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| | <StructureSection load='3d2z' size='340' side='right'caption='[[3d2z]], [[Resolution|resolution]] 2.80Å' scene=''> | | <StructureSection load='3d2z' size='340' side='right'caption='[[3d2z]], [[Resolution|resolution]] 2.80Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3d2z]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_mg1655 Escherichia coli mg1655]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3D2Z OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3D2Z FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3d2z]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_str._K-12_substr._MG1655 Escherichia coli str. K-12 substr. MG1655]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3D2Z OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3D2Z FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.8Å</td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=FGA:GAMMA-D-GLUTAMIC+ACID'>FGA</scene></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=FGA:GAMMA-D-GLUTAMIC+ACID'>FGA</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2bgx|2bgx]], [[2bh7|2bh7]], [[3d2y|3d2y]]</div></td></tr>
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| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">amiD, ybjR, b0867, JW0851 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=511145 Escherichia coli MG1655])</td></tr>
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| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/N-acetylmuramoyl-L-alanine_amidase N-acetylmuramoyl-L-alanine amidase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.28 3.5.1.28] </span></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=3d2z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3d2z OCA], [https://pdbe.org/3d2z PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3d2z RCSB], [https://www.ebi.ac.uk/pdbsum/3d2z PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3d2z ProSAT]</span></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=3d2z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3d2z OCA], [https://pdbe.org/3d2z PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3d2z RCSB], [https://www.ebi.ac.uk/pdbsum/3d2z PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3d2z ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/AMID_ECOLI AMID_ECOLI] |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | <jmolCheckbox> | | <jmolCheckbox> |
| | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/d2/3d2z_consurf.spt"</scriptWhenChecked> | | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/d2/3d2z_consurf.spt"</scriptWhenChecked> |
| - | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | + | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked> |
| | <text>to colour the structure by Evolutionary Conservation</text> | | <text>to colour the structure by Evolutionary Conservation</text> |
| | </jmolCheckbox> | | </jmolCheckbox> |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Escherichia coli mg1655]] | + | [[Category: Escherichia coli str. K-12 substr. MG1655]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: N-acetylmuramoyl-L-alanine amidase]]
| + | [[Category: Charlier P]] |
| - | [[Category: Charlier, P]] | + | [[Category: Frere JM]] |
| - | [[Category: Frere, J M]] | + | [[Category: Herman R]] |
| - | [[Category: Herman, R]] | + | [[Category: Joris B]] |
| - | [[Category: Joris, B]] | + | [[Category: Kerff F]] |
| - | [[Category: Kerff, F]] | + | [[Category: Luxen A]] |
| - | [[Category: Luxen, A]] | + | [[Category: Mercier F]] |
| - | [[Category: Mercier, F]] | + | [[Category: Petrella S]] |
| - | [[Category: Petrella, S]] | + | [[Category: Sauvage E]] |
| - | [[Category: Sauvage, E]] | + | |
| - | [[Category: Ampd]]
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| - | [[Category: Cell wall biogenesis/degradation]]
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| - | [[Category: Hydrolase]]
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| - | [[Category: Lipoprotein]]
| + | |
| - | [[Category: Membrane]]
| + | |
| - | [[Category: Metal-binding]]
| + | |
| - | [[Category: N-acetylmuramyl-l-alanine amidase]]
| + | |
| - | [[Category: Outer membrane]]
| + | |
| - | [[Category: Palmitate]]
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| - | [[Category: Peptidoglycan recognizing protein]]
| + | |
| - | [[Category: Pgrp]]
| + | |
| - | [[Category: Zinc amidase]]
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| Structural highlights
Function
AMID_ECOLI
Evolutionary Conservation
Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.
Publication Abstract from PubMed
AmiD is the fifth identified N-acetylmuramoyl-L-alanine zinc amidase of Escherichia coli. This periplasmic lipoprotein is anchored in the outer membrane and has a broad specificity. AmiD is capable of cleaving the intact peptidoglycan (PG) as well as soluble fragments containing N-acetylmuramic acid regardless of the presence of an anhydro form or not, unlike the four other amidases, AmiA, AmiB, AmiC, and AmpD, which have some specificity. AmiD function is, however, not clearly established but it could be part of the enzymatic machinery involved in the PG turnover in E. coli. We solved three structures of the E. coli zinc amidase AmiD devoid of its lipidic anchorage: the holoenzyme, the apoenzyme in complex with the substrate anhydro-N-acetylmuramic-acid-L-Ala-gamma-d-Glu-L-Lys, and the holoenzyme in complex with the L-Ala-gamma-D-Glu-L-Lys peptide, the product of the hydrolysis of this substrate by AmiD. The AmiD structure shows a relatively flexible N-terminal extension that allows an easy reach of the PG by the enzyme inserted into the outer membrane. The C-terminal domain provides a potential extended geometrical complementarity to the substrate. AmiD shares a common fold with AmpD, the bacteriophage T7 lysozyme, and the PG recognition proteins, which are receptor proteins involved in the innate immune responses of a wide range of organisms. Analysis of the different structures reveals the similarity between the catalytic mechanism of zinc amidases of the AmiD family and the thermolysin-related zinc peptidases.
Specific structural features of the N-acetylmuramoyl-L-alanine amidase AmiD from Escherichia coli and mechanistic implications for enzymes of this family.,Kerff F, Petrella S, Mercier F, Sauvage E, Herman R, Pennartz A, Zervosen A, Luxen A, Frere JM, Joris B, Charlier P J Mol Biol. 2010 Mar 19;397(1):249-59. Epub 2009 Dec 28. PMID:20036252[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Kerff F, Petrella S, Mercier F, Sauvage E, Herman R, Pennartz A, Zervosen A, Luxen A, Frere JM, Joris B, Charlier P. Specific structural features of the N-acetylmuramoyl-L-alanine amidase AmiD from Escherichia coli and mechanistic implications for enzymes of this family. J Mol Biol. 2010 Mar 19;397(1):249-59. Epub 2009 Dec 28. PMID:20036252 doi:10.1016/j.jmb.2009.12.038
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