1SLY

COMPLEX OF THE 70-KDA SOLUBLE LYTIC TRANSGLYCOSYLASE WITH BULGECIN A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.185 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure of the 70-kDa soluble lytic transglycosylase complexed with bulgecin A. Implications for the enzymatic mechanism.

Thunnissen, A.M.Rozeboom, H.J.Kalk, K.H.Dijkstra, B.W.

(1995) Biochemistry 34: 12729-12737

  • DOI: 10.1021/bi00039a032
  • Primary Citation of Related Structures:  
    1SLY

  • PubMed Abstract: 
  • Bulgecins are O-sulfonated glycopeptides that are able to enhance the antibacterial activity of beta-lactam antibiotics. The 70-kDa soluble lytic transglycosylase (SLT70) from Escherichia coli forms a specific target of these compounds. Using X-ray crystallography, the three-dimensional structure of a complex of SLT70 with bulgecin A has been determined to 2 ...

    Bulgecins are O-sulfonated glycopeptides that are able to enhance the antibacterial activity of beta-lactam antibiotics. The 70-kDa soluble lytic transglycosylase (SLT70) from Escherichia coli forms a specific target of these compounds. Using X-ray crystallography, the three-dimensional structure of a complex of SLT70 with bulgecin A has been determined to 2.8-A resolution and refined to an R factor of 19.5%. The model contains all 618 amino acids of SLT70 and a single molecule of bound bulgecin, located in the active site of the enzyme. The glycopeptide inhibitor is bound in an extended conformation occupying sites analogous to the B, C, and D subsites of lysozyme. Upon binding of bulgecin, the three-stranded antiparallel beta-sheet in the C domain shows a pronounced shift toward the inhibitor. In subsite D, the proposed catalytic residue Glu478 forms a hydrogen bond to the hydroxymethyl oxygen of the proline part of bulgecin and interacts electrostatically with the proline NH2+ group. These interactions, in addition to the interactions observed for the 2-acetamido group of the N-acetylglucosamine residue bound in subsite C, may explain the strong inhibition of SLT70 activity by bulgecin, suggesting that bulgecin acts as an analogue of an oxocarbonium ion intermediate in the reaction catalyzed by SLT70. The structure of the SLT70--bulgecin A complex may be of assistance in the rational design of novel antibiotics.


    Related Citations: 
    • The Catalytic Domain of a Bacterial Lytic Transglycosylase Defines a Novel Class of Lysozymes
      Thunnissen, A.M., Isaacs, N.W., Dijkstra, B.W.
      (1995) Proteins 22: 245
    • 'Holy' Proteins. II: The Soluble Lytic Transglycosylase
      Dijkstra, B.W., Thunnissen, A.M.
      (1994) Curr Opin Struct Biol 4: 810
    • Doughnut-Shaped Structure of a Bacterial Muramidase Revealed by X-Ray Crystallography
      Thunnissen, A.M., Dijkstra, A.J., Kalk, K.H., Rozeboom, H.J., Engel, H., Keck, W., Dijkstra, B.W.
      (1994) Nature 367: 750

    Organizational Affiliation

    Laboratory of Biophysical Chemistry, University of Groningen, The Netherlands.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
70-KDA SOLUBLE LYTIC TRANSGLYCOSYLASEA618Escherichia coliMutation(s): 0 
EC: 3.2.1 (PDB Primary Data), 4.2.2 (UniProt)
UniProt
Find proteins for P0AGC3 (Escherichia coli (strain K12))
Explore P0AGC3 
Go to UniProtKB:  P0AGC3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0AGC3
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BLG
Query on BLG

Download Ideal Coordinates CCD File 
B [auth A]4-O-(4-O-SULFONYL-N-ACETYLGLUCOSAMININYL)-5-METHYLHYDROXY-L-PROLINE-TAURINE
C16 H30 N3 O14 S2
RPNZWZDLNYCCIG-HMMVDTEZSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.185 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.31α = 90
b = 88.47β = 90
c = 133.06γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
KBRANIdata reduction
X-PLORmodel building
X-PLORrefinement
BIOMOLdata scaling
X-PLORphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1996-08-17
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance