2exa

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[[Image:2exa.gif|left|200px]]
 
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{{Structure
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==Crystal structure of penicillin binding protein 4 (dacB) from Escherichia coli, complexed with FAROM==
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|PDB= 2exa |SIZE=350|CAPTION= <scene name='initialview01'>2exa</scene>, resolution 1.70&Aring;
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<StructureSection load='2exa' size='340' side='right'caption='[[2exa]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=FRO:(5R,6S)-6-[(1R)-1-HYDROXYETHYL]-7-OXO-3-[(2R)-TETRAHYDROFURAN-2-YL]-4-THIA-1-AZABICYCLO[3.2.0]HEPT-2-ENE-2-CARBOXYLATE'>FRO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>
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<table><tr><td colspan='2'>[[2exa]] 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=2EXA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2EXA FirstGlance]. <br>
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|ACTIVITY=
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.7&#8491;</td></tr>
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|GENE= dacb ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])
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<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>
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|DOMAIN=
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<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>
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|RELATEDENTRY=[[2ex2|2EX2]], [[2ex6|2EX6]], [[2ex8|2EX8]], [[2ex9|2EX9]], [[2exb|2EXB]]
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</table>
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2exa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2exa OCA], [http://www.ebi.ac.uk/pdbsum/2exa PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2exa RCSB]</span>
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== Evolutionary Conservation ==
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}}
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ex/2exa_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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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.
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'''Crystal structure of penicillin binding protein 4 (dacB) from Escherichia coli, complexed with FAROM'''
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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&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 2exa" style="background-color:#fffaf0;"></div>
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==Overview==
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==See Also==
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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.
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*[[Penicillin-binding protein 3D structures|Penicillin-binding protein 3D structures]]
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== References ==
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==About this Structure==
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<references/>
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2EXA is a [[Single protein]] structure of 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=2EXA OCA].
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__TOC__
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</StructureSection>
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==Reference==
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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:[http://www.ncbi.nlm.nih.gov/pubmed/16411754 16411754]
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[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
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[[Category: Single protein]]
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[[Category: Large Structures]]
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[[Category: Kishida, H.]]
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[[Category: Kishida H]]
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[[Category: Lloyd, A.]]
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[[Category: Lloyd A]]
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[[Category: Park, S Y.]]
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[[Category: Park S-Y]]
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[[Category: Roper, D I.]]
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[[Category: Roper DI]]
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[[Category: Tame, J R.H.]]
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[[Category: Tame JRH]]
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[[Category: Unzai, S.]]
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[[Category: Unzai S]]
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[[Category: d-alanyl-d-alanine-carboxypeptidase]]
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[[Category: d-alanyl-d-alanine-endopeptidase]]
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[[Category: farom]]
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[[Category: penem]]
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[[Category: penicillin,cephem]]
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[[Category: penicillin-binding protein]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 02:55:00 2008''
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Current revision

Crystal structure of penicillin binding protein 4 (dacB) from Escherichia coli, complexed with FAROM

PDB ID 2exa

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