1LSP

THE CRYSTAL STRUCTURE OF A BULGECIN-INHIBITED G-TYPE LYSOZYME FROM THE EGG-WHITE OF THE AUSTRALIAN BLACK SWAN. A COMPARISON OF THE BINDING OF BULGECIN TO THREE MURAMIDASES


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structure of a bulgecin-inhibited g-type lysozyme from the egg white of the Australian black swan. A comparison of the binding of bulgecin to three muramidases.

Karlsen, S.Hough, E.Rao, Z.H.Isaacs, N.W.

(1996) Acta Crystallogr.,Sect.D 52: 105-114

  • DOI: 10.1107/S0907444995008468

  • PubMed Abstract: 
  • Bulgecin A, a bacterial metabolite, has been shown to bind in the active-site groove of the chicken-type lysozyme from the rainbow trout (RBTL) and in the lysozyme-like C-terminal domain, of a soluble lytic transglycosylase (C-SLT) from Escherichia c ...

    Bulgecin A, a bacterial metabolite, has been shown to bind in the active-site groove of the chicken-type lysozyme from the rainbow trout (RBTL) and in the lysozyme-like C-terminal domain, of a soluble lytic transglycosylase (C-SLT) from Escherichia coli. These enzymes are muramidases that cleave the glycosidic bonds in the glycan strands of the murein polymer. Here we report the crystal structure of a complex between the goose-type lysozyme from the egg white of the Australian black swan (SEWL) and bulgecin A at 2.45 A resolution. As is the case for the C-SLT/bulgecin and RBTL/bulgecin complexes, the ligand binds with the N-acetylglucosamine ring in subsite C and the proline moiety in site D where it interacts with the catalytic glutamic acid. The taurine residue interacts with the beta-sheet region. Comparisons of the three buigecin complexes show that the inhibitor has the same binding mode to the muramidases with similar protein-ligand interactions, particularly for SEWL and RBTL. From our results, it seems likely that bulgecin, in general, inhibits enzymes with lysozyme-like domains and thus might represent a novel class of natural antibiotics that act on murein-degrading rather than murein-synthesizing enzymes.


    Related Citations: 
    • Three-Dimensional Structure of Goose-Type Lysozyme from the Egg White of the Australian Black Swan, Cygnus Atratus
      Isaacs, N.W.,Machin, K.J.,Masakuni, M.
      (1985) Aust.J.Biol.Sci. 38: 12
    • The Crystal Structure of a Complex between Bulgecin, a Bacterial Metabolite, and Lysozyme from the Rainbow Trout
      Karlsen, S.,Hough, E.
      () TO BE PUBLISHED --: --
    • Structures of Bulgecins, Bacterial Metabolites with Bulge-Inducing Activity
      Shinagawa, S.,Kasahara, F.,Wada, Y.,Harada, S.,Asai, M.
      (1984) Tetrahedron 40: 3465


    Organizational Affiliation

    Protein Crystallography Group, Institute of Mathematical and Physical Science, University of Tromsø, Norway.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
LYSOZYME
A
185Cygnus atratusEC: 3.2.1.17
Find proteins for P00717 (Cygnus atratus)
Go to UniProtKB:  P00717
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BUL
Query on BUL

Download SDF File 
Download CCD File 
A
BULGECIN A
C16 H29 N3 O14 S2
RPNZWZDLNYCCIG-HMMVDTEZSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 91.690α = 90.00
b = 65.330β = 90.00
c = 38.150γ = 90.00
Software Package:
Software NamePurpose
PROLSQrefinement
XDSdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1996-01-01
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2014-03-19
    Type: Other