1W17

Structure of Bacillus subtilis PdaA, a family 4 Carbohydrate esterase.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.201 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structures of Bacillus subtilis PdaA, a family 4 carbohydrate esterase, and a complex with N-acetyl-glucosamine.

Blair, D.E.van Aalten, D.M.

(2004) FEBS Lett. 570: 13-19

  • DOI: 10.1016/j.febslet.2004.06.013
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Family 4 carbohydrate esterases deacetylate polymeric carbohydrate substrates such as chitin, acetyl xylan and peptidoglycan. Although some of these enzymes have recently been enzymologically characterised, neither their structure nor their reaction ...

    Family 4 carbohydrate esterases deacetylate polymeric carbohydrate substrates such as chitin, acetyl xylan and peptidoglycan. Although some of these enzymes have recently been enzymologically characterised, neither their structure nor their reaction mechanism has been defined. Sequence conservation in this family has pointed to a conserved core, termed the NodB homology domain. We describe the cloning, purification and 1.9 A crystal structure of PdaA, a peptidoglycan deacetylase from Bacillus subtilis. The enzyme assumes a fold related to a (beta/alpha)8 barrel, with a long groove on the surface of the protein that harbours all conserved residues. A complex with the substrate analogue N-acetyl-glucosamine was refined to 2.25 A resolution, revealing interactions of an aspartic acid and three histidines, all conserved in the NodB homology domain, with the ligand. The PdaA structure provides a template for interpreting the wealth of sequence data on family 4 carbohydrate esterases in a structural context and represents a first step towards understanding the reaction mechanism of this family of enzymes.


    Organizational Affiliation

    Division of Biological Chemistry and Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROBABLE POLYSACCHARIDE DEACETYLASE PDAA
A, B
263Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: pdaA (yfjS)
EC: 3.5.1.-
Find proteins for O34928 (Bacillus subtilis (strain 168))
Go to UniProtKB:  O34928
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.201 
  • Space Group: P 65
Unit Cell:
Length (Å)Angle (°)
a = 88.115α = 90.00
b = 88.115β = 90.00
c = 120.957γ = 120.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
CNSrefinement
DENZOdata reduction
MLPHAREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-01-10
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2018-02-28
    Type: Advisory, Database references, Source and taxonomy, Structure summary