Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 44.75 kDa 
• Atom Count: 2754 
• Residue Count: 348 
• Unique protein chains: 1

4BIN

Crystal structure of the E. coli N-acetylmuramoyl-L-alanine amidase AmiC

• DOI: 10.2210/pdb4BIN/pdb

• Classification: HYDROLASE
• Organism(s): Escherichia coli K-12
• Mutation(s): No 


• Deposited: 2013-04-12 Released: 2013-08-21 
• Deposition Author(s): Kerff, F., Rocaboy, M., Herman, R., Sauvage, E., Charlier, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.49 Å
• R-Value Free: 0.231 
• R-Value Work: 0.176 
• R-Value Observed: 0.178 

Literature

The Crystal Structure of the Cell Division Amidase Amic Reveals the Fold of the Amin Domain, a New Peptidoglycan Binding Domain.

Rocaboy, M., Herman, R., Sauvage, E., Remaut, H., Moonens, K., Terrak, M., Charlier, P., Kerff, F.

(2013) Mol Microbiol 90: 267

• PubMed: 23927005 
• DOI: 10.1111/mmi.12361
• Primary Citation of Related Structures:  
  4BIN


• PubMed Abstract: 
  

Binary fission is the ultimate step of the prokaryotic cell cycle. In Gram-negative bacteria like Escherichia coli, this step implies the invagination of three biological layers (cytoplasmic membrane, peptidoglycan and outer membrane), biosynthesis of the new poles and eventually, daughter cells separation. The latter requires the coordinated action of the N-acetylmuramyl-L-alanine amidases AmiA/B/C and their LytM activators EnvC and NlpD to cleave the septal peptidoglycan. We present here the 2.5 Å crystal structure of AmiC which includes the first report of an AMIN domain structure, a β-sandwich of two symmetrical four-stranded β-sheets exposing highly conserved motifs on the two outer faces. We show that this N-terminal domain, involved in the localization of AmiC at the division site, is a new peptidoglycan-binding domain. The C-terminal catalytic domain shows an auto-inhibitory alpha helix obstructing the active site. AmiC lacking this helix exhibits by itself an activity comparable to that of the wild type AmiC activated by NlpD. We also demonstrate the interaction between AmiC and NlpD by microscale thermophoresis and confirm the importance of the active site blocking alpha helix in the regulation of the amidase activity.

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Organizational Affiliation: 

Centre d'Ingénierie des Protéines, University of Liège, Liège, Belgium.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
N-ACETYLMURAMOYL-L-ALANINE AMIDASE AMIC	A	403	Escherichia coli K-12	Mutation(s): 0  Gene Names: amiC, ygdN, b2817, JW5449 EC: 3.5.1.28
Find proteins for P63883 (Escherichia coli (strain K12)) Explore P63883  Go to UniProtKB:  P63883

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	A	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
NA	A	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.49 Å
• R-Value Free: 0.231 
• R-Value Work: 0.176 
• R-Value Observed: 0.178 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.032	α = 90
b = 68.442	β = 90
c = 90.576	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-04-12 
• Released Date: 2013-08-21 
Deposition Author(s): Kerff, F., Rocaboy, M., Herman, R., Sauvage, E., Charlier, P.

Revision History 

• Version 1.0: 2013-08-21
  Type: Initial release
  
• Version 1.1: 2013-10-30
  Changes: Database references