6H8N

Structure of peptidoglycan deacetylase PdaC from Bacillus subtilis - mutant D285S


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.26 Å
  • R-Value Free: 0.174 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.161 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure-function relationships underlying the dualN-acetylmuramic andN-acetylglucosamine specificities of the bacterial peptidoglycan deacetylase PdaC.

Grifoll-Romero, L.Sainz-Polo, M.A.Albesa-Jove, D.Guerin, M.E.Biarnes, X.Planas, A.

(2019) J Biol Chem 294: 19066-19080

  • DOI: https://doi.org/10.1074/jbc.RA119.009510
  • Primary Citation of Related Structures:  
    6H8L, 6H8N

  • PubMed Abstract: 
  • Bacillus subtilis PdaC ( Bs PdaC) is a membrane-bound, multidomain peptidoglycan N- deacetylase acting on N -acetylmuramic acid (MurNAc) residues and conferring lysozyme resistance to modified cell wall peptidoglycans. Bs PdaC contains a C-terminal family 4 carbohydrate esterase (CE4) catalytic domain, but unlike other MurNAc deacetylases, Bs PdaC also has GlcNAc deacetylase activity on chitooligosaccharides (COSs), characteristic of chitin deacetylases ...

    Bacillus subtilis PdaC ( Bs PdaC) is a membrane-bound, multidomain peptidoglycan N- deacetylase acting on N -acetylmuramic acid (MurNAc) residues and conferring lysozyme resistance to modified cell wall peptidoglycans. Bs PdaC contains a C-terminal family 4 carbohydrate esterase (CE4) catalytic domain, but unlike other MurNAc deacetylases, Bs PdaC also has GlcNAc deacetylase activity on chitooligosaccharides (COSs), characteristic of chitin deacetylases. To uncover the molecular basis of this dual activity, here we determined the X-ray structure of the Bs PdaC CE4 domain at 1.54 Å resolution and analyzed its mode of action on COS substrates. We found that the minimal substrate is GlcNAc 3 and that activity increases with the degree of glycan polymerization. COS deacetylation kinetics revealed that Bs PdaC operates by a multiple-chain mechanism starting at the internal GlcNAc units and leading to deacetylation of all but the reducing-end GlcNAc residues. Interestingly, Bs PdaC shares higher sequence similarity with the peptidoglycan GlcNAc deacetylase Sp PgdaA than with other MurNAc deacetylases. Therefore, we used ligand-docking simulations to analyze the dual GlcNAc- and MurNAc-binding specificities of Bs PdaC and compared them with those of Sp PgdA and Bs PdaA, representing peptidoglycan deacetylases highly specific for GlcNAc or MurNAc residues, respectively. Bs PdaC retains the conserved Asp-His-His metal-binding triad characteristic of CE4 enzymes acting on GlcNAc residues, differing from MurNAc deacetylases that lack the metal-coordinating Asp residue. Bs PdaC contains short loops similar to those in Sp PgdA, resulting in an open binding cleft that can accommodate polymeric substrates. We propose that PdaC is the first member of a new subclass of peptidoglycan MurNAc deacetylases.


    Organizational Affiliation

    Laboratory of Biochemistry, Institut Químic de Sarrià, University Ramon Llull, 08017 Barcelona, Spain antoni.planas@iqs.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Peptidoglycan-N-acetylmuramic acid deacetylase PdaC
A, B
212Bacillus subtilis subsp. subtilis str. 168Mutation(s): 1 
Gene Names: pdaCyjeABSU12100
EC: 3.5.1
UniProt
Find proteins for O34798 (Bacillus subtilis (strain 168))
Explore O34798 
Go to UniProtKB:  O34798
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO34798
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.26 Å
  • R-Value Free: 0.174 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.161 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.42α = 90
b = 61.8β = 90
c = 130.99γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data reduction
xia2data scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-11-13
    Type: Initial release
  • Version 1.1: 2020-03-25
    Changes: Database references
  • Version 1.2: 2020-04-01
    Changes: Database references