2ex2: Difference between revisions

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-[[Image:2ex2.png|left|200px]]
-{{STRUCTURE_2ex2|  PDB=2ex2  |  SCENE=  }}
+==Crystal structure of penicillin binding protein 4 (dacB) from Escherichia coli==
+<StructureSection load='2ex2' size='340' side='right'caption='[[2ex2]], [[Resolution|resolution]] 1.55&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[2ex2]] 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=2EX2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2EX2 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]] 1.55&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</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=2ex2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ex2 OCA], [https://pdbe.org/2ex2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ex2 RCSB], [https://www.ebi.ac.uk/pdbsum/2ex2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ex2 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/DACB_ECOLI DACB_ECOLI] Not involved in transpeptidation but exclusively catalyzes a DD-carboxypeptidase and DD-endopeptidase reaction.<ref>PMID:2046551</ref>
+== 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/ex/2ex2_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=2ex2 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The crystal structure of penicillin binding protein 4 (PBP4) from Escherichia coli, which has both DD-endopeptidase and DD-carboxypeptidase activity, is presented. PBP4 is one of 12 penicillin binding proteins in E. coli involved in the synthesis and maintenance of the cell wall. The model contains a penicillin binding domain similar to known structures, but includes a large insertion which folds into domains with unique folds. The structures of the protein covalently attached to five different antibiotics presented here show the active site residues are unmoved compared to the apoprotein, but nearby surface loops and helices are displaced in some cases. The altered geometry of conserved active site residues compared with those of other PBPs suggests a possible cause for the slow deacylation rate of PBP4.
-===Crystal structure of penicillin binding protein 4 (dacB) from Escherichia coli===
+Crystal structure of penicillin binding protein 4 (dacB) from Escherichia coli, both in the native form and covalently linked to various antibiotics.,Kishida H, Unzai S, Roper DI, Lloyd A, Park SY, Tame JR Biochemistry. 2006 Jan 24;45(3):783-92. PMID:16411754<ref>PMID:16411754</ref>
-{{ABSTRACT_PUBMED_16411754}}
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
-==About this Structure==
+<div class="pdbe-citations 2ex2" style="background-color:#fffaf0;"></div>
-[[2ex2]] is a 1 chain structure of [[Penicillin-binding protein]] 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=2EX2 OCA].
 ==See Also==
-*[[Penicillin-binding protein|Penicillin-binding protein]]
+*[[Penicillin-binding protein 3D structures|Penicillin-binding protein 3D structures]]
+== References ==
-==Reference==
+<references/>
-<ref group="xtra">PMID:016411754</ref><references group="xtra"/>
+__TOC__
+</StructureSection>
 [[Category: Escherichia coli]]
-[[Category: Kishida, H.]]
+[[Category: Large Structures]]
-[[Category: Lloyd, A.]]
+[[Category: Kishida H]]
-[[Category: Park, S Y.]]
+[[Category: Lloyd A]]
-[[Category: Roper, D I.]]
+[[Category: Park S-Y]]
-[[Category: Tame, J R.H.]]
+[[Category: Roper DI]]
-[[Category: Unzai, S.]]
+[[Category: Tame JRH]]
-[[Category: Cephem]]
+[[Category: Unzai S]]
-[[Category: D-alanyl-d-alanine-carboxypeptidase]]
-[[Category: D-alanyl-d-alanine-endopeptidase]]
-[[Category: Hydrolase]]
-[[Category: Penem]]
-[[Category: Penicillin]]
-[[Category: Penicillin-binding protein]]