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3iiq

From Proteopedia

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[[Image:3iiq.png|left|200px]]
 
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==Crystallographic analysis of bacterial signal peptidase in ternary complex with Arylomycin A2 and a beta-sultam inhibitor==
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The line below this paragraph, containing "STRUCTURE_3iiq", creates the "Structure Box" on the page.
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<StructureSection load='3iiq' size='340' side='right'caption='[[3iiq]], [[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'>[[3iiq]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12] and [https://en.wikipedia.org/wiki/Streptomyces_sp. Streptomyces sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IIQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3IIQ 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=5PG:(2S)-(4-HYDROXYPHENYL)(METHYLAMINO)ETHANOIC+ACID'>5PG</scene>, <scene name='pdbligand=CCN:ACETONITRILE'>CCN</scene>, <scene name='pdbligand=DAL:D-ALANINE'>DAL</scene>, <scene name='pdbligand=DSE:N-METHYL-D-SERINE'>DSE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=JZA:4-[(1,1-DIOXIDO-1,2-THIAZETIDIN-2-YL)CARBONYL]MORPHOLINE'>JZA</scene>, <scene name='pdbligand=M12:10-METHYLUNDECANOIC+ACID'>M12</scene>, <scene name='pdbligand=TRT:FRAGMENT+OF+TRITON+X-100'>TRT</scene></td></tr>
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{{STRUCTURE_3iiq| PDB=3iiq | 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=3iiq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3iiq OCA], [https://pdbe.org/3iiq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3iiq RCSB], [https://www.ebi.ac.uk/pdbsum/3iiq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3iiq ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/LEP_ECOLI LEP_ECOLI]
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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/ii/3iiq_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=3iiq 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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Bacterial type I signal peptidase (SPase I), an essential membrane-bound endopeptidase with a unique Ser/Lys dyad mechanism, is being investigated as a potential novel antibiotic target. We present here binding and inhibition assays along with crystallographic data that shows that the lipohexapeptide-based natural product arylomycin A2 and the morpholino-beta-sultam derivative (BAL0019193) inhibit SPase I by binding to non-overlapping subsites near the catalytic center. The 2.0 A resolution crystal structure of the soluble catalytic domain of Escherichia coli SPase I (SPase I Delta2-75) in ternary complex with arylomycin A2 and BAL0019193 reveals the position of BAL0019193 adjacent to arylomycin A2 within the SPase I binding site. BAL0019193 binds in a noncovalent manner in close proximity to SPase I residues Ser88, Ser90, Lys145, Asn277, Ala279, and Glu307, as well as atom O45 of arylomycin A2. The binding mode of arylomycin A2 in this 2.0 A resolution ternary complex is compared to that seen in the previous 2.5 A resolution arylomycin A2-SPase cocrystal structure. This work contributes to our understanding of SPase I inhibitor/substrate recognition and should prove helpful in the further development of novel antibiotics based on the inhibition of SPase I.
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===Crystallographic analysis of bacterial signal peptidase in ternary complex with Arylomycin A2 and a beta-sultam inhibitor===
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Crystallographic analysis of bacterial signal peptidase in ternary complex with arylomycin A2 and a beta-sultam inhibitor.,Luo C, Roussel P, Dreier J, Page MG, Paetzel M Biochemistry. 2009 Sep 29;48(38):8976-84. PMID:19655811<ref>PMID:19655811</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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The line below this paragraph, {{ABSTRACT_PUBMED_19655811}}, adds the Publication Abstract to the page
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<div class="pdbe-citations 3iiq" style="background-color:#fffaf0;"></div>
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(as it appears on PubMed at http://www.pubmed.gov), where 19655811 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_19655811}}
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__TOC__
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</StructureSection>
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==About this Structure==
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[[Category: Escherichia coli K-12]]
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[[3iiq]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] and [http://en.wikipedia.org/wiki/Streptomyces_sp. Streptomyces sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IIQ OCA].
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[[Category: Large Structures]]
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[[Category: Streptomyces sp]]
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==Reference==
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[[Category: Paetzel M]]
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<ref group="xtra">PMID:019655811</ref><references group="xtra"/>
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[[Category: Escherichia coli]]
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[[Category: Signal peptidase I]]
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[[Category: Streptomyces sp.]]
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[[Category: Paetzel, M.]]
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[[Category: Antibiotic]]
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[[Category: Biaryl bridge]]
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[[Category: Hydrolase-antibiotic-inhibitor complex]]
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[[Category: Lipopeptide]]
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[[Category: Morpholino beta-sultam]]
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[[Category: Peptidase]]
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[[Category: Ser/lys dyad]]
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[[Category: Serine protease]]
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Current revision

Crystallographic analysis of bacterial signal peptidase in ternary complex with Arylomycin A2 and a beta-sultam inhibitor

PDB ID 3iiq

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