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1j3g

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(New page: 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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[[Image:1j3g.jpg|left|200px]]<br /><applet load="1j3g" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1j3g" />
 
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'''Solution structure of Citrobacter Freundii AmpD'''<br />
 
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==Overview==
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==Solution structure of Citrobacter Freundii AmpD==
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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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<StructureSection load='1j3g' size='340' side='right'caption='[[1j3g]]' scene=''>
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== Structural highlights ==
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<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>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
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<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>
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<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>
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</table>
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== Function ==
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[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.
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/j3/1j3g_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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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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==About this Structure==
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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>
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1J3G is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Citrobacter_freundii Citrobacter freundii] with ZN as [http://en.wikipedia.org/wiki/ligand ligand]. This structure superseeds the now removed PDB entries 1IYA and 1J2S. Active as [http://en.wikipedia.org/wiki/N-acetylmuramoyl-L-alanine_amidase N-acetylmuramoyl-L-alanine amidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.28 3.5.1.28] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1J3G OCA].
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==Reference==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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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:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=12654266 12654266]
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</div>
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<div class="pdbe-citations 1j3g" style="background-color:#fffaf0;"></div>
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== References ==
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<references/>
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__TOC__
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</StructureSection>
[[Category: Citrobacter freundii]]
[[Category: Citrobacter freundii]]
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[[Category: N-acetylmuramoyl-L-alanine amidase]]
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[[Category: Large Structures]]
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[[Category: Single protein]]
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[[Category: Dehareng D]]
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[[Category: Dehareng, D.]]
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[[Category: Genereux C]]
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[[Category: Genereux, C.]]
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[[Category: Joris B]]
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[[Category: Joris, B.]]
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[[Category: Liepinsh E]]
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[[Category: Liepinsh, E.]]
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[[Category: Otting G]]
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[[Category: Otting, G.]]
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[[Category: ZN]]
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[[Category: mixed alpha-beta]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 17:54:39 2007''
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Current revision

Solution structure of Citrobacter Freundii AmpD

PDB ID 1j3g

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