6p56 - Revision history

OCA at 14:53, 13 March 2024

OCA — Wed, 13 Mar 2024 14:53:54 GMT

←Older revision		Revision as of 14:53, 13 March 2024
Line 3:		Line 3:
	<StructureSection load='6p56' size='340' side='right'caption='[[6p56]], [[Resolution\|resolution]] 1.92Å' scene=''>		<StructureSection load='6p56' size='340' side='right'caption='[[6p56]], [[Resolution\|resolution]] 1.92Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6p56]] is a 2 chain structure with sequence from [~~http~~://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=6P56 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6P56 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6p56]] 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=6P56 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6P56 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=PO4:PHOSPHATE+ION'>PO4</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]] 1.92Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>penA ([http://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=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b></td><td class="sblockDat"><span class='plainlinks~~'>[http://en.wikipedia.org/wiki/Serine-type_D-Ala-D-Ala_carboxypeptidase Serine-type D-Ala-D-Ala carboxypeptidase], with EC number [http://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=6p56 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6p56 OCA], [https://pdbe.org/6p56 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6p56 RCSB], [https://www.ebi.ac.uk/pdbsum/6p56 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6p56 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=6p56 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6p56 OCA], [~~http~~://pdbe.org/6p56 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6p56 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6p56 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6p56 ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://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;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	Resistance of Neisseria gonorrhoeae to extended-spectrum cephalosporins (ESCs) has become a major threat to human health. The primary mechanism by which N. gonorrhoeae becomes resistant to ESCs is by acquiring a mosaic penA gene, encoding penicillin-binding protein 2 (PBP2) variants. Such variants contain up to 62 mutations compared with wild-type, of which a subset contribute to resistance. To interpret molecular mechanisms underpinning cephalosporin resistance, it is necessary to know how PBP2 is acylated by ESCs. Here, we report the crystal structures of the transpeptidase domain of wild-type PBP2 in complex with cefixime and ceftriaxone, along with structures of PBP2 in apo form and with a phosphate ion bound in the active site at resolutions of 1-7-1.9 A. These structures reveal that acylation of PBP2 by ESCs is accompanied by rotation of the Thr498 sidechain in the KTG motif to contact the cephalosporin carboxylate, twisting of the beta3 strand to form the oxyanion hole, and rolling of the beta3-beta4 loop toward the active site. Recognition of the cephalosporin carboxylate appears to be the key trigger for formation of an acylation-competent state of PBP2. The structures also begin to explain the impact of mutations implicated in ESC resistance. In particular, a G545S mutation may hinder twisting of beta3 because its sidechain hydroxyl forms a hydrogen bond with Thr498. Overall, our data suggest that acylation is initiated by conformational changes elicited or trapped by binding of ESCs and that these movements are restricted by mutations associated with resistance against ESCs.	+
-		+
-	Recognition of the beta-lactam Carboxylate Triggers Acylation of Neisseria gonorrhoeae Penicillin-Binding Protein 2.,Singh A, Tomberg J, Nicholas RA, Davies C J Biol Chem. 2019 Jul 30. pii: RA119.009942. doi: 10.1074/jbc.RA119.009942. PMID:31362987<ref>PMID:31362987</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 6p56" style="background-color:#fffaf0;"></div>~~	+

	==See Also==		==See Also==
	*[[Penicillin-binding protein 3D structures\|Penicillin-binding protein 3D structures]]		*[[Penicillin-binding protein 3D structures\|Penicillin-binding protein 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Serine-type D-Ala-D-Ala carboxypeptidase]]
-	[[Category: Davies, C]]
-	[[Category: Singh, A]]
-	[[Category: Antibiotic resistance]]
-	[[Category: Hydrolase]]
	[[Category: Neisseria gonorrhoeae]]		[[Category: Neisseria gonorrhoeae]]
-	[[Category: ~~Penicillin-binding protein~~]]	+	[[Category: Davies C]]
-	[[Category: ~~Transpeptidase domain~~]]	+	[[Category: Singh A]]

OCA at 12:03, 1 January 2020

OCA — Wed, 01 Jan 2020 12:03:26 GMT

←Older revision		Revision as of 12:03, 1 January 2020
Line 20:		Line 20:
	</div>		</div>
	<div class="pdbe-citations 6p56" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6p56" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Penicillin-binding protein 3D structures\|Penicillin-binding protein 3D structures]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 17:31, 14 August 2019

OCA — Wed, 14 Aug 2019 17:31:05 GMT

←Older revision		Revision as of 17:31, 14 August 2019
Line 3:		Line 3:
	<StructureSection load='6p56' size='340' side='right'caption='[[6p56]], [[Resolution\|resolution]] 1.92Å' scene=''>		<StructureSection load='6p56' size='340' side='right'caption='[[6p56]], [[Resolution\|resolution]] 1.92Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6p56]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6P56 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6P56 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6p56]] is a 2 chain structure with sequence from [http://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=6P56 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6P56 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">penA ([http://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'>[http://en.wikipedia.org/wiki/Serine-type_D-Ala-D-Ala_carboxypeptidase Serine-type D-Ala-D-Ala carboxypeptidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.16.4 3.4.16.4] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Serine-type_D-Ala-D-Ala_carboxypeptidase Serine-type D-Ala-D-Ala carboxypeptidase], with EC number [http://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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6p56 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6p56 OCA], [http://pdbe.org/6p56 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6p56 RCSB], [http://www.ebi.ac.uk/pdbsum/6p56 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6p56 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=6p56 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6p56 OCA], [http://pdbe.org/6p56 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6p56 RCSB], [http://www.ebi.ac.uk/pdbsum/6p56 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6p56 ProSAT]</span></td></tr>
Line 10:		Line 11:
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/PBP2_NEIGO PBP2_NEIGO]] Synthesis of cross-linked peptidoglycan from the lipid intermediates.		[[http://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 of Neisseria gonorrhoeae to extended-spectrum cephalosporins (ESCs) has become a major threat to human health. The primary mechanism by which N. gonorrhoeae becomes resistant to ESCs is by acquiring a mosaic penA gene, encoding penicillin-binding protein 2 (PBP2) variants. Such variants contain up to 62 mutations compared with wild-type, of which a subset contribute to resistance. To interpret molecular mechanisms underpinning cephalosporin resistance, it is necessary to know how PBP2 is acylated by ESCs. Here, we report the crystal structures of the transpeptidase domain of wild-type PBP2 in complex with cefixime and ceftriaxone, along with structures of PBP2 in apo form and with a phosphate ion bound in the active site at resolutions of 1-7-1.9 A. These structures reveal that acylation of PBP2 by ESCs is accompanied by rotation of the Thr498 sidechain in the KTG motif to contact the cephalosporin carboxylate, twisting of the beta3 strand to form the oxyanion hole, and rolling of the beta3-beta4 loop toward the active site. Recognition of the cephalosporin carboxylate appears to be the key trigger for formation of an acylation-competent state of PBP2. The structures also begin to explain the impact of mutations implicated in ESC resistance. In particular, a G545S mutation may hinder twisting of beta3 because its sidechain hydroxyl forms a hydrogen bond with Thr498. Overall, our data suggest that acylation is initiated by conformational changes elicited or trapped by binding of ESCs and that these movements are restricted by mutations associated with resistance against ESCs.
		+
		+	Recognition of the beta-lactam Carboxylate Triggers Acylation of Neisseria gonorrhoeae Penicillin-Binding Protein 2.,Singh A, Tomberg J, Nicholas RA, Davies C J Biol Chem. 2019 Jul 30. pii: RA119.009942. doi: 10.1074/jbc.RA119.009942. PMID:31362987<ref>PMID:31362987</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6p56" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 06:00, 7 August 2019

OCA — Wed, 07 Aug 2019 06:00:14 GMT

←Older revision		Revision as of 06:00, 7 August 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6p56 is ~~ON HOLD~~	+	==Crystal structure of the transpeptidase domain of a T498A mutant of PBP2 from Neisseria gonorrhoeae==
-		+	<StructureSection load='6p56' size='340' side='right'caption='[[6p56]], [[Resolution\|resolution]] 1.92Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6p56]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6P56 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6P56 FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Serine-type_D-Ala-D-Ala_carboxypeptidase Serine-type D-Ala-D-Ala carboxypeptidase], with EC number [http://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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6p56 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6p56 OCA], [http://pdbe.org/6p56 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6p56 RCSB], [http://www.ebi.ac.uk/pdbsum/6p56 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6p56 ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/PBP2_NEIGO PBP2_NEIGO]] Synthesis of cross-linked peptidoglycan from the lipid intermediates.
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Serine-type D-Ala-D-Ala carboxypeptidase]]
		+	[[Category: Davies, C]]
		+	[[Category: Singh, A]]
		+	[[Category: Antibiotic resistance]]
		+	[[Category: Hydrolase]]
		+	[[Category: Neisseria gonorrhoeae]]
		+	[[Category: Penicillin-binding protein]]
		+	[[Category: Transpeptidase domain]]

OCA: Protected "6p56" [edit=sysop:move=sysop]

OCA — Wed, 05 Jun 2019 21:15:30 GMT

Protected "6p56" [edit=sysop:move=sysop]

←Older revision

Revision as of 21:15, 5 June 2019

OCA: New page: '''Unreleased structure''' The entry 6p56 is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 05 Jun 2019 21:15:29 GMT

New page: '''Unreleased structure''' The entry 6p56 is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6p56 is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]