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| | <StructureSection load='1t7d' size='340' side='right'caption='[[1t7d]], [[Resolution|resolution]] 2.47Å' scene=''> | | <StructureSection load='1t7d' size='340' side='right'caption='[[1t7d]], [[Resolution|resolution]] 2.47Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[1t7d]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895] and [http://en.wikipedia.org/wiki/Chainia_sp. Chainia 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 [http://proteopedia.org/fgij/fg.htm?mol=1T7D FirstGlance]. <br> | + | <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> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=M12:10-METHYLUNDECANOIC+ACID'>M12</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]] 2.47Å</td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><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></td></tr> | + | <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> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1b12|1b12]], [[1kn9|1kn9]], [[3iiq|3iiq]]</div></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=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> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">LEPB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>
| + | |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Signal_peptidase_I Signal peptidase I], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.89 3.4.21.89] </span></td></tr>
| + | |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=1t7d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1t7d OCA], [http://pdbe.org/1t7d PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1t7d RCSB], [http://www.ebi.ac.uk/pdbsum/1t7d PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1t7d ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/LEP_ECOLI LEP_ECOLI] |
| | == 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: Bacillus coli migula 1895]] | + | [[Category: Escherichia coli]] |
| - | [[Category: Chainia sp]]
| + | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Signal peptidase I]] | + | [[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: Biaryl bridge]]
| + | |
| - | [[Category: Hydrolase]]
| + | |
| - | [[Category: Hydrolase-antibiotic complex]]
| + | |
| - | [[Category: Lipopeptide]]
| + | |
| - | [[Category: Ser/lys dyad]]
| + | |
| - | [[Category: Signal peptidase]]
| + | |
| Structural highlights
Function
LEP_ECOLI
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
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.
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[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Paetzel M, Goodall JJ, Kania M, Dalbey RE, Page MG. Crystallographic and biophysical analysis of a bacterial signal peptidase in complex with a lipopeptide-based inhibitor. J Biol Chem. 2004 Jul 16;279(29):30781-90. Epub 2004 May 10. PMID:15136583 doi:10.1074/jbc.M401686200
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