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
  • R-Value Observed: 0.175 

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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 D Biol Crystallogr 52: 105-114

  • DOI: 10.1107/S0907444995008468
  • Primary Citation of Related Structures:  
    1LSP

  • 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 coli. These enzymes are muramidases that cleave the glycosidic bonds in the glycan strands of the murein polymer ...

    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: 
    • The Crystal Structure of a Complex between Bulgecin, a Bacterial Metabolite, and Lysozyme from the Rainbow Trout
      Karlsen, S., Hough, E.
      () To be published --: --
    • 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
    • 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
LYSOZYMEA185Cygnus atratusMutation(s): 0 
EC: 3.2.1.17
UniProt
Find proteins for P00717 (Cygnus atratus)
Explore P00717 
Go to UniProtKB:  P00717
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00717
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BUL
Query on BUL

Download Ideal Coordinates CCD File 
B [auth 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
  • R-Value Observed: 0.175 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.69α = 90
b = 65.33β = 90
c = 38.15γ = 90
Software Package:
Software NamePurpose
XDSdata scaling
PROLSQrefinement
XDSdata reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

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