6TA9 | pdb_00006ta9

Bd0314 DslA wild-type form 1

• PDB DOI: https://doi.org/10.2210/pdb6TA9/pdb

• Classification: HYDROLASE
• Organism(s): Bdellovibrio bacteriovorus HD100
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-10-29 Released: 2020-07-15 
• Deposition Author(s): Lovering, A.L., Harding, C.J.
• Funding Organization(s): Biotechnology and Biological Sciences Research Council

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.36 Å
• R-Value Free: 
  0.180 (Depositor), 0.187 (DCC) 
• R-Value Work: 
  0.140 (Depositor), 0.151 (DCC) 
• R-Value Observed: 
  0.142 (Depositor) 

Starting Model: other

Literature

A lysozyme with altered substrate specificity facilitates prey cell exit by the periplasmic predator Bdellovibrio bacteriovorus.

Harding, C.J., Huwiler, S.G., Somers, H., Lambert, C., Ray, L.J., Till, R., Taylor, G., Moynihan, P.J., Sockett, R.E., Lovering, A.L.

(2020) Nat Commun 11: 4817-4817

• PubMed: 32968056 
• DOI: https://doi.org/10.1038/s41467-020-18139-8
• Primary Citation Related Structures: 
  6TA9, 6TAB, 6TAD, 6TAF


• PubMed Abstract: 
  

  Lysozymes are among the best-characterized enzymes, acting upon the cell wall substrate peptidoglycan. Here, examining the invasive bacterial periplasmic predator Bdellovibrio bacteriovorus, we report a diversified lysozyme, DslA, which acts, unusually, upon (GlcNAc-) deacetylated peptidoglycan. B. bacteriovorus are known to deacetylate the peptidoglycan of the prey bacterium, generating an important chemical difference between prey and self walls and implying usage of a putative deacetyl-specific "exit enzyme". DslA performs this role, and ΔDslA strains exhibit a delay in leaving from prey. The structure of DslA reveals a modified lysozyme superfamily fold, with several adaptations. Biochemical assays confirm DslA specificity for deacetylated cell wall, and usage of two glutamate residues for catalysis. Exogenous DslA, added ex vivo, is able to prematurely liberate B. bacteriovorus from prey, part-way through the predatory lifecycle. We define a mechanism for specificity that invokes steric selection, and use the resultant motif to identify wider DslA homologues.

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Organizational Affiliation: 
• Institute for Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, B15 2TT, UK.
Medical School, School of Life Sciences, Queen's Medical Centre, University of Nottingham, Nottingham, NG7 2UH, UK.
Medical School, School of Life Sciences, Queen's Medical Centre, University of Nottingham, Nottingham, NG7 2UH, UK. [e-mail].
Institute for Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, B15 2TT, 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: 28.28 kDa 
• Atom Count: 1,673 
• Modeled Residue Count: 182 
• Deposited Residue Count: 254 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SLT domain-containing protein	A	254	Bdellovibrio bacteriovorus HD100	Mutation(s): 0  Gene Names: Bd0314
UniProt
Find proteins for Q6MQY8 (Bdellovibrio bacteriovorus (strain ATCC 15356 / DSM 50701 / NCIMB 9529 / HD100)) Explore Q6MQY8  Go to UniProtKB:  Q6MQY8

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A], C [auth A], D [auth A], E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.36 Å
• R-Value Free:  0.180 (Depositor), 0.187 (DCC) 
• R-Value Work:  0.140 (Depositor), 0.151 (DCC) 
• R-Value Observed: 0.142 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.696	α = 90
b = 47.818	β = 90
c = 49.191	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-07-15 
Deposition Author(s): Lovering, A.L., Harding, C.J.

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Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council	United Kingdom	studentship

Revision History  

• Version 1.0: 2020-07-15
  Type: Initial release
  
• Version 1.1: 2020-10-07
  Changes: Database references, Refinement description
• Version 1.2: 2024-05-01
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2024-11-20
  Changes: Structure summary