1j3g: Difference between revisions
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New page: left|200px<br /><applet load="1j3g" size="450" color="white" frame="true" align="right" spinBox="true" caption="1j3g" /> '''Solution structure of Citrobacter Freundii A... |
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== | ==Solution structure of Citrobacter Freundii AmpD== | ||
AmpD is a bacterial amidase involved in the recycling of cell-wall | <StructureSection load='1j3g' size='340' side='right'caption='[[1j3g]]' scene=''> | ||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[1j3g]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Citrobacter_freundii Citrobacter freundii]. This structure supersedes the now removed PDB entries [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1iya 1iya] and [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1j2s 1j2s]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1J3G OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1J3G FirstGlance]. <br> | |||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr> | |||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1j3g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1j3g OCA], [https://pdbe.org/1j3g PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1j3g RCSB], [https://www.ebi.ac.uk/pdbsum/1j3g PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1j3g ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/AMPD_CITFR AMPD_CITFR] Involved in both cell wall peptidoglycans recycling and beta-lactamase induction. Specifically cleaves the amide bond between the lactyl group of N-acetylmuramic acid and the alpha-amino group of the L-alanine in degradation products containing an anhydro N-acetylmuramyl moiety. | |||
== Evolutionary Conservation == | |||
[[Image:Consurf_key_small.gif|200px|right]] | |||
Check<jmol> | |||
<jmolCheckbox> | |||
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/j3/1j3g_consurf.spt"</scriptWhenChecked> | |||
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | |||
<text>to colour the structure by Evolutionary Conservation</text> | |||
</jmolCheckbox> | |||
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1j3g ConSurf]. | |||
<div style="clear:both"></div> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
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. | |||
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<ref>PMID:12654266</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 1j3g" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Citrobacter freundii]] | [[Category: Citrobacter freundii]] | ||
[[Category: | [[Category: Large Structures]] | ||
[[Category: Dehareng D]] | |||
[[Category: Dehareng | [[Category: Genereux C]] | ||
[[Category: Genereux | [[Category: Joris B]] | ||
[[Category: Joris | [[Category: Liepinsh E]] | ||
[[Category: Liepinsh | [[Category: Otting G]] | ||
[[Category: Otting | |||
