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| | <StructureSection load='2i8c' size='340' side='right'caption='[[2i8c]], [[Resolution|resolution]] 2.46Å' scene=''> | | <StructureSection load='2i8c' size='340' side='right'caption='[[2i8c]], [[Resolution|resolution]] 2.46Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2i8c]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Staac Staac]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2I8C OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2I8C FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[2i8c]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Staphylococcus_aureus_subsp._aureus_COL Staphylococcus aureus subsp. aureus COL]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2I8C OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2I8C FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 2.46Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2i80|2i80]], [[2i87|2i87]]</div></td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=93062 STAAC])</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=2i8c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2i8c OCA], [https://pdbe.org/2i8c PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2i8c RCSB], [https://www.ebi.ac.uk/pdbsum/2i8c PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2i8c 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=2i8c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2i8c OCA], [https://pdbe.org/2i8c PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2i8c RCSB], [https://www.ebi.ac.uk/pdbsum/2i8c PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2i8c 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). |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: D-alanine--D-alanine ligase]] | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Staac]] | + | [[Category: Staphylococcus aureus subsp. aureus COL]] |
| - | [[Category: Chang, J S]] | + | [[Category: Chang JS]] |
| - | [[Category: Herberg, J T]] | + | [[Category: Herberg JT]] |
| - | [[Category: Horng, M]] | + | [[Category: Horng M]] |
| - | [[Category: Lin, A H]] | + | [[Category: Lin AH]] |
| - | [[Category: Liu, S]] | + | [[Category: Liu S]] |
| - | [[Category: Marotti, K R]] | + | [[Category: Marotti KR]] |
| - | [[Category: Tomich, P K]] | + | [[Category: Tomich PK]] |
| - | [[Category: Adp complex]]
| + | |
| - | [[Category: D-alanine:d-alanine ligase]]
| + | |
| - | [[Category: Lyase]]
| + | |
| - | [[Category: Staphylococcus aureus]]
| + | |
| Structural highlights
Function
DDL_STAAC Cell wall formation (By similarity).
Evolutionary Conservation
Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.
Publication Abstract from PubMed
D-alanine:D-alanine ligase (DDl) is an essential enzyme in bacterial cell wall biosynthesis and an important target for developing new antibiotics. It catalyzes the formation of D-alanine:D-alanine dipeptide, sequentially by using one D-alanine and one ATP as substrates for the first-half reaction, and a second D-alanine substrate to complete the reaction. Some gain of function DDl mutants can use an alternate second substrate, causing resistance to vancomycin, one of the last lines of defense against life-threatening Gram-positive infections. Here, we report the crystal structure of Staphylococcus aureus DDl (StaDDl) and its cocrystal structures with 3-chloro-2,2-dimethyl-N-[4(trifluoromethyl)phenyl]propanamide (inhibitor 1) (Ki=4 microM against StaDDl) and with ADP, one of the reaction products, at resolutions of 2.0, 2.2, and 2.6 A, respectively. The overall structure of StaDDl can be divided into three distinct domains. The inhibitor binds to a hydrophobic pocket at the interface of the first and the third domain. This inhibitor-binding pocket is adjacent to the first D-alanine substrate site but does not overlap with any substrate sites. An allosteric inhibition mechanism of StaDDl by this compound was proposed. The mechanism provides the basis for developing new antibiotics targeting D-alanine:D-alanine ligase. Because this compound only interacts with residues from the first D-alanine site, inhibitors with this binding mode potentially could overcome vancomycin resistance.
Allosteric inhibition of Staphylococcus aureus D-alanine:D-alanine ligase revealed by crystallographic studies.,Liu S, Chang JS, Herberg JT, Horng MM, Tomich PK, Lin AH, Marotti KR Proc Natl Acad Sci U S A. 2006 Oct 10;103(41):15178-83. Epub 2006 Oct 2. PMID:17015835[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Liu S, Chang JS, Herberg JT, Horng MM, Tomich PK, Lin AH, Marotti KR. Allosteric inhibition of Staphylococcus aureus D-alanine:D-alanine ligase revealed by crystallographic studies. Proc Natl Acad Sci U S A. 2006 Oct 10;103(41):15178-83. Epub 2006 Oct 2. PMID:17015835
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