MEPA, inactive form without ZN in P21

Experimental Data Snapshot

  • Resolution: 1.40 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.184 

wwPDB Validation   3D Report Full Report

This is version 1.3 of the entry. See complete history


Peptidoglycan amidase MepA is a LAS metallopeptidase

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

(2004) J Biol Chem 279: 43982-43989

  • DOI: https://doi.org/10.1074/jbc.M406735200
  • Primary Citation of Related Structures:  
    1TZP, 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 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.

  • Organizational Affiliation

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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Penicillin-insensitive murein endopeptidase
A, B
255Escherichia coliMutation(s): 0 
Gene Names: mepA
EC: 3.4.99
Find proteins for P0C0T5 (Escherichia coli (strain K12))
Explore P0C0T5 
Go to UniProtKB:  P0C0T5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0C0T5
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
E [auth A]
F [auth A]
G [auth B]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth B],
H [auth B],
I [auth B],
J [auth B],
K [auth B]
O4 S
Query on BU1

Download Ideal Coordinates CCD File 
L [auth B]1,4-BUTANEDIOL
C4 H10 O2
Experimental Data & Validation

Experimental Data

  • Resolution: 1.40 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.184 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.949α = 90
b = 115.143β = 94.08
c = 49.154γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
CCP4data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-09-07
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-04-03
    Changes: Data collection, Database references, Derived calculations, Refinement description