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| | <StructureSection load='3n8d' size='340' side='right'caption='[[3n8d]], [[Resolution|resolution]] 2.30Å' scene=''> | | <StructureSection load='3n8d' size='340' side='right'caption='[[3n8d]], [[Resolution|resolution]] 2.30Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3n8d]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/"micrococcus_aureus"_(rosenbach_1884)_zopf_1885 "micrococcus aureus" (rosenbach 1884) zopf 1885]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3N8D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3N8D FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3n8d]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Staphylococcus_aureus Staphylococcus aureus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3N8D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3N8D FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 2.3Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2i87|2i87]], [[2i80|2i80]], [[2i8c|2i8c]]</div></td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ddl ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1280 "Micrococcus aureus" (Rosenbach 1884) Zopf 1885])</td></tr> | + | |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/D-alanine--D-alanine_ligase D-alanine--D-alanine ligase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.3.2.4 6.3.2.4] </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=3n8d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3n8d OCA], [https://pdbe.org/3n8d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3n8d RCSB], [https://www.ebi.ac.uk/pdbsum/3n8d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3n8d 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=3n8d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3n8d OCA], [https://pdbe.org/3n8d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3n8d RCSB], [https://www.ebi.ac.uk/pdbsum/3n8d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3n8d ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[https://www.uniprot.org/uniprot/DDL_STAAC DDL_STAAC]] Cell wall formation (By similarity).
| + | [https://www.uniprot.org/uniprot/DDL_STAAC DDL_STAAC] Cell wall formation (By similarity). |
| | <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: D-alanine--D-alanine ligase]] | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Haouz, A]] | + | [[Category: Staphylococcus aureus]] |
| - | [[Category: Meziane-Cherif, D]] | + | [[Category: Haouz A]] |
| - | [[Category: Saul, F A]]
| + | [[Category: Meziane-Cherif D]] |
| - | [[Category: Cell wall synthesis]] | + | [[Category: Saul FA]] |
| - | [[Category: D-ala:d-ala ligase]]
| + | |
| - | [[Category: Ligase]] | + | |
| - | [[Category: Vancomycin dependence]]
| + | |
| Structural highlights
Function
DDL_STAAC Cell wall formation (By similarity).
Publication Abstract from PubMed
The vancomycin-resistant Staphylococcus aureus VRSA-9 clinical isolate was partially dependent on glycopeptide for growth. The responsible vanA operon had the same organization as that of Tn1546 and was located on a plasmid. The chromosomal D-Ala:D-Ala ligase (ddl) gene had two point mutations that led to Q260K and A283E substitutions, resulting in a 200-fold decrease in enzymatic activity compared to that of the wild-type strain VRSA-6. To gain insight into the mechanism of enzyme impairment, we determined the crystal structure of VRSA-9 Ddl and showed that the A283E mutation induces new ion pair/hydrogen bond interactions, leading to an asymmetric rearrangement of side chains in the dimer interface. The Q260K substitution is located in an exposed external loop and did not induce any significant conformational change. The VRSA-9 strain was susceptible to oxacillin due to synthesis of pentadepsipeptide precursors ending in D-alanyl-D-lactate which are not substrates for the beta-lactam-resistant penicillin binding protein PBP2'. Comparison with the partially vancomycin-dependent VRSA-7, whose Ddl is 5-fold less efficient than that of VRSA-9, indicated that the levels of vancomycin dependence and susceptibility to beta-lactams correlate with the degree of Ddl impairment. Ddl drug targeting could therefore be an effective strategy against vancomycin-resistant S. aureus.
Molecular basis of vancomycin dependence in VanA-type Staphylococcus aureus VRSA-9.,Meziane-Cherif D, Saul FA, Moubareck C, Weber P, Haouz A, Courvalin P, Perichon B J Bacteriol. 2010 Oct;192(20):5465-71. Epub 2010 Aug 20. PMID:20729361[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Meziane-Cherif D, Saul FA, Moubareck C, Weber P, Haouz A, Courvalin P, Perichon B. Molecular basis of vancomycin dependence in VanA-type Staphylococcus aureus VRSA-9. J Bacteriol. 2010 Oct;192(20):5465-71. Epub 2010 Aug 20. PMID:20729361 doi:10.1128/JB.00613-10
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