5hld - Revision history

OCA at 10:45, 16 August 2023

2023-08-16T10:45:48Z

←Older revision		Revision as of 10:45, 16 August 2023
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	<StructureSection load='5hld' size='340' side='right'caption='[[5hld]], [[Resolution\|resolution]] 2.31Å' scene=''>		<StructureSection load='5hld' size='340' side='right'caption='[[5hld]], [[Resolution\|resolution]] 2.31Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5hld]] 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=5HLD OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5HLD FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5hld]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5HLD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5HLD FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=63V:(2S)-5-METHYLIDENE-2-{(1R)-2-OXO-1-[(THIOPHEN-2-YLACETYL)AMINO]ETHYL}-5,6-DIHYDRO-2H-1,3-THIAZINE-4-CARBOXYLIC+ACID'>63V</scene>, <scene name='pdbligand=M0E:MOENOMYCIN'>M0E</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]] 2.31Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5hl9\|5hl9]], [[5hla\|5hla]], [[5hlb\|5hlb]]</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=63V:(2S)-5-METHYLIDENE-2-{(1R)-2-OXO-1-[(THIOPHEN-2-YLACETYL)AMINO]ETHYL}-5,6-DIHYDRO-2H-1,3-THIAZINE-4-CARBOXYLIC+ACID'>63V</scene>, <scene name='pdbligand=M0E:MOENOMYCIN'>M0E</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">mrcB, pbpF, ponB, b0149, JW0145 ([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'>[https://proteopedia.org/fgij/fg.htm?mol=5hld FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5hld OCA], [https://pdbe.org/5hld PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5hld RCSB], [https://www.ebi.ac.uk/pdbsum/5hld PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5hld 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=5hld FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5hld OCA], [~~http~~://pdbe.org/5hld PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5hld RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5hld PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5hld ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/PBPB_ECOLI PBPB_ECOLI]] Cell wall formation. Synthesis of cross-linked peptidoglycan from the lipid intermediates. The enzyme has a penicillin-insensitive transglycosylase N-terminal domain (formation of linear glycan strands) and a penicillin-sensitive transpeptidase C-terminal domain (cross-linking of the peptide subunits).	+	[https://www.uniprot.org/uniprot/PBPB_ECOLI PBPB_ECOLI] Cell wall formation. Synthesis of cross-linked peptidoglycan from the lipid intermediates. The enzyme has a penicillin-insensitive transglycosylase N-terminal domain (formation of linear glycan strands) and a penicillin-sensitive transpeptidase C-terminal domain (cross-linking of the peptide subunits).
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Ecoli~~]]	+	[[Category: Escherichia coli K-12]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: King~~, D T~~]]	+	[[Category: King DT]]
-	[[Category: Strynadka~~, N C.J]]~~	+	[[Category: Strynadka NCJ]]
-	~~[[Category: Inhibitor complex]]~~	+
-	~~[[Category: Penicillin-binding protein]]~~	+
-	~~[[Category: Transferase-transferase inhibitor complex]]~~	+
-	~~[[Category: Transglycosylase]]~~	+
-	~~[[Category: Transpeptidase~~]]	+

OCA at 16:16, 20 November 2019

2019-11-20T16:16:34Z

←Older revision		Revision as of 16:16, 20 November 2019
Line 1:		Line 1:

	==E. coli PBP1b in complex with acyl-CENTA and moenomycin==		==E. coli PBP1b in complex with acyl-CENTA and moenomycin==
-	<StructureSection load='5hld' size='340' side='right' caption='[[5hld]], [[Resolution\|resolution]] 2.31Å' scene=''>	+	<StructureSection load='5hld' size='340' side='right'caption='[[5hld]], [[Resolution\|resolution]] 2.31Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5hld]] 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=5HLD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5HLD FirstGlance]. <br>		<table><tr><td colspan='2'>[[5hld]] 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=5HLD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5HLD FirstGlance]. <br>
Line 20:		Line 20:
	</div>		</div>
	<div class="pdbe-citations 5hld" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5hld" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Penicillin-binding protein 3D structures\|Penicillin-binding protein 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
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	</StructureSection>		</StructureSection>
	[[Category: Ecoli]]		[[Category: Ecoli]]
		+	[[Category: Large Structures]]
	[[Category: King, D T]]		[[Category: King, D T]]
	[[Category: Strynadka, N C.J]]		[[Category: Strynadka, N C.J]]

OCA at 17:25, 15 November 2017

2017-11-15T17:25:24Z

←Older revision		Revision as of 17:25, 15 November 2017
Line 3:		Line 3:
	<StructureSection load='5hld' size='340' side='right' caption='[[5hld]], [[Resolution\|resolution]] 2.31Å' scene=''>		<StructureSection load='5hld' size='340' side='right' caption='[[5hld]], [[Resolution\|resolution]] 2.31Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5hld]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5HLD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5HLD FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5hld]] 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=5HLD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5HLD FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=63V:(2S)-5-METHYLIDENE-2-{(1R)-2-OXO-1-[(THIOPHEN-2-YLACETYL)AMINO]ETHYL}-5,6-DIHYDRO-2H-1,3-THIAZINE-4-CARBOXYLIC+ACID'>63V</scene>, <scene name='pdbligand=M0E:MOENOMYCIN'>M0E</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=63V:(2S)-5-METHYLIDENE-2-{(1R)-2-OXO-1-[(THIOPHEN-2-YLACETYL)AMINO]ETHYL}-5,6-DIHYDRO-2H-1,3-THIAZINE-4-CARBOXYLIC+ACID'>63V</scene>, <scene name='pdbligand=M0E:MOENOMYCIN'>M0E</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5hl9\|5hl9]], [[5hla\|5hla]], [[5hlb\|5hlb]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5hl9\|5hl9]], [[5hla\|5hla]], [[5hlb\|5hlb]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">mrcB, pbpF, ponB, b0149, JW0145 ([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=5hld FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5hld OCA], [http://pdbe.org/5hld PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5hld RCSB], [http://www.ebi.ac.uk/pdbsum/5hld PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5hld 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=5hld FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5hld OCA], [http://pdbe.org/5hld PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5hld RCSB], [http://www.ebi.ac.uk/pdbsum/5hld PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5hld ProSAT]</span></td></tr>
	</table>		</table>
Line 23:		Line 24:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Ecoli]]
	[[Category: King, D T]]		[[Category: King, D T]]
	[[Category: Strynadka, N C.J]]		[[Category: Strynadka, N C.J]]

OCA at 19:07, 15 December 2016

2016-12-15T19:07:45Z

←Older revision		Revision as of 19:07, 15 December 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5hld is ~~ON HOLD until Paper~~ Publication	+	==E. coli PBP1b in complex with acyl-CENTA and moenomycin==
		+	<StructureSection load='5hld' size='340' side='right' caption='[[5hld]], [[Resolution\|resolution]] 2.31Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5hld]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5HLD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5HLD FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=63V:(2S)-5-METHYLIDENE-2-{(1R)-2-OXO-1-[(THIOPHEN-2-YLACETYL)AMINO]ETHYL}-5,6-DIHYDRO-2H-1,3-THIAZINE-4-CARBOXYLIC+ACID'>63V</scene>, <scene name='pdbligand=M0E:MOENOMYCIN'>M0E</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5hl9\|5hl9]], [[5hla\|5hla]], [[5hlb\|5hlb]]</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=5hld FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5hld OCA], [http://pdbe.org/5hld PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5hld RCSB], [http://www.ebi.ac.uk/pdbsum/5hld PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5hld ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/PBPB_ECOLI PBPB_ECOLI]] Cell wall formation. Synthesis of cross-linked peptidoglycan from the lipid intermediates. The enzyme has a penicillin-insensitive transglycosylase N-terminal domain (formation of linear glycan strands) and a penicillin-sensitive transpeptidase C-terminal domain (cross-linking of the peptide subunits).
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	In Escherichia coli, the peptidoglycan cell wall is synthesized by bifunctional penicillin-binding proteins such as PBP1b that have both transpeptidase and transglycosylase activities. The PBP1b transpeptidase domain is a major target of beta-lactams and therefore it is important to attain a detailed understanding of its inhibition. The peptidoglycan glycosyltransferase domain of PBP1b is also considered an excellent antibiotic target, yet is not exploited by any clinically approved antibacterials. Herein, we adapt a pyrophosphate sensor assay to monitor PBP1b catalyzed glycosyltransfer and present an improved crystallographic model for inhibition of the PBP1b glycosyltransferase domain by the potent substrate analogue moenomycin. We elucidate the structure of a previously disordered region in the glycosyltransferase active site and discuss its implications with regards to peptidoglycan polymerization. Furthermore, we solve the crystal structures of E. coli PBP1b bound to multiple different beta-lactams in the transpeptidase active site, and complement this data with gel based competition assays to provide a detailed structural understanding of its inhibition. Taken together, this biochemical and structural data allows us to propose new insights into inhibition of both enzymatic domains in PBP1b.

-	~~Authors~~:	+	Escherichia coli Penicillin-Binding Protein 1B: Structural Insights into Inhibition.,King DT, Wasney GA, Nosella M, Fong A, Strynadka NC J Biol Chem. 2016 Nov 29. pii: jbc.M116.718403. PMID:27899450<ref>PMID:27899450</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5hld" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: King, D T]]
		+	[[Category: Strynadka, N C.J]]
		+	[[Category: Inhibitor complex]]
		+	[[Category: Penicillin-binding protein]]
		+	[[Category: Transferase-transferase inhibitor complex]]
		+	[[Category: Transglycosylase]]
		+	[[Category: Transpeptidase]]

OCA at 13:42, 15 May 2016

2016-05-15T13:42:12Z

←Older revision		Revision as of 13:42, 15 May 2016
Line 3:		Line 3:
	The entry 5hld is ON HOLD until Paper Publication		The entry 5hld is ON HOLD until Paper Publication

-	Authors: ~~King, D.T., Strynadka, N.C.J.~~	+	Authors:

	Description:		Description:
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Strynadka, N.C.J]]
-	[[Category: King, D.T]]

OCA at 15:25, 10 February 2016

2016-02-10T15:25:29Z

←Older revision		Revision as of 15:25, 10 February 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5hld is ON HOLD	+	The entry 5hld is ON HOLD until Paper Publication

	Authors: King, D.T., Strynadka, N.C.J.		Authors: King, D.T., Strynadka, N.C.J.

OCA: Protected "5hld" [edit=sysop:move=sysop]

2016-01-20T15:42:39Z

Protected "5hld" [edit=sysop:move=sysop]

←Older revision

Revision as of 15:42, 20 January 2016

OCA: New page: '''Unreleased structure''' The entry 5hld is ON HOLD Authors: King, D.T., Strynadka, N.C.J. Description: Category: Unreleased Structures Category: Strynadka, N.C.J [[Category:...

2016-01-20T15:42:37Z

New page: '''Unreleased structure''' The entry 5hld is ON HOLD Authors: King, D.T., Strynadka, N.C.J. Description: Category: Unreleased Structures Category: Strynadka, N.C.J [[Category:...

New page

'''Unreleased structure'''

The entry 5hld is ON HOLD

Authors: King, D.T., Strynadka, N.C.J.

Description:
[[Category: Unreleased Structures]]
[[Category: Strynadka, N.C.J]]
[[Category: King, D.T]]