3g5k: Difference between revisions
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[[Image: | ==Structure and activity of human mitochondrial peptide deformylase, a novel cancer target== | ||
<StructureSection load='3g5k' size='340' side='right' caption='[[3g5k]], [[Resolution|resolution]] 1.70Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[3g5k]] 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=3G5K OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3G5K FirstGlance]. <br> | |||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BB2:ACTINONIN'>BB2</scene>, <scene name='pdbligand=CO:COBALT+(II)+ION'>CO</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]], [[3g5p|3g5p]]</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=3g5k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3g5k OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3g5k RCSB], [http://www.ebi.ac.uk/pdbsum/3g5k 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/g5/3g5k_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: Actinonin]] | [[Category: Actinonin]] | ||
[[Category: Hydrolase]] | [[Category: Hydrolase]] | ||
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[[Category: Metal-binding]] | [[Category: Metal-binding]] | ||
[[Category: Mitochondrion]] | [[Category: Mitochondrion]] | ||
[[Category: Protein biosynthesis]] | [[Category: Protein biosynthesis]] | ||
[[Category: Transit peptide]] | [[Category: Transit peptide]] | ||
Revision as of 10:12, 3 December 2014
Structure and activity of human mitochondrial peptide deformylase, a novel cancer target
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