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==Crystal structure of penicillin binding protein 4 (dacB) from Escherichia coli, complexed with FLOMOX== | ==Crystal structure of penicillin binding protein 4 (dacB) from Escherichia coli, complexed with FLOMOX== | ||
<StructureSection load='2exb' size='340' side='right' caption='[[2exb]], [[Resolution|resolution]] 1.75Å' scene=''> | <StructureSection load='2exb' size='340' side='right'caption='[[2exb]], [[Resolution|resolution]] 1.75Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[2exb]] is a 1 chain structure with sequence from [ | <table><tr><td colspan='2'>[[2exb]] 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=2EXB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2EXB FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FXM:2,2-DIMETHYLPROPANOYLOXYMETHYL+( | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.75Å</td></tr> | ||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FXM:2,2-DIMETHYLPROPANOYLOXYMETHYL+(2R)-5-(AMINOCARBONYLOXYMETHYL)-2-[(1R)-1-[[(Z)-2-(2-AZANYL-1,3-THIAZOL-4-YL)PENT-2-ENOYL]AMINO]-2-OXIDANYLIDENE-ETHYL]-3,6-DIHYDRO-2H-1,3-THIAZINE-4-CARBOXYLATE'>FXM</scene>, <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=2exb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2exb OCA], [https://pdbe.org/2exb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2exb RCSB], [https://www.ebi.ac.uk/pdbsum/2exb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2exb ProSAT]</span></td></tr> | |||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | |||
</table> | </table> | ||
== Function == | == 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 == | == Evolutionary Conservation == | ||
[[Image:Consurf_key_small.gif|200px|right]] | [[Image:Consurf_key_small.gif|200px|right]] | ||
Check<jmol> | Check<jmol> | ||
<jmolCheckbox> | <jmolCheckbox> | ||
<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ex/2exb_consurf.spt"</scriptWhenChecked> | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ex/2exb_consurf.spt"</scriptWhenChecked> | ||
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/ | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked> | ||
<text>to colour the structure by Evolutionary Conservation</text> | <text>to colour the structure by Evolutionary Conservation</text> | ||
</jmolCheckbox> | </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/ | </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=2exb ConSurf]. | ||
<div style="clear:both"></div> | <div style="clear:both"></div> | ||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
| Line 28: | Line 28: | ||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
</div> | </div> | ||
<div class="pdbe-citations 2exb" style="background-color:#fffaf0;"></div> | |||
==See Also== | ==See Also== | ||
*[[Penicillin-binding protein|Penicillin-binding protein]] | *[[Penicillin-binding protein 3D structures|Penicillin-binding protein 3D structures]] | ||
== References == | == References == | ||
<references/> | <references/> | ||
| Line 36: | Line 37: | ||
</StructureSection> | </StructureSection> | ||
[[Category: Escherichia coli]] | [[Category: Escherichia coli]] | ||
[[Category: Kishida | [[Category: Large Structures]] | ||
[[Category: Lloyd | [[Category: Kishida H]] | ||
[[Category: Park | [[Category: Lloyd A]] | ||
[[Category: Roper | [[Category: Park S-Y]] | ||
[[Category: Tame | [[Category: Roper DI]] | ||
[[Category: Unzai | [[Category: Tame JRH]] | ||
[[Category: Unzai S]] | |||
Latest revision as of 10:58, 30 October 2024
Crystal structure of penicillin binding protein 4 (dacB) from Escherichia coli, complexed with FLOMOXCrystal structure of penicillin binding protein 4 (dacB) from Escherichia coli, complexed with FLOMOX
Structural highlights
FunctionDACB_ECOLI Not involved in transpeptidation but exclusively catalyzes a DD-carboxypeptidase and DD-endopeptidase reaction.[1] Evolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMedThe 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[2] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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