3g5k

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[[Image:3g5k.png|left|200px]]
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==Structure and activity of human mitochondrial peptide deformylase, a novel cancer target==
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<StructureSection load='3g5k' size='340' side='right' caption='[[3g5k]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
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== Structural highlights ==
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<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>
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</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>
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<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>
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<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>
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<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>
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<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>
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</table>
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/g5/3g5k_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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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.
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{{STRUCTURE_3g5k| PDB=3g5k | SCENE= }}
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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>
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===Structure and activity of human mitochondrial peptide deformylase, a novel cancer target===
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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{{ABSTRACT_PUBMED_19236878}}
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== References ==
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<references/>
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==About this Structure==
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__TOC__
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[[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].
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</StructureSection>
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==Reference==
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<ref group="xtra">PMID:019236878</ref><references group="xtra"/>
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[[Category: Homo sapiens]]
[[Category: Homo sapiens]]
[[Category: Peptide deformylase]]
[[Category: Peptide deformylase]]
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[[Category: Escobar-Alvarez, S.]]
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[[Category: Escobar-Alvarez, S]]
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[[Category: Goldgur, Y.]]
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[[Category: Goldgur, Y]]
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[[Category: Li, Y.]]
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[[Category: Li, Y]]
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[[Category: Ouerfelli, O.]]
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[[Category: Ouerfelli, O]]
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[[Category: Scheinberg, D A.]]
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[[Category: Scheinberg, D A]]
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[[Category: Yang, G.]]
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[[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]]
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[[Category: Peptide deformylase]]
 
[[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

3g5k, resolution 1.70Å

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