3pn3: Difference between revisions

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-[[Image:3pn3.png|left|200px]]
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+==Crystal structure of Arabidopsis thaliana petide deformylase 1B (AtPDF1B) in complex with inhibitor 21==
-The line below this paragraph, containing "STRUCTURE_3pn3", creates the "Structure Box" on the page.
+<StructureSection load='3pn3' size='340' side='right'caption='[[3pn3]], [[Resolution|resolution]] 1.30&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[3pn3]] is a 2 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=3PN3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3PN3 FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.3&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PN3:TERT-BUTYL+{(2S)-1-[FORMYL(HYDROXY)AMINO]-3-PHENYLPROPAN-2-YL}CARBAMATE'>PN3</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-{{STRUCTURE_3pn3|  PDB=3pn3  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3pn3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3pn3 OCA], [https://pdbe.org/3pn3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3pn3 RCSB], [https://www.ebi.ac.uk/pdbsum/3pn3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3pn3 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/DEF1B_ARATH DEF1B_ARATH] Removes the formyl group from the N-terminal Met of newly synthesized proteins. Has a preferred substrate specificity towards the photosystem II (PS II) D1 polypeptide.<ref>PMID:11060042</ref>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+For several decades, molecular recognition has been considered one of the most fundamental processes in biochemistry. For enzymes, substrate binding is often coupled to conformational changes that alter the local environment of the active site to align the reactive groups for efficient catalysis and to reach the transition state. Adaptive substrate recognition is a well-known concept; however, it has been poorly characterized at a structural level because of its dynamic nature. Here, we provide a detailed mechanism for an induced-fit process at atomic resolution. We take advantage of a slow, tight binding inhibitor-enzyme system, actinonin-peptide deformylase. Crystal structures of the initial open state and final closed state were solved, as well as those of several intermediate mimics captured during the process. Ligand-induced reshaping of a hydrophobic pocket drives closure of the active site, which is finally "zipped up" by additional binding interactions. Together with biochemical analyses, these data allow a coherent reconstruction of the sequence of events leading from the encounter complex to the key-lock binding state of the enzyme. A "movie" that reconstructs this entire process can be further extrapolated to catalysis.
-===Crystal structure of Arabidopsis thaliana petide deformylase 1B (AtPDF1B) in complex with inhibitor 21===
+Trapping conformational States along ligand-binding dynamics of Peptide deformylase: the impact of induced fit on enzyme catalysis.,Fieulaine S, Boularot A, Artaud I, Desmadril M, Dardel F, Meinnel T, Giglione C PLoS Biol. 2011 May;9(5):e1001066. Epub 2011 May 24. PMID:21629676<ref>PMID:21629676</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-<!--
+</div>
-The line below this paragraph, {{ABSTRACT_PUBMED_21629676}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 3pn3" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 21629676 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_21629676}}
+__TOC__
+</StructureSection>
-==About this Structure==
-[[3pn3]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3PN3 OCA].
-==Reference==
-<ref group="xtra">PMID:021629676</ref><references group="xtra"/>
 [[Category: Arabidopsis thaliana]]
-[[Category: Peptide deformylase]]
+[[Category: Large Structures]]
-[[Category: Fieulaine, S.]]
+[[Category: Fieulaine S]]
-[[Category: Giglione, C.]]
+[[Category: Giglione C]]
-[[Category: Meinnel, T.]]
+[[Category: Meinnel T]]
-[[Category: 1b]]
-[[Category: Hydrolase-hydrolase inhibitor complex]]
-[[Category: Induced-fit]]
-[[Category: N-terminal excision pathway]]
-[[Category: Nme]]
-[[Category: Pdf]]
-[[Category: Peptide deformylase]]