Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 20.94 kDa 
• Atom Count: 1472 
• Modelled Residue Count: 187 
• Deposited Residue Count: 187 
• Unique protein chains: 1

1J3G

Solution structure of Citrobacter Freundii AmpD

• PDB DOI: 10.2210/pdb1J3G/pdb
• Entry: 1J3G supersedes: 1IYA, 1J2S
• BMRB: 5483

• Classification: HYDROLASE
• Organism(s): Citrobacter freundii
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2003-01-31 Released: 2003-02-18 
• Deposition Author(s): Liepinsh, E., Genereux, C., Dehareng, D., Joris, B., Otting, G.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 20 
• Conformers Submitted: 20 
• Selection Criteria: all calculated structures submitted 

Literature

NMR Structure of Citrobacter freundii AmpD, Comparison with Bacteriophage T7 Lysozyme and Homology with PGRP Domains

Liepinsh, E., Genereux, C., Dehareng, D., Joris, B., Otting, G.

(2003) J Mol Biol 327: 833-842

• PubMed: 12654266 
• DOI: 10.1016/s0022-2836(03)00185-2
• Primary Citation of Related Structures:  
  1J3G


• PubMed Abstract: 
  

AmpD is a bacterial amidase involved in the recycling of cell-wall fragments in Gram-negative bacteria. Inactivation of AmpD leads to derepression of beta-lactamase expression, presenting a major pathway for the acquisition of constitutive antibiotic resistance. Here, we report the NMR structure of AmpD from Citrobacter freundii (PDB accession code 1J3G). A deep substrate-binding pocket explains the observed specificity for low molecular mass substrates. The fold is related to that of bacteriophage T7 lysozyme. Both proteins bind zinc at a conserved site and require zinc for amidase activity, although the enzymatic mechanism seems to differ in detail. The structure-based sequence alignment identifies conserved features that are also conserved in the eukaryotic peptidoglycan recognition protein (PGRP) domains, including the zinc-coordination site in several of them. PGRP domains thus belong to the same fold family and, where zinc-binding residues are conserved, may have amidase activity. This hypothesis is supported by the observation that human serum N-acetylmuramyl-L-alanine amidase seems to be identical with a soluble form of human PGRP-L.

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Organizational Affiliation: 

Department of Medical Biochemistry, Karolinska Institute, S-17177 Stockholm, Sweden.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
AmpD protein	A	187	Citrobacter freundii	Mutation(s): 0  Gene Names: ampD EC: 3.5.1.28
UniProt
Find proteins for P82974 (Citrobacter freundii) Explore P82974  Go to UniProtKB:  P82974

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 20 
• Conformers Submitted: 20 
• Selection Criteria: all calculated structures submitted 
• OLDERADO: 1J3G Olderado

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-01-31 
• Released Date: 2003-02-18 
Deposition Author(s): Liepinsh, E., Genereux, C., Dehareng, D., Joris, B., Otting, G.
• This entry supersedes: 1IYA, 1J2S

Revision History  

• Version 1.0: 2003-02-18
  Type: Initial release
  
• Version 1.1: 2007-10-21
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2022-02-23
  Changes: Database references, Derived calculations