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| | <StructureSection load='3u7n' size='340' side='right'caption='[[3u7n]], [[Resolution|resolution]] 2.30Å' scene=''> | | <StructureSection load='3u7n' size='340' side='right'caption='[[3u7n]], [[Resolution|resolution]] 2.30Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3u7n]] is a 1 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=3U7N OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3U7N FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3u7n]] is a 1 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=3U7N OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3U7N FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=UHF:N-((2R,4S)-2-BUTYL-5-METHYL-4-(3-(5-METHYLPYRIDIN-2-YL)UREIDO)-3-OXOHEXYL)-N-HYDROXYFORMAMIDE'>UHF</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 2.3Å</td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSD:3-SULFINOALANINE'>CSD</scene></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CSD:3-SULFINOALANINE'>CSD</scene>, <scene name='pdbligand=UHF:N-((2R,4S)-2-BUTYL-5-METHYL-4-(3-(5-METHYLPYRIDIN-2-YL)UREIDO)-3-OXOHEXYL)-N-HYDROXYFORMAMIDE'>UHF</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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;'>[[3u7k|3u7k]], [[3u7l|3u7l]], [[3u7m|3u7m]]</div></td></tr>
| + | |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">sacol1100 ([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/Peptide_deformylase Peptide deformylase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.88 3.5.1.88] </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=3u7n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3u7n OCA], [https://pdbe.org/3u7n PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3u7n RCSB], [https://www.ebi.ac.uk/pdbsum/3u7n PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3u7n 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=3u7n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3u7n OCA], [https://pdbe.org/3u7n PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3u7n RCSB], [https://www.ebi.ac.uk/pdbsum/3u7n PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3u7n ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[https://www.uniprot.org/uniprot/DEF_STAAC DEF_STAAC]] Removes the formyl group from the N-terminal Met of newly synthesized proteins. Requires at least a dipeptide for an efficient rate of reaction. N-terminal L-methionine is a prerequisite for activity but the enzyme has broad specificity at other positions.[HAMAP-Rule:MF_00163]
| + | [https://www.uniprot.org/uniprot/DEF_STAAC DEF_STAAC] Removes the formyl group from the N-terminal Met of newly synthesized proteins. Requires at least a dipeptide for an efficient rate of reaction. N-terminal L-methionine is a prerequisite for activity but the enzyme has broad specificity at other positions.[HAMAP-Rule:MF_00163] |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | </StructureSection> | | </StructureSection> |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Peptide deformylase]] | + | [[Category: Staphylococcus aureus subsp. aureus COL]] |
| - | [[Category: Staac]] | + | [[Category: Kim KK]] |
| - | [[Category: Kim, K K]] | + | [[Category: Lee BJ]] |
| - | [[Category: Lee, B J]] | + | [[Category: Lee HH]] |
| - | [[Category: Lee, H H]] | + | [[Category: Lee S-J]] |
| - | [[Category: Lee, S J]] | + | [[Category: Lee SJ]] |
| - | [[Category: Lee, S K]] | + | [[Category: Lee SK]] |
| - | [[Category: Suh, S W]] | + | [[Category: Suh SW]] |
| - | [[Category: Yoon, H J]] | + | [[Category: Yoon H-J]] |
| - | [[Category: Hydrolase]]
| + | |
| - | [[Category: Hydrolase-hydrolase inhibitor complex]]
| + | |
| - | [[Category: Pdf]]
| + | |
| - | [[Category: Pdf-inhibitor]]
| + | |
| Structural highlights
Function
DEF_STAAC Removes the formyl group from the N-terminal Met of newly synthesized proteins. Requires at least a dipeptide for an efficient rate of reaction. N-terminal L-methionine is a prerequisite for activity but the enzyme has broad specificity at other positions.[HAMAP-Rule:MF_00163]
Publication Abstract from PubMed
Peptide deformylase (PDF) catalyzes the removal of the formyl group from the N-terminal methionine residue in newly synthesized polypeptides, which is an essential process in bacteria. Four new inhibitors of PDF that belong to two different classes, hydroxamate/pseudopeptide compounds [PMT387 (7a) and PMT497] and reverse-hydroxamate/nonpeptide compounds [PMT1039 (15e) and PMT1067], have been developed. These compounds inhibited the growth of several pathogens involved in respiratory-tract infections, such as Streptococcus pneumoniae, Moraxella catarrhalis and Haemophilus influenzae, and leading nosocomial pathogens such as Staphylococcus aureus and Klebsiella pneumoniae with a minimum inhibitory concentration (MIC) in the range 0.1-0.8 mg ml(-1). Interestingly, the reverse-hydroxamate/nonpeptide compounds showed a 250-fold higher antimicrobial activity towards S. aureus, although the four compounds showed similar K(i) values against S. aureus PDF enzymes, with K(i) values in the 11-85 nM range. To provide a structural basis for the discovery of additional PDF inhibitors, the crystal structures of S. aureus PDF in complex with the four inhibitors were determined at resolutions of 1.90-2.30 A. The inhibitor-bound structures displayed distinct deviations depending on the inhibitor class. The distance between the Zn(2+) ion and the carbonyl O atom of the hydroxamate inhibitors (or the hydroxyl O atom of the reverse-hydroxamate inhibitors) appears to be correlated to S. aureus inhibition activity. The structural information reported in this study should aid in the discovery of new PDF inhibitors that can be used as novel antibacterial drugs.
Structures of Staphylococcus aureus peptide deformylase in complex with two classes of new inhibitors.,Lee SJ, Lee SJ, Lee SK, Yoon HJ, Lee HH, Kim KK, Lee BJ, Lee BI, Suh SW Acta Crystallogr D Biol Crystallogr. 2012 Jul;68(Pt 7):784-93. doi:, 10.1107/S0907444912011912. Epub 2012 Jun 15. PMID:22751663[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Lee SJ, Lee SJ, Lee SK, Yoon HJ, Lee HH, Kim KK, Lee BJ, Lee BI, Suh SW. Structures of Staphylococcus aureus peptide deformylase in complex with two classes of new inhibitors. Acta Crystallogr D Biol Crystallogr. 2012 Jul;68(Pt 7):784-93. doi:, 10.1107/S0907444912011912. Epub 2012 Jun 15. PMID:22751663 doi:http://dx.doi.org/10.1107/S0907444912011912
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