2i87

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{{Seed}}
 
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[[Image:2i87.png|left|200px]]
 
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==Allosteric inhibition of Staphylococcus aureus D-alanine:D-alanine ligase revealed by crystallographic studies==
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The line below this paragraph, containing "STRUCTURE_2i87", creates the "Structure Box" on the page.
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<StructureSection load='2i87' size='340' side='right'caption='[[2i87]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[2i87]] 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=2I87 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2I87 FirstGlance]. <br>
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or leave the SCENE parameter empty for the default display.
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</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&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
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{{STRUCTURE_2i87| PDB=2i87 | SCENE= }}
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2i87 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2i87 OCA], [https://pdbe.org/2i87 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2i87 RCSB], [https://www.ebi.ac.uk/pdbsum/2i87 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2i87 ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/DDL_STAAC DDL_STAAC] Cell wall formation (By similarity).
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/i8/2i87_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2i87 ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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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.
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===Allosteric inhibition of Staphylococcus aureus D-alanine:D-alanine ligase revealed by crystallographic studies===
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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<ref>PMID:17015835</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 2i87" style="background-color:#fffaf0;"></div>
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==See Also==
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The line below this paragraph, {{ABSTRACT_PUBMED_17015835}}, adds the Publication Abstract to the page
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*[[D-alanine-D-alanine ligase 3D structures|D-alanine-D-alanine ligase 3D structures]]
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(as it appears on PubMed at http://www.pubmed.gov), where 17015835 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_17015835}}
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__TOC__
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</StructureSection>
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==About this Structure==
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[[Category: Large Structures]]
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2I87 is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Staphylococcus_aureus Staphylococcus aureus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2I87 OCA].
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[[Category: Staphylococcus aureus subsp. aureus COL]]
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[[Category: Chang JS]]
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==Reference==
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[[Category: Herberg JT]]
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<ref group="xtra">PMID:17015835</ref><references group="xtra"/>
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[[Category: Horng M]]
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[[Category: D-alanine--D-alanine ligase]]
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[[Category: Lin AH]]
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[[Category: Staphylococcus aureus]]
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[[Category: Liu S]]
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[[Category: Chang, J S.]]
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[[Category: Marotti KR]]
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[[Category: Herberg, J T.]]
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[[Category: Tomich PK]]
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[[Category: Horng, M.]]
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[[Category: Lin, A H.]]
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[[Category: Liu, S.]]
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[[Category: Marotti, K R.]]
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[[Category: Tomich, P K.]]
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[[Category: Apo]]
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[[Category: D-alanine:d-alanine ligase]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 22:52:44 2009''
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Current revision

Allosteric inhibition of Staphylococcus aureus D-alanine:D-alanine ligase revealed by crystallographic studies

PDB ID 2i87

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