Biological Assembly 1  

 3D View: Structure | Electron Density | Validation Report

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 1 generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 55.53 kDa 
• Atom Count: 3246 
• Modelled Residue Count: 413 
• Deposited Residue Count: 478 
• Unique protein chains: 2

6NKL

2.2 A resolution structure of VapBC-1 from nontypeable Haemophilus influenzae

• DOI: 10.2210/pdb6NKL/pdb

• Classification: ANTITOXIN
• Organism(s): Haemophilus influenzae
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2019-01-07 Released: 2019-04-10 
• Deposition Author(s): Lovell, S., Kashipathy, M.M., Battaile, K.P., Molinaro, A.L., Daines, D.A.
• Funding Organization(s): National Institutes of Health/National Institute on Deafness and Other Communication Disorders (NIH/NIDCD), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.234 
• R-Value Work: 0.186 
• R-Value Observed: 0.189 

Literature

Crystal Structure of VapBC-1 from Nontypeable Haemophilus influenzae and the Effect of PIN Domain Mutations on Survival during Infection.

Molinaro, A.L., Kashipathy, M.M., Lovell, S., Battaile, K.P., Coussens, N.P., Shen, M., Daines, D.A.

(2019) J Bacteriol 201

• PubMed: 30936373 
• DOI: 10.1128/JB.00026-19
• Primary Citation of Related Structures:  
  6NKL


• PubMed Abstract: 
  

Toxin-antitoxin (TA) gene pairs have been identified in nearly all bacterial genomes sequenced to date and are thought to facilitate persistence and antibiotic tolerance. TA loci are classified into various types based upon the characteristics of their antitoxins, with those in type II expressing proteic antitoxins. Many toxins from type II modules are ribonucleases that maintain a PilT N-terminal (PIN) domain containing conserved amino acids considered essential for activity. The vapBC ( v irulence- a ssociated p rotein) TA system is the largest subfamily in this class and has been linked to pathogenesis of nontypeable Haemophilus influenzae (NTHi). In this study, the crystal structure of the VapBC-1 complex from NTHi was determined to 2.20 Å resolution. Based on this structure, aspartate-to-asparagine and glutamate-to-glutamine mutations of four conserved residues in the PIN domain of the VapC-1 toxin were constructed and the effects of the mutations on protein-protein interactions, growth of Escherichia coli , and pathogenesis ex vivo were tested. Finally, a novel model system was designed and utilized that consists of an NTHi Δ vapBC-1 strain complemented in cis with the TA module containing a mutated or wild-type toxin at an ectopic site on the chromosome. This enabled the analysis of the effect of PIN domain toxin mutants in tandem with their wild-type antitoxin under the control of the vapBC-1 native promoter and in single copy. This is the first report of a system facilitating the study of TA mutant operons in the background of NTHi during infections of primary human tissues ex vivo IMPORTANCE Herein the crystal structure of the VapBC-1 complex from nontypeable Haemophilus influenzae (NTHi) is described. Our results show that some of the mutations in the PIN domain of the VapC-1 toxin were associated with decreased toxicity in E. coli , but the mutants retained the ability to homodimerize and to heterodimerize with the wild-type cognate antitoxin, VapB-1. A new system was designed and constructed to quantify the effects of these mutations on NTHi survival during infections of primary human tissues ex vivo Any mutation to a conserved amino acid in the PIN domain significantly decreased the number of survivors compared to that of the in cis wild-type toxin under the same conditions.

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Organizational Affiliation: 

Office of the Dean, College of Sciences, Old Dominion University, Norfolk, Virginia, USA [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribonuclease VapC	A, B	143	Haemophilus influenzae	Mutation(s): 0  Gene Names: vapC1, vapC, BV136_01367, BVZ80_01200, CH628_04345, NCTC11872_02278 EC: 3.1
UniProt
Find proteins for Q57122 (Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd)) Explore Q57122  Go to UniProtKB:  Q57122

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Antitoxin VapB1	C, D	96	Haemophilus influenzae	Mutation(s): 0  Gene Names: vapB1, BV136_01366, BVZ80_01199, CH628_04350
UniProt
Find proteins for Q57534 (Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd)) Explore Q57534  Go to UniProtKB:  Q57534

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.234 
• R-Value Work: 0.186 
• R-Value Observed: 0.189 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.88	α = 90
b = 57.325	β = 90
c = 175.745	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
Aimless	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2019-01-07 
• Released Date: 2019-04-10 
Deposition Author(s): Lovell, S., Kashipathy, M.M., Battaile, K.P., Molinaro, A.L., Daines, D.A.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute on Deafness and Other Communication Disorders (NIH/NIDCD)	United States	U01 DC014756
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	P30 GM110761

Revision History  

• Version 1.0: 2019-04-10
  Type: Initial release
  
• Version 1.1: 2019-06-05
  Changes: Data collection, Database references
• Version 1.2: 2019-12-18
  Changes: Author supporting evidence
• Version 1.3: 2020-05-06
  Changes: Structure summary