1t7d: Difference between revisions

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{{Seed}}
[[Image:1t7d.png|left|200px]]


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==Crystal structure of Escherichia coli type I signal peptidase in complex with a lipopeptide inhibitor==
The line below this paragraph, containing "STRUCTURE_1t7d", creates the "Structure Box" on the page.
<StructureSection load='1t7d' size='340' side='right'caption='[[1t7d]], [[Resolution|resolution]] 2.47&Aring;' scene=''>
You may change the PDB parameter (which sets the PDB file loaded into the applet)  
== Structural highlights ==
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
<table><tr><td colspan='2'>[[1t7d]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] 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=1T7D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1T7D FirstGlance]. <br>
or leave the SCENE parameter empty for the default display.
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.47&#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=DAL:D-ALANINE'>DAL</scene>, <scene name='pdbligand=DSE:N-METHYL-D-SERINE'>DSE</scene>, <scene name='pdbligand=M12:10-METHYLUNDECANOIC+ACID'>M12</scene></td></tr>
{{STRUCTURE_1t7d|  PDB=1t7d  |  SCENE=  }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1t7d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1t7d OCA], [https://pdbe.org/1t7d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1t7d RCSB], [https://www.ebi.ac.uk/pdbsum/1t7d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1t7d ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/LEP_ECOLI LEP_ECOLI]
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
  <jmolCheckbox>
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/t7/1t7d_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
    <text>to colour the structure by Evolutionary Conservation</text>
  </jmolCheckbox>
</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=1t7d ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
We report here the crystallographic and biophysical analysis of a soluble, catalytically active fragment of the Escherichia coli type I signal peptidase (SPase Delta2-75) in complex with arylomycin A2. The 2.5-A resolution structure revealed that the inhibitor is positioned with its COOH-terminal carboxylate oxygen (O45) within hydrogen bonding distance of all the functional groups in the catalytic center of the enzyme (Ser90 O-gamma, Lys145 N-zeta, and Ser88 O-gamma) and that it makes beta-sheet type interactions with the beta-strands that line each side of the binding site. Ligand binding studies, calorimetry, fluorescence spectroscopy, and stopped-flow kinetics were also used to analyze the binding mode of this unique non-covalently bound inhibitor. The crystal structure was solved in the space group P4(3)2(1)2. A detailed comparison is made to the previously published acyl-enzyme inhibitor complex structure (space group: P2(1)2(1)2) and the apo-enzyme structure (space group: P4(1)2(1)2). Together this work provides insights into the binding of pre-protein substrates to signal peptidase and will prove helpful in the development of novel antibiotics.


===Crystal structure of Escherichia coli type I signal peptidase in complex with a lipopeptide inhibitor===
Crystallographic and biophysical analysis of a bacterial signal peptidase in complex with a lipopeptide-based inhibitor.,Paetzel M, Goodall JJ, Kania M, Dalbey RE, Page MG J Biol Chem. 2004 Jul 16;279(29):30781-90. Epub 2004 May 10. PMID:15136583<ref>PMID:15136583</ref>


 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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The line below this paragraph, {{ABSTRACT_PUBMED_15136583}}, adds the Publication Abstract to the page
<div class="pdbe-citations 1t7d" style="background-color:#fffaf0;"></div>
(as it appears on PubMed at http://www.pubmed.gov), where 15136583 is the PubMed ID number.
== References ==
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<references/>
{{ABSTRACT_PUBMED_15136583}}
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</StructureSection>
==About this Structure==
1T7D is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1T7D OCA].
 
==Reference==
Crystallographic and biophysical analysis of a bacterial signal peptidase in complex with a lipopeptide-based inhibitor., Paetzel M, Goodall JJ, Kania M, Dalbey RE, Page MG, J Biol Chem. 2004 Jul 16;279(29):30781-90. Epub 2004 May 10. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15136583 15136583]
[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
[[Category: Signal peptidase I]]
[[Category: Large Structures]]
[[Category: Single protein]]
[[Category: Streptomyces sp]]
[[Category: Dalbey, R E.]]
[[Category: Dalbey RE]]
[[Category: Goodall, J J.]]
[[Category: Goodall JJ]]
[[Category: Kania, M.]]
[[Category: Kania M]]
[[Category: Paetzel, M.]]
[[Category: Paetzel M]]
[[Category: Page, M G.P.]]
[[Category: Page MGP]]
[[Category: Antibiotic]]
[[Category: Leader peptidase]]
[[Category: Leader peptide]]
[[Category: Lysine general base]]
[[Category: Non-covalently bound inhibitor]]
[[Category: Non-ribosomal peptide synthesis]]
[[Category: Peptide]]
[[Category: Secondary metabolite]]
[[Category: Ser/lys dyad]]
[[Category: Signal peptidase]]
[[Category: Signal peptide]]
 
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Retrieved from "https://proteopedia.org/1t7d"