6xqy - Revision history

OCA at 14:59, 18 October 2023

OCA — Wed, 18 Oct 2023 14:59:29 GMT

←Older revision		Revision as of 14:59, 18 October 2023
Line 3:		Line 3:
	<StructureSection load='6xqy' size='340' side='right'caption='[[6xqy]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='6xqy' size='340' side='right'caption='[[6xqy]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6xqy]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"diplococcus_gonorrhoeae"_(zopf_1885)_lehmann_and_neumann_1896 "diplococcus~~ gonorrhoeae~~" (zopf 1885) lehmann and neumann 1896~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6XQY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6XQY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6xqy]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Neisseria_gonorrhoeae Neisseria gonorrhoeae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6XQY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6XQY FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>~~</td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 1.9Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>penA ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~485~~ "~~Diplococcus gonorrhoeae~~" ~~(Zopf 1885) Lehmann and Neumann 1896])</td~~><~~/tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b></td><td class="sblockDat"><span class='plainlinks~~'>[https://en.wikipedia.org/wiki/Serine-type_D-Ala-D-Ala_carboxypeptidase Serine-type D-Ala-D-Ala carboxypeptidase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.16.4 3.4.16.4] </~~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=6xqy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6xqy OCA], [https://pdbe.org/6xqy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6xqy RCSB], [https://www.ebi.ac.uk/pdbsum/6xqy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6xqy 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=6xqy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6xqy OCA], [https://pdbe.org/6xqy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6xqy RCSB], [https://www.ebi.ac.uk/pdbsum/6xqy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6xqy ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/PBP2_NEIGO PBP2_NEIGO]] Synthesis of cross-linked peptidoglycan from the lipid intermediates.	+	[https://www.uniprot.org/uniprot/PBP2_NEIGO PBP2_NEIGO] Synthesis of cross-linked peptidoglycan from the lipid intermediates.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 28:		Line 27:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Serine-type D-Ala-D-Ala carboxypeptidase~~]]	+	[[Category: Neisseria gonorrhoeae]]
-	[[Category: Davies, C]]	+	[[Category: Davies C]]
-	[[Category: Fenton~~, B A~~]]	+	[[Category: Fenton BA]]
-	[[Category: Zhou, P]]	+	[[Category: Zhou P]]
-	~~[[Category: Antibiotic target]]~~	+
-	~~[[Category: Beta-lactam]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Pbp2]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 07:07, 2 February 2022

OCA — Wed, 02 Feb 2022 07:07:49 GMT

←Older revision		Revision as of 07:07, 2 February 2022
Line 1:		Line 1:

	==Crystal structure of the catalytic domain of PBP2 S310A from Neisseria gonorrhoeae at pH 9.5==		==Crystal structure of the catalytic domain of PBP2 S310A from Neisseria gonorrhoeae at pH 9.5==
-	<StructureSection load='6xqy' size='340' side='right'caption='[[6xqy]]' scene=''>	+	<StructureSection load='6xqy' size='340' side='right'caption='[[6xqy]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6XQY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6XQY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6xqy]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/"diplococcus_gonorrhoeae"_(zopf_1885)_lehmann_and_neumann_1896 "diplococcus gonorrhoeae" (zopf 1885) lehmann and neumann 1896]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6XQY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6XQY FirstGlance]. <br>
-	</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=6xqy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6xqy OCA], [https://pdbe.org/6xqy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6xqy RCSB], [https://www.ebi.ac.uk/pdbsum/6xqy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6xqy ProSAT]</span></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">penA ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=485 "Diplococcus gonorrhoeae" (Zopf 1885) Lehmann and Neumann 1896])</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Serine-type_D-Ala-D-Ala_carboxypeptidase Serine-type D-Ala-D-Ala carboxypeptidase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.16.4 3.4.16.4] </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=6xqy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6xqy OCA], [https://pdbe.org/6xqy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6xqy RCSB], [https://www.ebi.ac.uk/pdbsum/6xqy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6xqy ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[https://www.uniprot.org/uniprot/PBP2_NEIGO PBP2_NEIGO]] Synthesis of cross-linked peptidoglycan from the lipid intermediates.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Resistance to the extended-spectrum cephalosporin ceftriaxone in the pathogenic bacteria Neisseria gonorrhoeae is conferred by mutations in penicillin-binding protein 2 (PBP2), the lethal target of the antibiotic, but how these mutations exert their effect at the molecular level is unclear. Using solution NMR, X-ray crystallography, and isothermal titration calorimetry, we report that WT PBP2 exchanges dynamically between a low-affinity state with an extended beta3-beta4 loop conformation and a high-affinity state with an inward beta3-beta4 loop conformation. Histidine-514, which is located at the boundary of the beta4 strand, plays an important role during the exchange between these two conformational states. We also find that mutations present in PBP2 from H041, a ceftriaxone-resistant strain of N. gonorrhoeae, increase resistance to ceftriaxone by destabilizing the inward beta3-beta4 loop conformation or stabilizing the extended beta3-beta4 loop conformation to favor the low-affinity drug-binding state. These observations reveal a unique mechanism for ceftriaxone resistance, whereby mutations in PBP2 lower the proportion of target molecules in the high-affinity drug-binding state and thus reduce inhibition at lower drug concentrations.
		+
		+	Mutations in PBP2 from ceftriaxone-resistant Neisseria gonorrhoeae alter the dynamics of the beta3-beta4 loop to favor a low-affinity drug-binding state.,Fenton BA, Tomberg J, Sciandra CA, Nicholas RA, Davies C, Zhou P J Biol Chem. 2021 Oct;297(4):101188. doi: 10.1016/j.jbc.2021.101188. Epub 2021, Sep 13. PMID:34529975<ref>PMID:34529975</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6xqy" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Penicillin-binding protein 3D structures\|Penicillin-binding protein 3D structures]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Davies C]]	+	[[Category: Serine-type D-Ala-D-Ala carboxypeptidase]]
-	[[Category: Fenton BA]]	+	[[Category: Davies, C]]
-	[[Category: Zhou P]]	+	[[Category: Fenton, B A]]
		+	[[Category: Zhou, P]]
		+	[[Category: Antibiotic target]]
		+	[[Category: Beta-lactam]]
		+	[[Category: Hydrolase]]
		+	[[Category: Pbp2]]
		+	[[Category: Transferase]]

OCA at 08:55, 21 July 2021

OCA — Wed, 21 Jul 2021 08:55:29 GMT

←Older revision		Revision as of 08:55, 21 July 2021
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6xqy is ~~ON HOLD until Paper Publication~~	+	==Crystal structure of the catalytic domain of PBP2 S310A from Neisseria gonorrhoeae at pH 9.5==
-		+	<StructureSection load='6xqy' size='340' side='right'caption='[[6xqy]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6XQY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6XQY FirstGlance]. <br>
-	~~Description~~:	+	</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=6xqy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6xqy OCA], [https://pdbe.org/6xqy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6xqy RCSB], [https://www.ebi.ac.uk/pdbsum/6xqy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6xqy ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Davies C]]
		+	[[Category: Fenton BA]]
		+	[[Category: Zhou P]]

OCA at 09:25, 29 July 2020

OCA — Wed, 29 Jul 2020 09:25:10 GMT

←Older revision		Revision as of 09:25, 29 July 2020
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6xqy is ON HOLD	+	The entry 6xqy is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "6xqy" [edit=sysop:move=sysop]

OCA — Wed, 22 Jul 2020 06:54:54 GMT

Protected "6xqy" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:54, 22 July 2020

OCA: New page: '''Unreleased structure''' The entry 6xqy is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 22 Jul 2020 06:54:52 GMT

New page: '''Unreleased structure''' The entry 6xqy is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6xqy is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]