6NKL

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

PDB DOI: https://doi.org/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)

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

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

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 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/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.

Organizational Affiliation:

Office of the Dean, College of Sciences, Old Dominion University, Norfolk, Virginia, USA ddaines@odu.edu.

Macromolecules

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(by identity cutoff) | 3D Structure

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 Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q57122
Protein Feature View Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q57534
Protein Feature View Expand
Reference Sequence

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

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Entry History & Funding Information

Deposition Data

Released Date: 2019-04-10

Deposition Author(s):

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