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| | <StructureSection load='1zy1' size='340' side='right'caption='[[1zy1]], [[Resolution|resolution]] 3.00Å' scene=''> | | <StructureSection load='1zy1' size='340' side='right'caption='[[1zy1]], [[Resolution|resolution]] 3.00Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[1zy1]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Arath Arath]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ZY1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1ZY1 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[1zy1]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ZY1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1ZY1 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 3Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1zxz|1zxz]], [[1zy0|1zy0]]</div></td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">PDF1A ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 ARATH])</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=1zy1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1zy1 OCA], [https://pdbe.org/1zy1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1zy1 RCSB], [https://www.ebi.ac.uk/pdbsum/1zy1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1zy1 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=1zy1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1zy1 OCA], [https://pdbe.org/1zy1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1zy1 RCSB], [https://www.ebi.ac.uk/pdbsum/1zy1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1zy1 ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[https://www.uniprot.org/uniprot/DEF1A_ARATH DEF1A_ARATH]] Removes the formyl group from the N-terminal Met of newly synthesized proteins.<ref>PMID:11060042</ref>
| + | [https://www.uniprot.org/uniprot/DEF1A_ARATH DEF1A_ARATH] Removes the formyl group from the N-terminal Met of newly synthesized proteins.<ref>PMID:11060042</ref> |
| | == 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: Arath]] | |
| - | [[Category: Large Structures]] | |
| - | [[Category: Peptide deformylase]] | |
| - | [[Category: Dardel, F]] | |
| - | [[Category: Ferrer, J L]] | |
| - | [[Category: Fieulaine, S]] | |
| - | [[Category: Giglione, C]] | |
| - | [[Category: Juillan-Binard, C]] | |
| - | [[Category: Meinnel, T]] | |
| - | [[Category: Serero, A]] | |
| | [[Category: Arabidopsis thaliana]] | | [[Category: Arabidopsis thaliana]] |
| - | [[Category: Eukaryote]] | + | [[Category: Large Structures]] |
| - | [[Category: Higher plant]] | + | [[Category: Dardel F]] |
| - | [[Category: Hydrolase]] | + | [[Category: Ferrer J-L]] |
| - | [[Category: Pdf1a]] | + | [[Category: Fieulaine S]] |
| - | [[Category: Zinc ion]] | + | [[Category: Giglione C]] |
| | + | [[Category: Juillan-Binard C]] |
| | + | [[Category: Meinnel T]] |
| | + | [[Category: Serero A]] |
| Structural highlights
Function
DEF1A_ARATH Removes the formyl group from the N-terminal Met of newly synthesized proteins.[1]
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 (PDF) inhibitors have a strong potential to be used as a new class of antibiotics. However, recent studies have shown that the mitochondria of most eukaryotes, including humans, contain an essential PDF, PDF1A. The crystal structure of the Arabidopsis thaliana PDF1A (AtPDF1A), considered representative of PDF1As in general, has been determined. This structure displays several similarities to that of known bacterial PDFs. AtPDF1A behaves as a dimer, with the C-terminal residues responsible for linking the two subunits. This arrangement is similar to that of Leptospira interrogans PDF, the only other dimeric PDF identified to date. AtPDF1A is the first PDF for which zinc has been identified as the catalytic ion. However, the zinc binding pocket does not differ from the binding pockets of PDFs with iron rather than zinc. The crystal structure of AtPDF1A in complex with a substrate analog revealed that the substrate binding pocket of PDF1A displays strong modifications. The S1' binding pocket is significantly narrower, due to the creation of a floor from residues present in all PDF1As but not in bacterial PDFs. A true S3' pocket is created by the residues of a helical CD-loop, which is very long in PDF1As. Finally, these modified substrate binding pockets modify the position of the substrate in the active site. These differences provide guidelines for the design of bacterial PDF inhibitors that will not target mitochondrial PDFs.
The crystal structure of mitochondrial (Type 1A) peptide deformylase provides clear guidelines for the design of inhibitors specific for the bacterial forms.,Fieulaine S, Juillan-Binard C, Serero A, Dardel F, Giglione C, Meinnel T, Ferrer JL J Biol Chem. 2005 Dec 23;280(51):42315-24. Epub 2005 Sep 28. PMID:16192279[2]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Giglione C, Serero A, Pierre M, Boisson B, Meinnel T. Identification of eukaryotic peptide deformylases reveals universality of N-terminal protein processing mechanisms. EMBO J. 2000 Nov 1;19(21):5916-29. PMID:11060042 doi:10.1093/emboj/19.21.5916
- ↑ Fieulaine S, Juillan-Binard C, Serero A, Dardel F, Giglione C, Meinnel T, Ferrer JL. The crystal structure of mitochondrial (Type 1A) peptide deformylase provides clear guidelines for the design of inhibitors specific for the bacterial forms. J Biol Chem. 2005 Dec 23;280(51):42315-24. Epub 2005 Sep 28. PMID:16192279 doi:10.1074/jbc.M507155200
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