1TZP

MEPA, inactive form without ZN in P21


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.183 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Peptidoglycan amidase MepA is a LAS metallopeptidase

Marcyjaniak, M.Odintsov, S.G.Sabala, I.Bochtler, M.

(2004) J.Biol.Chem. 279: 43982-43989

  • DOI: 10.1074/jbc.M406735200
  • Primary Citation of Related Structures:  1U10

  • PubMed Abstract: 
  • LAS enzymes are a group of metallopeptidases that share an active site architecture and a core folding motif and have been named according to the group members lysostaphin, D-Ala-D-Ala carboxypeptidase and sonic hedgehog. Escherichia coli MepA is a p ...

    LAS enzymes are a group of metallopeptidases that share an active site architecture and a core folding motif and have been named according to the group members lysostaphin, D-Ala-D-Ala carboxypeptidase and sonic hedgehog. Escherichia coli MepA is a periplasmic, penicillin-insensitive murein endopeptidase that cleaves the D-alanyl-meso-2,6-diamino-pimelyl amide bond in E. coli peptidoglycan. The enzyme lacks sequence similarity with other peptidases, and is currently classified as a peptidase of unknown fold and catalytic class in all major data bases. Here, we build on our observation that two motifs, characteristic of the newly described LAS group of metallopeptidases, are conserved in MepA-type sequences. We demonstrate that recombinant E. coli MepA is sensitive to metal chelators and that mutations in the predicted Zn2+ ligands His-113, Asp-120, and His-211 inactivate the enzyme. Moreover, we present the crystal structure of MepA. The active site of the enzyme is most similar to the active sites of lysostaphin and D-Ala-D-Ala carboxypeptidase, and the fold is most closely related to the N-domain of sonic hedgehog. We conclude that MepA-type peptidases are LAS enzymes.


    Related Citations: 
    • Latent LytM at 1.3A resolution
      Odintsov, S.G.,Sabala, I.,Marcyjaniak, M.,Bochtler, M.
      (2004) J.Mol.Biol. 335: 775
    • Similar active sites in lysostaphins and D-Ala-D-Ala metallopeptidases
      Bochtler, M.,Odintsov, S.G.,Marcyjaniak, M.,Sabala, I.
      (2004) Protein Sci. 13: 854


    Organizational Affiliation

    International Institute of Molecular and Cell Biology, ul. Trojdena 4, 02-109 Warsaw, Poland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Penicillin-insensitive murein endopeptidase
A, B
255Escherichia coli (strain K12)Gene Names: mepA
EC: 3.4.24.-
Find proteins for P0C0T5 (Escherichia coli (strain K12))
Go to UniProtKB:  P0C0T5
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
BU1
Query on BU1

Download SDF File 
Download CCD File 
B
1,4-BUTANEDIOL
C4 H10 O2
WERYXYBDKMZEQL-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.183 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 45.949α = 90.00
b = 115.143β = 94.08
c = 49.154γ = 90.00
Software Package:
Software NamePurpose
CCP4data scaling
MOLREPphasing
MOSFLMdata reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-09-07
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance