Biological Assembly 1  

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Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 57617.57 
• Atom Count: 3779 
• Residue Count: 510 
• Unique protein chains: 1

1TZP

MEPA, inactive form without ZN in P21

• DOI: 10.2210/pdb1TZP/pdb

• Classification: HYDROLASE
• Organism(s): Escherichia coli (strain K12)
• Expression System: Escherichia coli BL21(DE3)


• Deposited: 2004-07-11 Released: 2004-09-07 
• Deposition Author(s): Marcyjaniak, M., Odintsov, S.G., Sabala, I., Bochtler, M.

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Experimental Data Snapshot

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

Literature

Peptidoglycan amidase MepA is a LAS metallopeptidase

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

(2004) J.Biol.Chem. 279: 43982-43989

• PubMed: 15292190 
• 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 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.

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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




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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
Molecule	Chains	Sequence Length	Organism	Details
Penicillin-insensitive murein endopeptidase	A, B	255	Escherichia coli (strain K12)	Mutation(s): 0  Gene Names: mepA EC: 3.4.24.-
Find proteins for P0C0T5 (Escherichia coli (strain K12)) Go to UniProtKB:  P0C0T5

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
SO4	A, B	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
BU1	B	1,4-BUTANEDIOL C4 H10 O2 WERYXYBDKMZEQL-UHFFFAOYSA-N

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 = 45.949	α = 90.00
b = 115.143	β = 94.08
c = 49.154	γ = 90.00

Software Package:

Software Name	Purpose
CCP4	data scaling
MOLREP	phasing
MOSFLM	data reduction
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-07-11 
• Released Date: 2004-09-07 
• Deposition Author(s): Marcyjaniak, M., Odintsov, S.G., Sabala, I., Bochtler, M.

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