View source for 5mtd


==Crystal structure of PDF from the Vibrio parahaemolyticus bacteriophage VP16T - crystal form II==
<StructureSection load='5mtd' size='340' side='right'caption='[[5mtd]], [[Resolution|resolution]] 1.50&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[5mtd]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Vibrio_phage_VP16T Vibrio phage VP16T]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5MTD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5MTD FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.5&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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=5mtd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5mtd OCA], [https://pdbe.org/5mtd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5mtd RCSB], [https://www.ebi.ac.uk/pdbsum/5mtd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5mtd ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/Q6VT21_9CAUD Q6VT21_9CAUD] 
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Prokaryotic proteins must be deformylated before the removal of their first methionine. Peptide deformylase (PDF) is indispensable and guarantees this mechanism. Recent metagenomics studies revealed new idiosyncratic PDF forms as the most abundant family of viral sequences. Little is known regarding these viral PDFs, including the capacity of the corresponding encoded proteins to ensure deformylase activity. We provide here the first evidence that viral PDFs, including the shortest PDF identified to date, Vp16 PDF, display deformylase activity in vivo, despite the absence of the key ribosome-interacting C-terminal region. Moreover, characterization of phage Vp16 PDF underscores unexpected structural and molecular features with the C-terminal Isoleucine residue significantly contributing to deformylase activity both in vitro and in vivo. This residue fully compensates for the absence of the usual long C-domain. Taken together, these data elucidate an unexpected mechanism of enzyme natural evolution and adaptation within viral sequences.

The C-terminal residue of phage Vp16 PDF, the smallest peptide deformylase, acts as an offset element locking the active conformation.,Grzela R, Nusbaum J, Fieulaine S, Lavecchia F, Bienvenut WV, Dian C, Meinnel T, Giglione C Sci Rep. 2017 Sep 8;7(1):11041. doi: 10.1038/s41598-017-11329-3. PMID:28887476<ref>PMID:28887476</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 5mtd" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Vibrio phage VP16T]]
[[Category: Fieulaine S]]
[[Category: Giglione C]]
[[Category: Grzela R]]
[[Category: Meinnel T]]