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2exa
From Proteopedia
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| - | [[Image:2exa.gif|left|200px]]<br /><applet load="2exa" size="350" color="white" frame="true" align="right" spinBox="true" | ||
| - | caption="2exa, resolution 1.70Å" /> | ||
| - | '''Crystal structure of penicillin binding protein 4 (dacB) from Escherichia coli, complexed with FAROM'''<br /> | ||
| - | == | + | ==Crystal structure of penicillin binding protein 4 (dacB) from Escherichia coli, complexed with FAROM== |
| + | <StructureSection load='2exa' size='340' side='right'caption='[[2exa]], [[Resolution|resolution]] 1.70Å' scene=''> | ||
| + | == Structural highlights == | ||
| + | <table><tr><td colspan='2'>[[2exa]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2EXA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2EXA FirstGlance]. <br> | ||
| + | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DGF:(2R,5R)-2-[(2S,3R)-3-HYDROXY-1-OXOBUTAN-2-YL]-5-[(2R)-TETRAHYDROFURAN-2-YL]-2,5-DIHYDRO-1,3-THIAZOLE-4-CARBOXYLIC+ACID'>DGF</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr> | ||
| + | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2ex2|2ex2]], [[2ex6|2ex6]], [[2ex8|2ex8]], [[2ex9|2ex9]], [[2exb|2exb]]</div></td></tr> | ||
| + | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">dacb ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</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=2exa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2exa OCA], [https://pdbe.org/2exa PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2exa RCSB], [https://www.ebi.ac.uk/pdbsum/2exa PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2exa 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/2exa_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=2exa 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. | 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, 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> | |
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| - | + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |
| - | + | </div> | |
| - | + | <div class="pdbe-citations 2exa" style="background-color:#fffaf0;"></div> | |
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| - | + | ==See Also== | |
| + | *[[Penicillin-binding protein 3D structures|Penicillin-binding protein 3D structures]] | ||
| + | == References == | ||
| + | <references/> | ||
| + | __TOC__ | ||
| + | </StructureSection> | ||
| + | [[Category: Bacillus coli migula 1895]] | ||
| + | [[Category: Large Structures]] | ||
| + | [[Category: Kishida, H]] | ||
| + | [[Category: Lloyd, A]] | ||
| + | [[Category: Park, S Y]] | ||
| + | [[Category: Roper, D I]] | ||
| + | [[Category: Tame, J R.H]] | ||
| + | [[Category: Unzai, S]] | ||
| + | [[Category: Cephem]] | ||
| + | [[Category: D-alanyl-d-alanine-carboxypeptidase]] | ||
| + | [[Category: D-alanyl-d-alanine-endopeptidase]] | ||
| + | [[Category: Farom]] | ||
| + | [[Category: Hydrolase]] | ||
| + | [[Category: Penem]] | ||
| + | [[Category: Penicillin]] | ||
| + | [[Category: Penicillin-binding protein]] | ||
Current revision
Crystal structure of penicillin binding protein 4 (dacB) from Escherichia coli, complexed with FAROM
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