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| | <StructureSection load='6a6a' size='340' side='right'caption='[[6a6a]], [[Resolution|resolution]] 2.26Å' scene=''> | | <StructureSection load='6a6a' size='340' side='right'caption='[[6a6a]], [[Resolution|resolution]] 2.26Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[6a6a]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6A6A OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6A6A FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[6a6a]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Enterococcus_faecalis_V583 Enterococcus faecalis V583]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6A6A OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6A6A FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=DAL:D-ALANINE'>DAL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</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]] 2.26Å</td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Serine-type_D-Ala-D-Ala_carboxypeptidase Serine-type D-Ala-D-Ala carboxypeptidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.16.4 3.4.16.4] </span></td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=DAL:D-ALANINE'>DAL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6a6a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6a6a OCA], [http://pdbe.org/6a6a PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6a6a RCSB], [http://www.ebi.ac.uk/pdbsum/6a6a PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6a6a 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=6a6a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6a6a OCA], [https://pdbe.org/6a6a PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6a6a RCSB], [https://www.ebi.ac.uk/pdbsum/6a6a PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6a6a ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/VANY_ENTFA VANY_ENTFA]] Vancomycin-inducible, penicillin-resistant, DD-carboxypeptidase that hydrolyzes depsipeptide- and D-alanyl-D-alanine-containing peptidoglycan precursors. Insensitive to beta-lactams. | + | [https://www.uniprot.org/uniprot/VANY_ENTFA VANY_ENTFA] Vancomycin-inducible, penicillin-resistant, DD-carboxypeptidase that hydrolyzes depsipeptide- and D-alanyl-D-alanine-containing peptidoglycan precursors. Insensitive to beta-lactams. |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| | + | [[Category: Enterococcus faecalis V583]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Serine-type D-Ala-D-Ala carboxypeptidase]]
| + | [[Category: Hahn H]] |
| - | [[Category: Hahn, H]] | + | [[Category: Kim HS]] |
| - | [[Category: Kim, H S]] | + | |
| - | [[Category: Hydrolase]]
| + | |
| - | [[Category: Metallopeptidase family m15]]
| + | |
| - | [[Category: Peptidase]]
| + | |
| - | [[Category: Vancomycin resistance]]
| + | |
| Structural highlights
6a6a is a 2 chain structure with sequence from Enterococcus faecalis V583. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Method: | X-ray diffraction, Resolution 2.26Å |
| Ligands: | , , , , |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
Function
VANY_ENTFA Vancomycin-inducible, penicillin-resistant, DD-carboxypeptidase that hydrolyzes depsipeptide- and D-alanyl-D-alanine-containing peptidoglycan precursors. Insensitive to beta-lactams.
Publication Abstract from PubMed
Vancomycin resistance in Enterococci and its transfer to methicillin-resistant Staphylococcus aureus are challenging problems in health care institutions worldwide. High-level vancomycin resistance is conferred by acquiring either transposable elements of the VanA or VanB type. Enterococcus faecalis VanYB in the VanB-type operon is a d,d-carboxypeptidase that recognizes the peptidyl-d-Ala(4)-d-Ala(5) extremity of peptidoglycan and hydrolyses the terminal d-Ala on the extracellular side of the cell wall, thereby increasing the level of glycopeptide antibiotics resistance. However, at the molecular level, it remains unclear how VanYB manipulates peptidoglycan peptides for vancomycin resistance. In this study, we have determined the crystal structures of E. faecalis VanYB in the d-Ala-d-Ala-bound, d-Ala-bound, and -unbound states. The interactions between VanYB and d-Ala-d-Ala observed in the crystal provide the molecular basis for the recognition of peptidoglycan substrates by VanYB. Moreover, comparisons with the related VanX and VanXY enzymes reveal distinct structural features of E. faecalis VanYB around the active-site cleft, thus shedding light on its unique substrate specificity. Our results could serve as the foundation for unravelling the molecular mechanism of vancomycin resistance and for developing novel antibiotics against the vancomycin-resistant Enterococcus species.
Structural basis for the substrate recognition of peptidoglycan pentapeptides by Enterococcus faecalis VanYB.,Kim HS, Hahn H, Kim J, Jang DM, Lee JY, Back JM, Im HN, Kim H, Han BW, Suh SW Int J Biol Macromol. 2018 Jul 27;119:335-344. doi:, 10.1016/j.ijbiomac.2018.07.081. PMID:30016658[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Kim HS, Hahn H, Kim J, Jang DM, Lee JY, Back JM, Im HN, Kim H, Han BW, Suh SW. Structural basis for the substrate recognition of peptidoglycan pentapeptides by Enterococcus faecalis VanYB. Int J Biol Macromol. 2018 Jul 27;119:335-344. doi:, 10.1016/j.ijbiomac.2018.07.081. PMID:30016658 doi:http://dx.doi.org/10.1016/j.ijbiomac.2018.07.081
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