1QSA

CRYSTAL STRUCTURE OF THE 70 KDA SOLUBLE LYTIC TRANSGLYCOSYLASE SLT70 FROM ESCHERICHIA COLI AT 1.65 ANGSTROMS RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.168 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

High resolution crystal structures of the Escherichia coli lytic transglycosylase Slt70 and its complex with a peptidoglycan fragment.

van Asselt, E.J.Thunnissen, A.M.Dijkstra, B.W.

(1999) J.Mol.Biol. 291: 877-898

  • DOI: 10.1006/jmbi.1999.3013
  • Primary Citation of Related Structures:  1QTE

  • PubMed Abstract: 
  • The 70 kDa soluble lytic transglycosylase (Slt70) from Escherichia coli is an exo-muramidase, that catalyses the cleavage of the glycosidic bonds between N -acetylmuramic acid and N -acetylglucosamine residues in peptidoglycan, the main structural co ...

    The 70 kDa soluble lytic transglycosylase (Slt70) from Escherichia coli is an exo-muramidase, that catalyses the cleavage of the glycosidic bonds between N -acetylmuramic acid and N -acetylglucosamine residues in peptidoglycan, the main structural component of the bacterial cell wall. This cleavage is accompanied by the formation of a 1,6-anhydro bond between the C1 and O6 atoms in the N -acetylmuramic acid residue (anhMurNAc). Crystallographic studies at medium resolution revealed that Slt70 is a multi-domain protein consisting of a large ring-shaped alpha-superhelix with on top a catalytic domain, which resembles the fold of goose-type lysozyme. Here we report the crystal structures of native Slt70 and of its complex with a 1,6-anhydromuropeptide solved at nominal resolutions of 1.65 A and 1.90 A, respectively. The high resolution native structure reveals the details on the hydrogen bonds, electrostatic and hydrophobic interactions that stabilise the catalytic domain and the alpha-superhelix. The building-block of the alpha-superhelix is an "up-down-up-down" four-alpha-helix bundle involving both parallel and antiparallel helix pairs. Stabilisation of the fold is provided through an extensive packing of apolar atoms, mostly from leucine and alanine residues. It lacks, however, an internal consensus sequence that characterises other super-secondary helical folds like the beta-helix in pectate lyase or the (beta-alpha)-helix in the ribonuclease inhibitor. The 1, 6-anhydromuropeptide product binds in a shallow groove adjacent to the peptidoglycan-binding groove of the catalytic domain. The groove is formed by conserved residues at the interface of the catalytic domain and the alpha-superhelix. The structure of the Slt70-1, 6-anhydromuropeptide complex confirms the presence of a specific binding-site for the peptide moieties of the peptidoglycan and it substantiates the notion that Slt70 starts the cleavage reaction at the anhMurNAc end of the peptidoglycan.


    Organizational Affiliation

    University of Groningen, Nijenborgh 4, Groningen, 9747 AG, The Netherlands.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (SOLUBLE LYTIC TRANSGLYCOSYLASE SLT70)
A
618Escherichia coli (strain K12)Gene Names: slt (sltY)
EC: 4.2.2.n1
Find proteins for P0AGC3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AGC3
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
ACT
Query on ACT

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Download CCD File 
A
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.168 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 78.009α = 90.00
b = 87.477β = 90.00
c = 132.906γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
DMmodel building
X-PLORphasing
DENZOdata reduction
DMphasing
X-PLORrefinement
X-PLORmodel building
PHASESphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-09-01
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance