1j3g
From Proteopedia
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Solution structure of Citrobacter Freundii AmpD
Overview
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.
About this Structure
1J3G is a Single protein structure of sequence from Citrobacter freundii with ZN as ligand. This structure superseeds the now removed PDB entries 1IYA and 1J2S. Active as N-acetylmuramoyl-L-alanine amidase, with EC number 3.5.1.28 Full crystallographic information is available from OCA.
Reference
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, J Mol Biol. 2003 Apr 4;327(4):833-42. PMID:12654266
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