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| | <StructureSection load='3g5k' size='340' side='right'caption='[[3g5k]], [[Resolution|resolution]] 1.70Å' scene=''> | | <StructureSection load='3g5k' size='340' side='right'caption='[[3g5k]], [[Resolution|resolution]] 1.70Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3g5k]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Human Human]. 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 [https://proteopedia.org/fgij/fg.htm?mol=3G5K FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3g5k]] is a 4 chain structure with sequence from [https://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 [https://proteopedia.org/fgij/fg.htm?mol=3G5K FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BB2:ACTINONIN'>BB2</scene>, <scene name='pdbligand=CO:COBALT+(II)+ION'>CO</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]] 1.7Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1g2a|1g2a]], [[1ix1|1ix1]], [[1lqw|1lqw]], [[1zy0|1zy0]], [[1zy1|1zy1]], [[3g5p|3g5p]]</div></td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BB2:ACTINONIN'>BB2</scene>, <scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">PDF, PDF1A ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=3g5k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3g5k OCA], [https://pdbe.org/3g5k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3g5k RCSB], [https://www.ebi.ac.uk/pdbsum/3g5k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3g5k 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=3g5k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3g5k OCA], [https://pdbe.org/3g5k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3g5k RCSB], [https://www.ebi.ac.uk/pdbsum/3g5k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3g5k ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[https://www.uniprot.org/uniprot/DEFM_HUMAN DEFM_HUMAN]] Removes the formyl group from the N-terminal Met of newly synthesized proteins.
| + | [https://www.uniprot.org/uniprot/DEFM_HUMAN DEFM_HUMAN] Removes the formyl group from the N-terminal Met of newly synthesized proteins. |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Human]] | + | [[Category: Homo sapiens]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[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 DA]] |
| - | [[Category: Scheinberg, D A]] | + | [[Category: Yang G]] |
| - | [[Category: Yang, G]] | + | |
| - | [[Category: Actinonin]]
| + | |
| - | [[Category: Hydrolase]]
| + | |
| - | [[Category: Iron]]
| + | |
| - | [[Category: Metal-binding]]
| + | |
| - | [[Category: Mitochondrion]]
| + | |
| - | [[Category: Protein biosynthesis]]
| + | |
| - | [[Category: Transit peptide]]
| + | |
| Structural highlights
Function
DEFM_HUMAN Removes the formyl group from the N-terminal Met of newly synthesized proteins.
Evolutionary Conservation
Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.
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[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Escobar-Alvarez S, Goldgur Y, Yang G, Ouerfelli O, Li Y, Scheinberg DA. Structure and activity of human mitochondrial peptide deformylase, a novel cancer target. J Mol Biol. 2009 Apr 17;387(5):1211-28. Epub 2009 Feb 21. PMID:19236878 doi:10.1016/j.jmb.2009.02.032
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