2WAG

The Structure of a family 25 Glycosyl hydrolase from Bacillus anthracis.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.187 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

The Crystal Structure of a Family Gh25 Lysozyme from Bacillus Anthracis Implies a Neighboring-Group Catalytic Mechanism with Retention of Anomeric Configuration

Martinez-Fleites, C.Korczynska, J.E.Cope, M.Turkenburg, J.P.Taylor, E.J.

(2009) Carbohydr.Res. 344: 1753

  • DOI: 10.1016/j.carres.2009.06.001

  • PubMed Abstract: 
  • Lysozymes are found in many of the sequence-based families of glycoside hydrolases (www.cazy.org) where they show considerable structural and mechanistic diversity. Lysozymes from glycoside hydrolase family GH25 adopt a (alpha/beta)(5)(beta)(3)-barre ...

    Lysozymes are found in many of the sequence-based families of glycoside hydrolases (www.cazy.org) where they show considerable structural and mechanistic diversity. Lysozymes from glycoside hydrolase family GH25 adopt a (alpha/beta)(5)(beta)(3)-barrel-like fold with a proposal in the literature that these enzymes act with inversion of anomeric configuration; the lack of a suitable substrate, however, means that no group has successfully demonstrated the configuration of the product. Here we report the 3-D structure of the GH25 enzyme from Bacillus anthracis at 1.4A resolution. We show that the active center is extremely similar to those from glycoside hydrolase families GH18, GH20, GH56, GH84, and GH85 implying that, in the absence of evidence to the contrary, GH25 enzymes also act with net retention of anomeric configuration using the neighboring-group catalytic mechanism that is common to this 'super-family' of enzymes.


    Organizational Affiliation

    Structural Biology Laboratory, Department of Chemistry, The University of York, YO10 5YW, United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
LYSOZYME, PUTATIVE
A
220Bacillus anthracisMutation(s): 0 
Find proteins for A0A0F7RB29 (Bacillus anthracis)
Go to UniProtKB:  A0A0F7RB29
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
15P
Query on 15P

Download SDF File 
Download CCD File 
A
POLYETHYLENE GLYCOL (N=34)
PEG 1500
C69 H140 O35
VUYXVWGKCKTUMF-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.187 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 100.522α = 90.00
b = 100.521β = 90.00
c = 106.720γ = 120.00
Software Package:
Software NamePurpose
AMoREphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-06-23
    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: 2019-10-16
    Type: Advisory, Data collection, Experimental preparation, Other