4e8w - Revision history

OCA at 14:55, 14 March 2024

2024-03-14T14:55:40Z

← Older revision		Revision as of 14:55, 14 March 2024
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4e8w]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Burkholderia_cenocepacia_J2315 Burkholderia cenocepacia J2315]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4E8W OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4E8W FirstGlance]. <br>		<table><tr><td colspan='2'>[[4e8w]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Burkholderia_cenocepacia_J2315 Burkholderia cenocepacia J2315]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4E8W OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4E8W FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=IHA:{[2-({[5-(2,6-DIMETHOXYPHENYL)-1,2,4-TRIAZIN-3-YL]AMINO}METHYL)-1,3-BENZOTHIAZOL-5-YL]OXY}ACETIC+ACID'>IHA</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</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]] 2.8654Å</td></tr>
			<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=IHA:{[2-({[5-(2,6-DIMETHOXYPHENYL)-1,2,4-TRIAZIN-3-YL]AMINO}METHYL)-1,3-BENZOTHIAZOL-5-YL]OXY}ACETIC+ACID'>IHA</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</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=4e8w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4e8w OCA], [https://pdbe.org/4e8w PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4e8w RCSB], [https://www.ebi.ac.uk/pdbsum/4e8w PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4e8w 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=4e8w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4e8w OCA], [https://pdbe.org/4e8w PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4e8w RCSB], [https://www.ebi.ac.uk/pdbsum/4e8w PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4e8w ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[https://www.uniprot.org/uniprot/B4EB35_BURCJ B4EB35_BURCJ]]		[https://www.uniprot.org/uniprot/B4EB35_BURCJ B4EB35_BURCJ]
	~~<div style="background-color:#fffaf0;">~~
	~~== Publication Abstract from PubMed ==~~
	As an essential constituent of the outer membrane of Gram-negative bacteria, lipopolysaccharide contributes significantly to virulence and antibiotic resistance. The lipopolysaccharide biosynthetic pathway therefore serves as a promising therapeutic target for antivirulence drugs and antibiotic adjuvants. Here we report the structural-functional studies of d-glycero-beta-d-manno-heptose 7-phosphate kinase (HldA), an absolutely conserved enzyme in this pathway, from Burkholderia cenocepacia. HldA is structurally similar to members of the PfkB carbohydrate kinase family and appears to catalyze heptose phosphorylation via an in-line mechanism mediated mainly by a conserved aspartate, Asp270. Moreover, we report the structures of HldA in complex with two potent inhibitors in which both inhibitors adopt a folded conformation and occupy the nucleotide-binding sites. Together, these results provide important insight into the mechanism of HldA-catalyzed heptose phosphorylation and necessary information for further development of HldA inhibitors.

	Structural-Functional Studies of Burkholderia cenocepaciad-Glycero-beta-d-manno-heptose 7-Phosphate Kinase (HldA) and Characterization of Inhibitors with Antibiotic Adjuvant and Antivirulence Properties.,Lee TW, Verhey TB, Antiperovitch PA, Atamanyuk D, Desroy N, Oliveira C, Denis A, Gerusz V, Drocourt E, Loutet SA, Hamad MA, Stanetty C, Andres SN, Sugiman-Marangos S, Kosma P, Valvano MA, Moreau F, Junop MS J Med Chem. 2013 Jan 22. PMID:23256532<ref>PMID:23256532</ref>

	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~
	~~</div>~~
	~~<div class="pdbe-citations 4e8w" style="background-color:#fffaf0;"></div>~~
	~~== References ==~~
	~~<references/>~~
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 06:57, 28 September 2022

2022-09-28T06:57:51Z

← Older revision		Revision as of 06:57, 28 September 2022
Line 1:		Line 1:

	==Crystal Structure of Burkholderia cenocepacia HldA in Complex with an ATP-competitive Inhibitor==		==Crystal Structure of Burkholderia cenocepacia HldA in Complex with an ATP-competitive Inhibitor==
	<StructureSection load='4e8w' size='340' side='right' caption='[[4e8w]], [[Resolution\|resolution]] 2.87Å' scene=''>		<StructureSection load='4e8w' size='340' side='right'caption='[[4e8w]], [[Resolution\|resolution]] 2.87Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4e8w]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Burcj Burcj~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4E8W OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4E8W FirstGlance]. <br>		<table><tr><td colspan='2'>[[4e8w]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Burkholderia_cenocepacia_J2315 Burkholderia cenocepacia J2315]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4E8W OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4E8W FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=IHA:{[2-({[5-(2,6-DIMETHOXYPHENYL)-1,2,4-TRIAZIN-3-YL]AMINO}METHYL)-1,3-BENZOTHIAZOL-5-YL]OXY}ACETIC+ACID'>IHA</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>~~</td></tr>~~		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=IHA:{[2-({[5-(2,6-DIMETHOXYPHENYL)-1,2,4-TRIAZIN-3-YL]AMINO}METHYL)-1,3-BENZOTHIAZOL-5-YL]OXY}ACETIC+ACID'>IHA</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene></td></tr>
	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4e84\|4e84]], [[4e8z\|4e8z]], [[4e8y\|4e8y]]</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=4e8w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4e8w OCA], [https://pdbe.org/4e8w PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4e8w RCSB], [https://www.ebi.ac.uk/pdbsum/4e8w PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4e8w ProSAT]</span></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">hldA, BceJ2315_28810, BCAL2945 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=216591 BURCJ])</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=4e8w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4e8w OCA], [~~http~~://pdbe.org/4e8w PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4e8w RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4e8w PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4e8w ProSAT]</span></td></tr>
	</table>		</table>
			== Function ==
			[[https://www.uniprot.org/uniprot/B4EB35_BURCJ B4EB35_BURCJ]]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 22:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Burcj~~]]		[[Category: Burkholderia cenocepacia J2315]]
	[[Category: ~~Junop, M S~~]]		[[Category: Large Structures]]
	[[Category: ~~Lee, T W~~]]		[[Category: Junop MS]]
	[[Category: ~~Verhey,~~ T ~~B]]~~		[[Category: Lee T-W]]
	~~[[Category: Beta~~-~~clasp dimerization region~~]]		[[Category: Verhey TB]]
	[[Category: ~~Lps-heptose biosynthesis]]~~
	~~[[Category: Pfkb carbohydrate kinase]]~~
	~~[[Category: Phosphorylation]]~~
	~~[[Category: Transferase-transferase inhibitor complex~~]]

OCA at 05:59, 5 August 2016

2016-08-05T05:59:53Z

← Older revision		Revision as of 05:59, 5 August 2016
Line 1:		Line 1:
	~~{{STRUCTURE_4e8w\| PDB=4e8w \| SCENE= }}~~
	~~===Crystal Structure of Burkholderia cenocepacia HldA in Complex with an ATP-competitive Inhibitor===~~
	~~{{ABSTRACT_PUBMED_23256532}}~~

	==~~About this~~ Structure==		==Crystal Structure of Burkholderia cenocepacia HldA in Complex with an ATP-competitive Inhibitor==
	[[4e8w]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Burkholderia_cenocepacia_j2315 Burkholderia cenocepacia j2315~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4E8W OCA].		<StructureSection load='4e8w' size='340' side='right' caption='[[4e8w]], [[Resolution\|resolution]] 2.87Å' scene=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[4e8w]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Burcj Burcj]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4E8W OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4E8W FirstGlance]. <br>
			</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=IHA:{[2-({[5-(2,6-DIMETHOXYPHENYL)-1,2,4-TRIAZIN-3-YL]AMINO}METHYL)-1,3-BENZOTHIAZOL-5-YL]OXY}ACETIC+ACID'>IHA</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene></td></tr>
			<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4e84\|4e84]], [[4e8z\|4e8z]], [[4e8y\|4e8y]]</td></tr>
			<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">hldA, BceJ2315_28810, BCAL2945 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=216591 BURCJ])</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=4e8w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4e8w OCA], [http://pdbe.org/4e8w PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4e8w RCSB], [http://www.ebi.ac.uk/pdbsum/4e8w PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4e8w ProSAT]</span></td></tr>
			</table>
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			As an essential constituent of the outer membrane of Gram-negative bacteria, lipopolysaccharide contributes significantly to virulence and antibiotic resistance. The lipopolysaccharide biosynthetic pathway therefore serves as a promising therapeutic target for antivirulence drugs and antibiotic adjuvants. Here we report the structural-functional studies of d-glycero-beta-d-manno-heptose 7-phosphate kinase (HldA), an absolutely conserved enzyme in this pathway, from Burkholderia cenocepacia. HldA is structurally similar to members of the PfkB carbohydrate kinase family and appears to catalyze heptose phosphorylation via an in-line mechanism mediated mainly by a conserved aspartate, Asp270. Moreover, we report the structures of HldA in complex with two potent inhibitors in which both inhibitors adopt a folded conformation and occupy the nucleotide-binding sites. Together, these results provide important insight into the mechanism of HldA-catalyzed heptose phosphorylation and necessary information for further development of HldA inhibitors.

	~~==Reference==~~		Structural-Functional Studies of Burkholderia cenocepaciad-Glycero-beta-d-manno-heptose 7-Phosphate Kinase (HldA) and Characterization of Inhibitors with Antibiotic Adjuvant and Antivirulence Properties.,Lee TW, Verhey TB, Antiperovitch PA, Atamanyuk D, Desroy N, Oliveira C, Denis A, Gerusz V, Drocourt E, Loutet SA, Hamad MA, Stanetty C, Andres SN, Sugiman-Marangos S, Kosma P, Valvano MA, Moreau F, Junop MS J Med Chem. 2013 Jan 22. PMID:23256532<ref>PMID:23256532</ref>
	<ref ~~group="xtra"~~>PMID:~~023256532~~</ref><~~references group~~="~~xtra~~"/><references/>
	[[Category: ~~Burkholderia cenocepacia j2315~~]]		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	[[Category: Junop, M S.]]		</div>
	[[Category: Lee, T W.]]		<div class="pdbe-citations 4e8w" style="background-color:#fffaf0;"></div>
	[[Category: Verhey, T B.]]		== References ==
			<references/>
			__TOC__
			</StructureSection>
			[[Category: Burcj]]
			[[Category: Junop, M S]]
			[[Category: Lee, T W]]
			[[Category: Verhey, T B]]
	[[Category: Beta-clasp dimerization region]]		[[Category: Beta-clasp dimerization region]]
	[[Category: Lps-heptose biosynthesis]]		[[Category: Lps-heptose biosynthesis]]

OCA at 07:09, 30 June 2013

2013-06-30T07:09:23Z

← Older revision		Revision as of 07:09, 30 June 2013
Line 1:		Line 1:
	~~'''Unreleased structure'''~~		{{STRUCTURE_4e8w\| PDB=4e8w \| SCENE= }}
			===Crystal Structure of Burkholderia cenocepacia HldA in Complex with an ATP-competitive Inhibitor===
			{{ABSTRACT_PUBMED_23256532}}

	~~The entry~~ 4e8w is ~~ON HOLD until Paper Publication~~		==About this Structure==
			[[4e8w]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Burkholderia_cenocepacia_j2315 Burkholderia cenocepacia j2315]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4E8W OCA].

	~~Authors~~: Lee, T.-W., Verhey, T.B.~~, Junop, M.S.~~		==Reference==
			<ref group="xtra">PMID:023256532</ref><references group="xtra"/><references/>
	~~Description~~: ~~Crystal Structure of Burkholderia cenocepacia HldA in Complex with an ATP~~-~~competitive Inhibitor~~		[[Category: Burkholderia cenocepacia j2315]]
			[[Category: Junop, M S.]]
			[[Category: Lee, T W.]]
			[[Category: Verhey, T B.]]
			[[Category: Beta-clasp dimerization region]]
			[[Category: Lps-heptose biosynthesis]]
			[[Category: Pfkb carbohydrate kinase]]
			[[Category: Phosphorylation]]
			[[Category: Transferase-transferase inhibitor complex]]

OCA at 05:25, 30 May 2012

2012-05-30T05:25:01Z

← Older revision		Revision as of 05:25, 30 May 2012
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

	The entry 4e8w is ON HOLD		The entry 4e8w is ON HOLD until Paper Publication

	Authors: Lee, T.-W., Verhey, T.B., Junop, M.S.		Authors: Lee, T.-W., Verhey, T.B., Junop, M.S.

	Description: Crystal Structure of Burkholderia cenocepacia HldA in Complex with an ATP-competitive Inhibitor		Description: Crystal Structure of Burkholderia cenocepacia HldA in Complex with an ATP-competitive Inhibitor

OCA: Protected "4e8w" [edit=sysop:move=sysop]

2012-03-28T07:24:57Z

Protected "4e8w" [edit=sysop:move=sysop]

← Older revision	Revision as of 07:24, 28 March 2012
(No difference)

OCA: New page: '''Unreleased structure''' The entry 4e8w is ON HOLD Authors: Lee, T.-W., Verhey, T.B., Junop, M.S. Description: Crystal Structure of Burkholderia cenocepacia HldA in Complex with an A...

2012-03-28T07:24:56Z

New page: '''Unreleased structure''' The entry 4e8w is ON HOLD Authors: Lee, T.-W., Verhey, T.B., Junop, M.S. Description: Crystal Structure of Burkholderia cenocepacia HldA in Complex with an A...

New page

'''Unreleased structure'''

The entry 4e8w is ON HOLD

Authors: Lee, T.-W., Verhey, T.B., Junop, M.S.

Description: Crystal Structure of Burkholderia cenocepacia HldA in Complex with an ATP-competitive Inhibitor