This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.
Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.
3g5p
From Proteopedia
(Difference between revisions)
m (Protected "3g5p" [edit=sysop:move=sysop]) |
|||
| Line 1: | Line 1: | ||
| - | [[ | + | ==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]] | ||
| Line 26: | Line 45: | ||
[[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
| |||||||||||
