20
  Changes: Data collection, Database references, Other, Refinement description