2PI8

Crystal structure of E. coli MltA with bound chitohexaose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.182 

wwPDB Validation 3D Report Full Report


This is version 1.5 of the entry. See complete history

Literature

Structure of Escherichia coli Lytic transglycosylase MltA with bound chitohexaose: implications for peptidoglycan binding and cleavage

van Straaten, K.E.Barends, T.R.M.Dijkstra, B.W.Thunnissen, A.M.W.H.

(2007) J.Biol.Chem. 282: 21197-21205

  • DOI: 10.1074/jbc.M701818200
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Crystal structures of an inactive mutant (D308A) of the lytic transglycosylase MltA from Escherichia coli have been determined in two different apo-forms, as well as in complex with the substrate analogue chitohexaose. The chitohexaose binds with all ...

    Crystal structures of an inactive mutant (D308A) of the lytic transglycosylase MltA from Escherichia coli have been determined in two different apo-forms, as well as in complex with the substrate analogue chitohexaose. The chitohexaose binds with all six saccharide residues in the active site groove, with an intact glycosidic bond at the bond cleavage center. Its binding induces a large reorientation of the two structural domains in MltA, narrowing the active site groove and allowing tight interactions of the oligosaccharide with residues from both domains. The structures identify residues in MltA with key roles in the binding and recognition of peptidoglycan and confirm that Asp-308 is the single catalytic residue, acting as a general acid/base. Moreover, the structures suggest that catalysis involves a high energy conformation of the scissile glycosidic linkage and that the putative oxocarbenium ion intermediate is stabilized by the dipole moment of a nearby alpha-helix.


    Related Citations: 
    • Crystal structure of MltA from Escherichia coli reveals a unique lytic transglycosylase fold
      van Straaten, K.E.,Dijkstra, B.W.,Vollmer, W.,Thunnissen, A.M.W.H.
      (2005) J.Mol.Biol. 352: 1068
    • Purification, crystallization and preliminary X-ray analysis of the lytic transglycosylase MltA from Escherichia coli
      van Straaten, K.E.,Dijkstra, B.W.,Thunnissen, A.M.W.H.
      (2004) Acta Crystallogr.,Sect.D 60: 758
    • Escherichia coli MltA: MAD phasing and refinement of a tetartohedrally twinned protein crystal structure
      Barends, T.R.M.,de Jong, R.M.,van Straaten, K.E.,Thunnissen, A.M.W.H.,Dijkstra, B.W.
      (2005) Acta Crystallogr.,Sect.D 61: 613


    Organizational Affiliation

    Laboratory of Biophysical Chemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Membrane-bound lytic murein transglycosylase A
A, B, C, D
345Escherichia coli (strain K12)Mutation(s): 1 
Gene Names: mltA (mlt, ygdM)
EC: 4.2.2.n1
Find proteins for P0A935 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A935
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A, B, C, D
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B, C, D
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.182 
  • Space Group: P 31
Unit Cell:
Length (Å)Angle (°)
a = 91.000α = 90.00
b = 91.000β = 90.00
c = 187.200γ = 120.00
Software Package:
Software NamePurpose
SOLVEphasing
RESOLVEphasing
ProDCdata collection
PDB_EXTRACTdata extraction
SCALEPACKdata scaling
CNSrefinement
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-05-08
    Type: Initial release
  • Version 1.1: 2007-11-19
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Source and taxonomy, Version format compliance
  • Version 1.3: 2012-06-13
    Type: Other
  • Version 1.4: 2017-10-18
    Type: Refinement description
  • Version 1.5: 2018-03-14
    Type: Data collection, Database references