1bsk: Difference between revisions

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-[[Image:1bsk.png|left|200px]]
-{{STRUCTURE_1bsk|  PDB=1bsk  |  SCENE=  }}
+==ZINC DEFORMYLASE INHIBITOR COMPLEX FROM E.COLI==
+<StructureSection load='1bsk' size='340' side='right'caption='[[1bsk]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1bsk]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BSK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1BSK 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]] 3&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MLN:(S)-2-(PHOSPHONOXY)CAPROYL-L-LEUCYL-P-NITROANILIDE'>MLN</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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=1bsk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bsk OCA], [https://pdbe.org/1bsk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1bsk RCSB], [https://www.ebi.ac.uk/pdbsum/1bsk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1bsk ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/DEF_ECOLI DEF_ECOLI] Removes the formyl group from the N-terminal Met of newly synthesized proteins. Requires at least a dipeptide for an efficient rate of reaction. N-terminal L-methionine is a prerequisite for activity but the enzyme has broad specificity at other positions.[HAMAP-Rule:MF_00163]
+== 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/bs/1bsk_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/main_output.php?pdb_ID=1bsk ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+While protein synthesis in bacteria begins with a formylated methionine, the formyl group of the nascent polypeptide is removed by peptide deformylase. Since eukaryotic protein synthesis does not involve formylation and deformylation at the N-terminus, there has been increasing interest in peptide deformylase as a potential target for antibacterial chemotherapy. Toward this end and to aid in the design of effective antibiotics targeting peptide deformylase, the structures of the protein-inhibitor complexes of both the cobalt and the zinc containing Escherichia coli peptide deformylase bound to the transition-state analogue, (S)-2-O-(H-phosphonoxy)-L-caproyl-L-leucyl-p-nitroanilide (PCLNA), have been determined. The proteins for both deformylase-inhibitor complexes show basically the same fold as for the native enzyme. The PCLNA inhibitor adopts an extended conformation and fits nicely into a hydrophobic cavity located near the metal site. On the basis of these structures, guidelines for the design of high-affinity deformylase inhibitors are suggested. As our results show that the protein residues which interact with the PCLNA inhibitor are conserved over a wide variety of species, we suggest that antibiotics targeting deformylase could have wide applicability.
-===ZINC DEFORMYLASE INHIBITOR COMPLEX FROM E.COLI===
+Structural basis for the design of antibiotics targeting peptide deformylase.,Hao B, Gong W, Rajagopalan PT, Zhou Y, Pei D, Chan MK Biochemistry. 1999 Apr 13;38(15):4712-9. PMID:10200158<ref>PMID:10200158</ref>
-{{ABSTRACT_PUBMED_10200158}}
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
-==About this Structure==
+<div class="pdbe-citations 1bsk" style="background-color:#fffaf0;"></div>
-[[1bsk]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BSK OCA].
+== References ==
+<references/>
-==Reference==
+__TOC__
-<ref group="xtra">PMID:010200158</ref><references group="xtra"/>
+</StructureSection>
 [[Category: Escherichia coli]]
-[[Category: N-formylmethionylaminoacyl-tRNA deformylase]]
+[[Category: Large Structures]]
-[[Category: Chan, M K.]]
+[[Category: Chan MK]]
-[[Category: Gong, W.]]
+[[Category: Gong W]]
-[[Category: Hao, B.]]
+[[Category: Hao B]]
-[[Category: Hu, Y.]]
+[[Category: Hu Y]]
-[[Category: Pei, D.]]
+[[Category: Pei D]]
-[[Category: Rajagopalan, P T.]]
+[[Category: Rajagopalan PT]]
-[[Category: Deformylase]]
-[[Category: Hydrolase]]
-[[Category: Inhibitor]]
-[[Category: Metalloproteinase]]