1D0L

THE ESCHERICHIA COLI LYTIC TRANSGLYCOSYLASE SLT35 IN COMPLEX WITH BULGECIN A

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.170 

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This is version 1.3 of the entry. See complete history. 


Literature

Crystallographic studies of the interactions of Escherichia coli lytic transglycosylase Slt35 with peptidoglycan.

van Asselt, E.J., Kalk, K.H., Dijkstra, B.W.

(2000) Biochemistry 39: 1924-1934

  • DOI: 10.1021/bi992161p
  • Primary Citation of Related Structures:  
    1D0K, 1D0L, 1D0M

  • PubMed Abstract: 

    • Lytic transglycosylases catalyze the cleavage of the beta-1, 4-glycosidic bond between N-acetylmuramic acid (MurNAc) and N-acetylglucosamine (GlcNAc) in peptidoglycan with concomitant formation of a 1,6-anhydro bond in the MurNAc residue. To understand the reaction mechanism of Escherichia coli lytic transglycosylase Slt35, three crystal structures have been determined of Slt35 in complex with two different peptidoglycan fragments and with the lytic transglycosylase inhibitor bulgecin A ...

    Lytic transglycosylases catalyze the cleavage of the beta-1, 4-glycosidic bond between N-acetylmuramic acid (MurNAc) and N-acetylglucosamine (GlcNAc) in peptidoglycan with concomitant formation of a 1,6-anhydro bond in the MurNAc residue. To understand the reaction mechanism of Escherichia coli lytic transglycosylase Slt35, three crystal structures have been determined of Slt35 in complex with two different peptidoglycan fragments and with the lytic transglycosylase inhibitor bulgecin A. The complexes define four sugar-binding subsites (-2, -1, +1, and +2) and two peptide-binding sites in a large cleft close to Glu162. The Glu162 side chain is between the -1 and +1 sugar-binding sites, in agreement with a function as catalytic acid/base. The complexes suggest additional contributions to catalysis from Ser216 and Asn339, residues which are conserved among the MltB/Slt35 lytic transglycosylases.

    Organizational Affiliation: 

    BIOSON Research Institute, Laboratory of Biophysical Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
35KD SOLUBLE LYTIC TRANSGLYCOSYLASEA322Escherichia coliMutation(s): 2 
EC: 4.2.2
UniProt
Find proteins for P41052 (Escherichia coli (strain K12))
Explore P41052 
Go to UniProtKB:  P41052
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP41052
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BLG
Query on BLG
Download Ideal Coordinates CCD File 
C [auth A]4-O-(4-O-SULFONYL-N-ACETYLGLUCOSAMININYL)-5-METHYLHYDROXY-L-PROLINE-TAURINE
C16 H30 N3 O14 S2
RPNZWZDLNYCCIG-HMMVDTEZSA-O		 Ligand Interaction
CA
Query on CA
Download Ideal Coordinates CCD File 
B [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.170 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.395α = 90
b = 67.785β = 90
c = 97.735γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-03-06
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2021-11-03
    Changes: Data collection, Database references, Derived calculations