PDBsum entry: 1j3g

Hydrolase

PDB id: 1j3g

Contents

Protein chain

187 a.a. *

Metals

_ZN

* Residue conservation analysis

PDB id:

1j3g

Name:

Hydrolase

Title:

Solution structure of citrobacter freundii ampd

Structure:

Ampd protein. Chain: a. Synonym: ampd. Engineered: yes

Source:

Citrobacter freundii. Organism_taxid: 546. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

NMR struc:

20 models

Authors:

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

Key ref:

E.Liepinsh et al. (2003). NMR structure of Citrobacter freundii AmpD, comparison with bacteriophage T7 lysozyme and homology with PGRP domains. J Mol Biol, 327, 833-842. PubMed id: 12654266 DOI: 10.1016/S0022-2836(03)00185-2

Date:

31-Jan-03 Release date: 18-Feb-03

Supersedes:

1j2s

Protein chain

P82974  (AMPD_CITFR) -  1,6-anhydro-N-acetylmuramyl-L-alanine amidase AmpD

Seq: 187 a.a.

Struc: 187 a.a.

Enzyme reactions

• Enzyme class: E.C.3.5.1.28 - N-acetylmuramoyl-L-alanine amidase.
• Reaction: Hydrolyzes the link between N-acetylmuramoyl residues and L-amino acid residues in certain bacterial cell-wall glycopeptides.

 Gene Ontology (GO) functional annotation 

• Cellular component: cytoplasm (1 term)
• Biological process: cell wall organization (2 terms)
• Biochemical function: hydrolase activity (3 terms)

DOI no: 10.1016/S0022-2836(03)00185-2

J Mol Biol 327:833-842 (2003)

PubMed id: 12654266

NMR structure of Citrobacter freundii AmpD, comparison with bacteriophage T7 lysozyme and homology with PGRP domains.

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

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.

Selected figure(s)

Figure 1.
Figure 1. Solution structure of AmpD and comparison with T7 lysozyme. (a) Ribbon representation of AmpD. The b-strands and a-helices are numbered as in Figure 2. White and yellow numbers distinguish strands and helices, respectively. The zinc ion is shown in purple. (b) Ribbon representation of T7 lysozyme (PDB code 1LBA). Second- ary-structure elements homologous to AmpD are coloured as in (a). (c) Stereo view of AmpD, showing a superposition of the backbone atoms in the 20 conformers representing the NMR structure (Table 1), in the same orientation as in (a). Numbers identify sequence positions. (d) Stereo view of the AmpD conformer closest to the mean structure of the 20 conformers shown in (c), using a heavy-atom representation in the same orientation as in (c). The polypeptide back- bone is drawn in green. The following colors were used for the side-chains: blue, Arg, Lys, positively charged His; red, Glu, Asp; yellow, Ala, Cys, Ile, Leu, Met, Phe, Pro, Trp, Val; gray, Asn, Gln, Ser, Thr, Tyr, uncharged His. The zinc ion is shown as a purple sphere, with the side-chains of the coordinating residues His34, His154 and Asp164 drawn in bold. Black spheres mark the C a positions of those residues, where point mutations have been found in con- stituitively b-lactamase expressing bacteria. 17

Figure 3.
Figure 3. Model of the AmpD-substrate complex. The solvent-accessible surface is shown with the following color code for different chemical groups: yellow, hydro- phobic; gray, hydrophilic; red, negatively charged; blue, positively charged. The zinc atom is displayed as a pur- ple sphere. The side-chains of the Zn 2⁺ -coordinating resi- dues and of Tyr63 were excluded from the surface calculation and drawn with green lines instead. The sub- strate, 1,6-anhydro MurNAc-L-alanyl-g-D-glutamyl-meso- diaminopimelic acid, is drawn in a line representation (blue) with carbonyl and carboxyl bonds in red.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2003, 327, 833-842) copyright 2003.

Figures were selected by the author.