3g5p
From Proteopedia
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| - | [[ | + | ==Structure and activity of human mitochondrial peptide deformylase, a novel cancer target== |
| + | <StructureSection load='3g5p' size='340' side='right' caption='[[3g5p]], [[Resolution|resolution]] 1.70Å' scene=''> | ||
| + | == Structural highlights == | ||
| + | <table><tr><td colspan='2'>[[3g5p]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3G5P OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3G5P FirstGlance]. <br> | ||
| + | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr> | ||
| + | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1g2a|1g2a]], [[1ix1|1ix1]], [[1lqw|1lqw]], [[1zy0|1zy0]], [[1zy1|1zy1]], [[3g5k|3g5k]]</td></tr> | ||
| + | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">PDF, PDF1A ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</td></tr> | ||
| + | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Peptide_deformylase Peptide deformylase], with EC number [http://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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3g5p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3g5p OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3g5p RCSB], [http://www.ebi.ac.uk/pdbsum/3g5p PDBsum]</span></td></tr> | ||
| + | </table> | ||
| + | == 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/g5/3g5p_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/chain_selection.php?pdb_ID=2ata ConSurf]. | ||
| + | <div style="clear:both"></div> | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | Peptide deformylase proteins (PDFs) participate in the N-terminal methionine excision pathway of newly synthesized peptides. We show that the human PDF (HsPDF) can deformylate its putative substrates derived from mitochondrial DNA-encoded proteins. The first structural model of a mammalian PDF (1.7 A), HsPDF, shows a dimer with conserved topology of the catalytic residues and fold as non-mammalian PDFs. The HsPDF C-terminus topology and the presence of a helical loop (H2 and H3), however, shape a characteristic active site entrance. The structure of HsPDF bound to the peptidomimetic inhibitor actinonin (1.7 A) identified the substrate-binding site. A defined S1' pocket, but no S2' or S3' substrate-binding pockets, exists. A conservation of PDF-actinonin interaction across PDFs was observed. Despite the lack of true S2' and S3' binding pockets, confirmed through peptide binding modeling, enzyme kinetics suggest a combined contribution from P2'and P3' positions of a formylated peptide substrate to turnover. | ||
| - | + | Structure and activity of human mitochondrial peptide deformylase, a novel cancer target.,Escobar-Alvarez S, Goldgur Y, Yang G, Ouerfelli O, Li Y, Scheinberg DA J Mol Biol. 2009 Apr 17;387(5):1211-28. Epub 2009 Feb 21. PMID:19236878<ref>PMID:19236878</ref> | |
| - | + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |
| - | + | </div> | |
| - | + | == References == | |
| - | + | <references/> | |
| - | + | __TOC__ | |
| - | + | </StructureSection> | |
| - | + | ||
| - | == | + | |
| - | < | + | |
[[Category: Homo sapiens]] | [[Category: Homo sapiens]] | ||
[[Category: Peptide deformylase]] | [[Category: Peptide deformylase]] | ||
| - | [[Category: Escobar-Alvarez, S | + | [[Category: Escobar-Alvarez, S]] |
| - | [[Category: Goldgur, Y | + | [[Category: Goldgur, Y]] |
| - | [[Category: Li, Y | + | [[Category: Li, Y]] |
| - | [[Category: Ouerfelli, O | + | [[Category: Ouerfelli, O]] |
| - | [[Category: Scheinberg, D A | + | [[Category: Scheinberg, D A]] |
| - | [[Category: Yang, G | + | [[Category: Yang, G]] |
[[Category: Human]] | [[Category: Human]] | ||
[[Category: Hydrolase]] | [[Category: Hydrolase]] | ||
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[[Category: Mitochondria]] | [[Category: Mitochondria]] | ||
[[Category: Mitochondrion]] | [[Category: Mitochondrion]] | ||
| - | [[Category: Peptide deformylase]] | ||
[[Category: Protein biosynthesis]] | [[Category: Protein biosynthesis]] | ||
[[Category: Transit peptide]] | [[Category: Transit peptide]] | ||
Revision as of 10:24, 3 December 2014
Structure and activity of human mitochondrial peptide deformylase, a novel cancer target
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