3it9: Difference between revisions
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<StructureSection load='3it9' size='340' side='right'caption='[[3it9]], [[Resolution|resolution]] 2.10Å' scene=''> | <StructureSection load='3it9' size='340' side='right'caption='[[3it9]], [[Resolution|resolution]] 2.10Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[3it9]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/ | <table><tr><td colspan='2'>[[3it9]] is a 4 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=3IT9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3IT9 FirstGlance]. <br> | ||
</td></tr><tr id=' | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.1Å</td></tr> | ||
<tr id=' | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FRU:FRUCTOSE'>FRU</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=PRD_900003:sucrose'>PRD_900003</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=3it9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3it9 OCA], [https://pdbe.org/3it9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3it9 RCSB], [https://www.ebi.ac.uk/pdbsum/3it9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3it9 ProSAT]</span></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=3it9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3it9 OCA], [https://pdbe.org/3it9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3it9 RCSB], [https://www.ebi.ac.uk/pdbsum/3it9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3it9 ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Function == | == Function == | ||
[https://www.uniprot.org/uniprot/DACC_ECOLI DACC_ECOLI] Removes C-terminal D-alanyl residues from sugar-peptide cell wall precursors. | |||
== Evolutionary Conservation == | == Evolutionary Conservation == | ||
[[Image:Consurf_key_small.gif|200px|right]] | [[Image:Consurf_key_small.gif|200px|right]] | ||
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__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: | [[Category: Escherichia coli]] | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: Chen Y]] | |||
[[Category: Chen | [[Category: Hesek D]] | ||
[[Category: Hesek | [[Category: Lee M]] | ||
[[Category: Lee | [[Category: Mobashery S]] | ||
[[Category: Mobashery | [[Category: Shi Q]] | ||
[[Category: Shi | [[Category: Shoichet BK]] | ||
[[Category: Shoichet | [[Category: Zhang W]] | ||
[[Category: Zhang | |||
Latest revision as of 10:57, 6 September 2023
Crystal structure of Penicillin-Binding Protein 6 (PBP6) from E. coli in apo stateCrystal structure of Penicillin-Binding Protein 6 (PBP6) from E. coli in apo state
Structural highlights
FunctionDACC_ECOLI Removes C-terminal D-alanyl residues from sugar-peptide cell wall precursors. 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 PubMedPenicillin-binding protein 6 (PBP6) is one of the two main DD-carboxypeptidases in Escherichia coli, which are implicated in maturation of bacterial cell wall and formation of cell shape. Here, we report the first X-ray crystal structures of PBP6, capturing its apo state (2.1 A), an acyl-enzyme intermediate with the antibiotic ampicillin (1.8 A), and for the first time for a PBP, a preacylation complex (a "Michaelis complex", determined at 1.8 A) with a peptidoglycan substrate fragment containing the full pentapeptide, NAM-(L-Ala-D-isoGlu-L-Lys-D-Ala-D-Ala). These structures illuminate the molecular interactions essential for ligand recognition and catalysis by DD-carboxypeptidases, and suggest a coupling of conformational flexibility of active site loops to the reaction coordinate. The substrate fragment complex structure, in particular, provides templates for models of cell wall recognition by PBPs, as well as substantiating evidence for the molecular mimicry by beta-lactam antibiotics of the peptidoglycan acyl-D-Ala-D-Ala moiety. Crystal structures of penicillin-binding protein 6 from Escherichia coli.,Chen Y, Zhang W, Shi Q, Hesek D, Lee M, Mobashery S, Shoichet BK J Am Chem Soc. 2009 Oct 14;131(40):14345-54. PMID:19807181[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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