4q5k
From Proteopedia
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== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[4q5k]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacteroides_uniformis_ATCC_8492 Bacteroides uniformis ATCC 8492]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4Q5K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4Q5K FirstGlance]. <br> | <table><tr><td colspan='2'>[[4q5k]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacteroides_uniformis_ATCC_8492 Bacteroides uniformis ATCC 8492]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4Q5K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4Q5K FirstGlance]. <br> | ||
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=2YP:(2R)-2-[[(1R,2S,3R,4R,5R)-4-ACETAMIDO-2-[(2S,3R,4R,5S,6R)-3-ACETAMIDO-6-(HYDROXYMETHYL)-4,5-BIS(OXIDANYL)OXAN-2-YL]OXY-6,8-DIOXABICYCLO[3.2.1]OCTAN-3-YL]OXY]PROPANOIC+ACID'>2YP</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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]] 1.3Å</td></tr> |
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=2YP:(2R)-2-[[(1R,2S,3R,4R,5R)-4-ACETAMIDO-2-[(2S,3R,4R,5S,6R)-3-ACETAMIDO-6-(HYDROXYMETHYL)-4,5-BIS(OXIDANYL)OXAN-2-YL]OXY-6,8-DIOXABICYCLO[3.2.1]OCTAN-3-YL]OXY]PROPANOIC+ACID'>2YP</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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=4q5k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4q5k OCA], [https://pdbe.org/4q5k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4q5k RCSB], [https://www.ebi.ac.uk/pdbsum/4q5k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4q5k 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=4q5k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4q5k OCA], [https://pdbe.org/4q5k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4q5k RCSB], [https://www.ebi.ac.uk/pdbsum/4q5k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4q5k ProSAT]</span></td></tr> | ||
</table> | </table> | ||
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GlcNAc-1,6-anhydro-MurNAc-tetrapeptide is a major peptidoglycan degradation intermediate and a cytotoxin. It is generated by lytic transglycosylases and further degraded and recycled by various enzymes. We have identified and characterized a highly specific N-acetylmuramoyl-L-alanine amidase (AmiA) from Bacteroides uniformis, a member of the DUF1460 protein family, that hydrolyzes GlcNAc-1,6-anhydro-MurNAc-peptide into disaccharide and stem peptide. The high-resolution apo structure at 1.15 A resolution shows that AmiA is related to NlpC/P60 gamma-D-Glu-meso-diaminopimelic acid amidases and shares a common catalytic core and cysteine peptidase-like active site. AmiA has evolved structural adaptations that reconfigure the substrate recognition site. The preferred substrates for AmiA were predicted in silico based on structural and bioinformatics data, and subsequently were characterized experimentally. Further crystal structures of AmiA in complexes with GlcNAc-1,6-anhydro-MurNAc and GlcNAc have enabled us to elucidate substrate recognition and specificity. DUF1460 is highly conserved in structure and defines another amidase family. | GlcNAc-1,6-anhydro-MurNAc-tetrapeptide is a major peptidoglycan degradation intermediate and a cytotoxin. It is generated by lytic transglycosylases and further degraded and recycled by various enzymes. We have identified and characterized a highly specific N-acetylmuramoyl-L-alanine amidase (AmiA) from Bacteroides uniformis, a member of the DUF1460 protein family, that hydrolyzes GlcNAc-1,6-anhydro-MurNAc-peptide into disaccharide and stem peptide. The high-resolution apo structure at 1.15 A resolution shows that AmiA is related to NlpC/P60 gamma-D-Glu-meso-diaminopimelic acid amidases and shares a common catalytic core and cysteine peptidase-like active site. AmiA has evolved structural adaptations that reconfigure the substrate recognition site. The preferred substrates for AmiA were predicted in silico based on structural and bioinformatics data, and subsequently were characterized experimentally. Further crystal structures of AmiA in complexes with GlcNAc-1,6-anhydro-MurNAc and GlcNAc have enabled us to elucidate substrate recognition and specificity. DUF1460 is highly conserved in structure and defines another amidase family. | ||
| - | Structure-guided functional characterization of DUF1460 reveals a highly specific NlpC/P60 amidase family.,Xu Q, Mengin-Lecreulx D, Patin D, Grant JC, Chiu HJ, Jaroszewski L, Knuth MW, Godzik A, Lesley SA, Elsliger MA, Deacon AM, Wilson IA Structure. 2014 Dec 2;22(12):1799-1809. doi: 10.1016/j.str.2014.09.018. Epub 2014, Nov 20. PMID:25465128<ref>PMID:25465128</ref> | + | Structure-guided functional characterization of DUF1460 reveals a highly specific NlpC/P60 amidase family.,Xu Q, Mengin-Lecreulx D, Patin D, Grant JC, Chiu HJ, Jaroszewski L, Knuth MW, Godzik A, Lesley SA, Elsliger MA, Deacon AM, Wilson IA Structure. 2014 Dec 2;22(12):1799-1809. doi: 10.1016/j.str.2014.09.018. Epub 2014 , Nov 20. PMID:25465128<ref>PMID:25465128</ref> |
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
Current revision
Crystal structure of a N-acetylmuramoyl-L-alanine amidase (BACUNI_02947) from Bacteroides uniformis ATCC 8492 at 1.30 A resolution
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