Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 36672.29 
• Atom Count: 2571 
• Residue Count: 322 
• Unique protein chains: 1

1D0L

THE ESCHERICHIA COLI LYTIC TRANSGLYCOSYLASE SLT35 IN COMPLEX WITH BULGECIN A

• DOI: 10.2210/pdb1D0L/pdb

• Classification: TRANSFERASE
• Organism(s): Escherichia coli (strain K12)
• Expression System: Escherichia coli
• Mutation(s): 2 


• Deposited: 1999-09-12 Released: 2000-03-06 
• Deposition Author(s): van Asselt, E.J., Kalk, K.H., Dijkstra, B.W.

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Experimental Data Snapshot

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

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

• PubMed: 10684641 
• Primary Citation of Related Structures:  
  1D0M, 1D0K


• 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. 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.

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Organizational Affiliation: 

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

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
35KD SOLUBLE LYTIC TRANSGLYCOSYLASE	A	322	Escherichia coli (strain K12)	Mutation(s): 2  Gene Names: mltB EC: 4.2.2.n1
Find proteins for P41052 (Escherichia coli (strain K12)) Go to UniProtKB:  P41052

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
CA	A	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
BLG	A	4-O-(4-O-SULFONYL-N-ACETYLGLUCOSAMININYL)-5-METHYLHYDROXY-L-PROLINE-TAURINE BULGECIN A C16 H30 N3 O14 S2 RPNZWZDLNYCCIG-HMMVDTEZSA-O

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.97 Å
• R-Value Free: 0.200 
• R-Value Work: 0.168 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 58.395	α = 90.00
b = 67.785	β = 90.00
c = 97.735	γ = 90.00

Software Package:

Software Name	Purpose
X-PLOR	model building
DENZO	data reduction
X-PLOR	phasing
SCALEPACK	data scaling
X-PLOR	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1999-09-12 
• Released Date: 2000-03-06 
• Deposition Author(s): van Asselt, E.J., Kalk, K.H., Dijkstra, B.W.

Revision History 

• Version 1.0: 2000-03-06
  Type: Initial release
• Version 1.1: 2008-04-27
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance