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6ntw
From Proteopedia
(Difference between revisions)
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<StructureSection load='6ntw' size='340' side='right'caption='[[6ntw]], [[Resolution|resolution]] 2.76Å' scene=''> | <StructureSection load='6ntw' size='340' side='right'caption='[[6ntw]], [[Resolution|resolution]] 2.76Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
| - | <table><tr><td colspan='2'>[[6ntw]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6NTW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6NTW FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[6ntw]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6NTW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6NTW FirstGlance]. <br> |
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MXR:(2S,3R,4S)-4-{[(3S,5R)-5-(DIMETHYLCARBAMOYL)PYRROLIDIN-3-YL]SULFANYL}-2-[(2S,3R)-3-HYDROXY-1-OXOBUTAN-2-YL]-3-METHYL-3,4-DIHYDRO-2H-PYRROLE-5-CARBOXYLIC+ACID'>MXR</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MXR:(2S,3R,4S)-4-{[(3S,5R)-5-(DIMETHYLCARBAMOYL)PYRROLIDIN-3-YL]SULFANYL}-2-[(2S,3R)-3-HYDROXY-1-OXOBUTAN-2-YL]-3-METHYL-3,4-DIHYDRO-2H-PYRROLE-5-CARBOXYLIC+ACID'>MXR</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> | ||
| + | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ycbB, b0925, JW0908 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr> | ||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6ntw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ntw OCA], [http://pdbe.org/6ntw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ntw RCSB], [http://www.ebi.ac.uk/pdbsum/6ntw PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ntw ProSAT]</span></td></tr> | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6ntw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ntw OCA], [http://pdbe.org/6ntw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ntw RCSB], [http://www.ebi.ac.uk/pdbsum/6ntw PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ntw ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Function == | == Function == | ||
[[http://www.uniprot.org/uniprot/YCBB_ECOLI YCBB_ECOLI]] Responsible, at least in part, for generating a meso-diaminopimelyl-3-a meso-diaminopimelyl-3 cross-link.<ref>PMID:18456808</ref> | [[http://www.uniprot.org/uniprot/YCBB_ECOLI YCBB_ECOLI]] Responsible, at least in part, for generating a meso-diaminopimelyl-3-a meso-diaminopimelyl-3 cross-link.<ref>PMID:18456808</ref> | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | The bacterial cell wall plays a crucial role in viability and is an important drug target. In Escherichia coli, the peptidoglycan crosslinking reaction to form the cell wall is primarily carried out by penicillin-binding proteins that catalyse D,D-transpeptidase activity. However, an alternate crosslinking mechanism involving the L,D-transpeptidase YcbB can lead to bypass of D,D-transpeptidation and beta-lactam resistance. Here, we show that the crystallographic structure of YcbB consists of a conserved L,D-transpeptidase catalytic domain decorated with a subdomain on the dynamic substrate capping loop, peptidoglycan-binding and large scaffolding domains. Meropenem acylation of YcbB gives insight into the mode of inhibition by carbapenems, the singular antibiotic class with significant activity against L,D-transpeptidases. We also report the structure of PBP5-meropenem to compare interactions mediating inhibition. Additionally, we probe the interaction network of this pathway and assay beta-lactam resistance in vivo. Our results provide structural insights into the mechanism of action and the inhibition of L,D-transpeptidation, and into YcbB-mediated antibiotic resistance. | ||
| + | |||
| + | Structural insight into YcbB-mediated beta-lactam resistance in Escherichia coli.,Caveney NA, Caballero G, Voedts H, Niciforovic A, Worrall LJ, Vuckovic M, Fonvielle M, Hugonnet JE, Arthur M, Strynadka NCJ Nat Commun. 2019 Apr 23;10(1):1849. doi: 10.1038/s41467-019-09507-0. PMID:31015395<ref>PMID:31015395</ref> | ||
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| + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
| + | </div> | ||
| + | <div class="pdbe-citations 6ntw" style="background-color:#fffaf0;"></div> | ||
== References == | == References == | ||
<references/> | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
| + | [[Category: Ecoli]] | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: Caballero, G]] | [[Category: Caballero, G]] | ||
Current revision
Crystal structure of E. coli YcbB
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