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| | ==Crystal structure of BaLdcB / VanY-like L,D-carboxypeptidase Zinc(II)-bound== | | ==Crystal structure of BaLdcB / VanY-like L,D-carboxypeptidase Zinc(II)-bound== |
| - | <StructureSection load='4mph' size='340' side='right' caption='[[4mph]], [[Resolution|resolution]] 2.03Å' scene=''> | + | <StructureSection load='4mph' size='340' side='right'caption='[[4mph]], [[Resolution|resolution]] 2.03Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4mph]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_cereus_var._anthracis"_(cohn_1872)_smith_et_al._1946 "bacillus cereus var. anthracis" (cohn 1872) smith et al. 1946]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4MPH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4MPH FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4mph]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_anthracis Bacillus anthracis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4MPH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4MPH FirstGlance]. <br> |
| - | </td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=PE3:3,6,9,12,15,18,21,24,27,30,33,36,39-TRIDECAOXAHENTETRACONTANE-1,41-DIOL'>PE3</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.0301Å</td></tr> |
| - | <tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4jid|4jid]]</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=PE3:3,6,9,12,15,18,21,24,27,30,33,36,39-TRIDECAOXAHENTETRACONTANE-1,41-DIOL'>PE3</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr> |
| - | <tr><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">BACI_C24940, BAS2349, BA_2526, DACA3, GBAA_2526, VANY ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1392 "Bacillus cereus var. anthracis" (Cohn 1872) Smith et al. 1946])</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=4mph FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4mph OCA], [https://pdbe.org/4mph PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4mph RCSB], [https://www.ebi.ac.uk/pdbsum/4mph PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4mph ProSAT]</span></td></tr> |
| - | <tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4mph FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4mph OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4mph RCSB], [http://www.ebi.ac.uk/pdbsum/4mph PDBsum]</span></td></tr>
| + | </table> |
| - | <table> | + | == Function == |
| - | <div style="background-color:#fffaf0;">
| + | [https://www.uniprot.org/uniprot/A0A6L8PDI9_BACAN A0A6L8PDI9_BACAN] |
| - | == Publication Abstract from PubMed == | + | |
| - | Peptidoglycan surrounds the bacterial cytoplasmic membrane to protect the cell against osmolysis. The biosynthesis of peptidoglycan, made of glycan strands crosslinked by short peptides, is the target of antibiotics like beta-lactams and glycopeptides. Nascent peptidoglycan contains pentapeptides that are trimmed by carboxypeptidases to tetra- and tripeptides. The well-characterized DD-carboxypeptidases hydrolyze the terminal D-alanine from the stem pentapeptide to produce a tetrapeptide. However, few LD-carboxypeptidases that produce tripeptides have been identified, and nothing is known about substrate specificity in these enzymes. We report biochemical properties and crystal structures of the LD-carboxypeptidases LdcB from Streptococcus pneumoniae, Bacillus anthracis, and Bacillus subtilis. The enzymes are active against bacterial cell wall tetrapeptides and adopt a zinc-carboxypeptidase fold characteristic of the LAS superfamily. We have also solved the structure of S. pneumoniae LdcB with a product mimic, elucidating the residues essential for peptidoglycan recognition and the conformational changes that occur on ligand binding.
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| - | Structure of the LdcB LD-Carboxypeptidase Reveals the Molecular Basis of Peptidoglycan Recognition.,Hoyland CN, Aldridge C, Cleverley RM, Duchene MC, Minasov G, Onopriyenko O, Sidiq K, Stogios PJ, Anderson WF, Daniel RA, Savchenko A, Vollmer W, Lewis RJ Structure. 2014 Jun 4. pii: S0969-2126(14)00139-7. doi:, 10.1016/j.str.2014.04.015. PMID:24909784<ref>PMID:24909784</ref>
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| - | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
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| - | </div>
| + | |
| - | == References ==
| + | |
| - | <references/>
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Anderson, W F.]] | + | [[Category: Bacillus anthracis]] |
| - | [[Category: CSGID, Center for Structural Genomics of Infectious Diseases.]] | + | [[Category: Large Structures]] |
| - | [[Category: Onopriyenko, O.]] | + | [[Category: Anderson WF]] |
| - | [[Category: Peterson, S N.]] | + | [[Category: Onopriyenko O]] |
| - | [[Category: Savchenko, A.]] | + | [[Category: Peterson SN]] |
| - | [[Category: Shatsman, S.]] | + | [[Category: Savchenko A]] |
| - | [[Category: Skarina, T.]] | + | [[Category: Shatsman S]] |
| - | [[Category: Stogios, P J.]] | + | [[Category: Skarina T]] |
| - | [[Category: Wawrzak, Z.]] | + | [[Category: Stogios PJ]] |
| - | [[Category: Baldcb]]
| + | [[Category: Wawrzak Z]] |
| - | [[Category: Center for structural genomics of infectious disease]]
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| - | [[Category: Csgid]]
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| - | [[Category: D-carboxypeptidase]]
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| - | [[Category: Hedgehog/dd-peptidase fold]]
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| - | [[Category: Hydrolase]]
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| - | [[Category: Merops family m15b]]
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| - | [[Category: National institute of allergy and infectious disease]]
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| - | [[Category: Niaid]]
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| - | [[Category: Peptidoglycan metallopeptidase]]
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| - | [[Category: Structural genomic]]
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| - | [[Category: Substrate l-ala-d-iso-gln-l-lys-d-ala]]
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| - | [[Category: Tetrapeptidase]]
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| - | [[Category: Vany-like family]]
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| - | [[Category: Zinc-dependent metallopeptidase]]
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