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| | ==Native Escherichia coli L,D-carboxypeptidase A (LdcA)== | | ==Native Escherichia coli L,D-carboxypeptidase A (LdcA)== |
| - | <StructureSection load='5z01' size='340' side='right' caption='[[5z01]], [[Resolution|resolution]] 1.75Å' scene=''> | + | <StructureSection load='5z01' size='340' side='right'caption='[[5z01]], [[Resolution|resolution]] 1.75Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[5z01]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Z01 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5Z01 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5z01]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Z01 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5Z01 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 1.75Å</td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ldcA, ycgQ, b1192, JW1181 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Muramoyltetrapeptide_carboxypeptidase Muramoyltetrapeptide carboxypeptidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.17.13 3.4.17.13] </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=5z01 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5z01 OCA], [https://pdbe.org/5z01 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5z01 RCSB], [https://www.ebi.ac.uk/pdbsum/5z01 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5z01 ProSAT]</span></td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5z01 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5z01 OCA], [http://pdbe.org/5z01 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5z01 RCSB], [http://www.ebi.ac.uk/pdbsum/5z01 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5z01 ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/LDCA_ECOLI LDCA_ECOLI]] Releases the terminal D-alanine residue from the cytoplasmic tetrapeptide recycling product L-Ala-gamma-D-Glu-meso-Dap-D-Ala. To a lesser extent, can also cleave D-Ala from murein derivatives containing the tetrapeptide, i.e. MurNAc-tetrapeptide, UDP-MurNAc-tetrapeptide, GlcNAc-MurNAc-tetrapeptide, and GlcNAc-anhMurNAc-tetrapeptide. Does not act on murein sacculi or cross-linked muropeptides. The tripeptides produced by the LcdA reaction can then be reused as peptidoglycan building blocks; LcdA is thereby involved in murein recycling. Is also essential for viability during stationary phase.<ref>PMID:10428950</ref> <ref>PMID:18535144</ref> | + | [https://www.uniprot.org/uniprot/LDCA_ECOLI LDCA_ECOLI] Releases the terminal D-alanine residue from the cytoplasmic tetrapeptide recycling product L-Ala-gamma-D-Glu-meso-Dap-D-Ala. To a lesser extent, can also cleave D-Ala from murein derivatives containing the tetrapeptide, i.e. MurNAc-tetrapeptide, UDP-MurNAc-tetrapeptide, GlcNAc-MurNAc-tetrapeptide, and GlcNAc-anhMurNAc-tetrapeptide. Does not act on murein sacculi or cross-linked muropeptides. The tripeptides produced by the LcdA reaction can then be reused as peptidoglycan building blocks; LcdA is thereby involved in murein recycling. Is also essential for viability during stationary phase.<ref>PMID:10428950</ref> <ref>PMID:18535144</ref> |
| - | <div style="background-color:#fffaf0;">
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| - | == Publication Abstract from PubMed ==
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| - | Bacterial peptidoglycan is constructed by cross-linking sugar chains carrying pentapeptide building blocks with two d-alanine residues at the C-terminus. Incorporation into the polymer and subsequent breakdown of peptidoglycan releases a tetrapeptide with a single d-alanine residue. Removal of this residue is necessary for the tripeptide to receive a new D-Ala-D-Ala dipeptide in the synthetic pathway, but proteases are generally unable to work with substrates having residues of unusual chirality close to the scissile bond. Processing of the tetrapeptide is carried out by a dedicated ld-carboxypeptidase, which is of interest as a novel drug target. We describe the high resolution crystal structure of the enzyme from E. coli, and demonstrate the dimeric structure is highly conserved.
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| - | The crystal structure and oligomeric form of Escherichia colil,d-carboxypeptidase A.,Meyer K, Addy C, Akashi S, Roper DI, Tame JRH Biochem Biophys Res Commun. 2018 May 15;499(3):594-599. doi:, 10.1016/j.bbrc.2018.03.195. Epub 2018 Apr 5. PMID:29601819<ref>PMID:29601819</ref>
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| - | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
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| - | </div>
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| - | <div class="pdbe-citations 5z01" style="background-color:#fffaf0;"></div>
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| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Ecoli]] | + | [[Category: Escherichia coli K-12]] |
| - | [[Category: Muramoyltetrapeptide carboxypeptidase]] | + | [[Category: Large Structures]] |
| - | [[Category: Meyer, K]] | + | [[Category: Meyer K]] |
| - | [[Category: Tame, J R.H]] | + | [[Category: Tame JRH]] |
| - | [[Category: Cell-wall]]
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| - | [[Category: Hydrolase]]
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| - | [[Category: Peptidoglycan]]
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| - | [[Category: Recycling]]
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