6und - Revision history

OCA at 07:54, 11 October 2023

2023-10-11T07:54:58Z

←Older revision		Revision as of 07:54, 11 October 2023
Line 3:		Line 3:
	<StructureSection load='6und' size='340' side='right'caption='[[6und]], [[Resolution\|resolution]] 1.55Å' scene=''>		<StructureSection load='6und' size='340' side='right'caption='[[6und]], [[Resolution\|resolution]] 1.55Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6und]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Psef5 Psef5~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6UND OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6UND FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6und]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_protegens_Pf-5 Pseudomonas protegens Pf-5]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6UND OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6UND FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=QCV:N~~-~~(4-nitrophenyl)methanimine'>QCV</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]] 1.55Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~inhA, PFL_4109 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=~~5&id=220664 PSEF5]~~)</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=QCV:N-(4-nitrophenyl)methanimine'>QCV</scene></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=6und FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6und OCA], [~~http~~://pdbe.org/6und PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6und RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6und PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6und 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=6und FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6und OCA], [https://pdbe.org/6und PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6und RCSB], [https://www.ebi.ac.uk/pdbsum/6und PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6und ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q4K977_PSEF5 Q4K977_PSEF5]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 22:		Line 24:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Psef5]]~~	+	[[Category: Pseudomonas protegens Pf-5]]
-	~~[[Category: Bedem, H van den~~]]	+	[[Category: Dasgupta M]]
-	[[Category: Dasgupta, M]]	+	[[Category: Wilson MA]]
-	[[Category: Wilson~~, M A~~]]	+	[[Category: Van den Bedem H]]
-	[[Category: ~~Covalent catalytic intermediate]]~~	+
-	~~[[Category: Lyase~~]]	+

OCA at 13:24, 18 December 2019

2019-12-18T13:24:05Z

←Older revision		Revision as of 13:24, 18 December 2019
Line 3:		Line 3:
	<StructureSection load='6und' size='340' side='right'caption='[[6und]], [[Resolution\|resolution]] 1.55Å' scene=''>		<StructureSection load='6und' size='340' side='right'caption='[[6und]], [[Resolution\|resolution]] 1.55Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6und]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6UND OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6UND FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6und]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Psef5 Psef5]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6UND OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6UND FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=QCV:N-(4-nitrophenyl)methanimine'>QCV</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=QCV:N-(4-nitrophenyl)methanimine'>QCV</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">inhA, PFL_4109 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=220664 PSEF5])</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=6und FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6und OCA], [http://pdbe.org/6und PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6und RCSB], [http://www.ebi.ac.uk/pdbsum/6und PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6und 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=6und FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6und OCA], [http://pdbe.org/6und PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6und RCSB], [http://www.ebi.ac.uk/pdbsum/6und PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6und ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	How changes in enzyme structure and dynamics facilitate passage along the reaction coordinate is a fundamental unanswered question. Here, we use time-resolved mix-and-inject serial crystallography (MISC) at an X-ray free electron laser (XFEL), ambient-temperature X-ray crystallography, computer simulations, and enzyme kinetics to characterize how covalent catalysis modulates isocyanide hydratase (ICH) conformational dynamics throughout its catalytic cycle. We visualize this previously hypothetical reaction mechanism, directly observing formation of a thioimidate covalent intermediate in ICH microcrystals during catalysis. ICH exhibits a concerted helical displacement upon active-site cysteine modification that is gated by changes in hydrogen bond strength between the cysteine thiolate and the backbone amide of the highly strained Ile152 residue. These catalysis-activated motions permit water entry into the ICH active site for intermediate hydrolysis. Mutations at a Gly residue (Gly150) that modulate helical mobility reduce ICH catalytic turnover and alter its pre-steady-state kinetic behavior, establishing that helical mobility is important for ICH catalytic efficiency. These results demonstrate that MISC can capture otherwise elusive aspects of enzyme mechanism and dynamics in microcrystalline samples, resolving long-standing questions about the connection between nonequilibrium protein motions and enzyme catalysis.
		+
		+	Mix-and-inject XFEL crystallography reveals gated conformational dynamics during enzyme catalysis.,Dasgupta M, Budday D, de Oliveira SHP, Madzelan P, Marchany-Rivera D, Seravalli J, Hayes B, Sierra RG, Boutet S, Hunter MS, Alonso-Mori R, Batyuk A, Wierman J, Lyubimov A, Brewster AS, Sauter NK, Applegate GA, Tiwari VK, Berkowitz DB, Thompson MC, Cohen AE, Fraser JS, Wall ME, van den Bedem H, Wilson MA Proc Natl Acad Sci U S A. 2019 Dec 4. pii: 1901864116. doi:, 10.1073/pnas.1901864116. PMID:31801874<ref>PMID:31801874</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6und" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
		+	[[Category: Psef5]]
	[[Category: Bedem, H van den]]		[[Category: Bedem, H van den]]
	[[Category: Dasgupta, M]]		[[Category: Dasgupta, M]]

OCA at 15:40, 20 November 2019

2019-11-20T15:40:15Z

←Older revision		Revision as of 15:40, 20 November 2019
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-	'''Unreleased structure'''

-	~~The entry~~ 6und is ~~ON HOLD~~	+	==Pseudomonas fluorescens isocyanide hydratase thioimidate intermediate at 298 K XFEL data==
-		+	<StructureSection load='6und' size='340' side='right'caption='[[6und]], [[Resolution\|resolution]] 1.55Å' scene=''>
-	~~Authors~~: ~~Dasgupta~~, M., ~~van den Bedem~~, H., ~~Wilson~~, M.A.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6und]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6UND OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6UND FirstGlance]. <br>
-	~~Description: Pseudomonas fluorescens isocyanide hydratase thioimidate intermediate at 298 K XFEL data~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=QCV:N-(4-nitrophenyl)methanimine'>QCV</scene></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	<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=6und FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6und OCA], [http://pdbe.org/6und PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6und RCSB], [http://www.ebi.ac.uk/pdbsum/6und PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6und ProSAT]</span></td></tr>
-	[[Category: ~~Van Den~~ Bedem, H]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Bedem, H van den]]
	[[Category: Dasgupta, M]]		[[Category: Dasgupta, M]]
-	[[Category: Wilson, M.A]]	+	[[Category: Wilson, M A]]
		+	[[Category: Covalent catalytic intermediate]]
		+	[[Category: Lyase]]

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

2019-10-23T05:12:10Z

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

←Older revision

Revision as of 05:12, 23 October 2019

OCA: New page: '''Unreleased structure''' The entry 6und is ON HOLD Authors: Dasgupta, M., van den Bedem, H., Wilson, M.A. Description: Pseudomonas fluorescens isocyanide hydratase thioimidate interm...

2019-10-23T05:12:08Z

New page: '''Unreleased structure''' The entry 6und is ON HOLD Authors: Dasgupta, M., van den Bedem, H., Wilson, M.A. Description: Pseudomonas fluorescens isocyanide hydratase thioimidate interm...

New page

'''Unreleased structure'''

The entry 6und is ON HOLD

Authors: Dasgupta, M., van den Bedem, H., Wilson, M.A.

Description: Pseudomonas fluorescens isocyanide hydratase thioimidate intermediate at 298 K XFEL data
[[Category: Unreleased Structures]]
[[Category: Van Den Bedem, H]]
[[Category: Dasgupta, M]]
[[Category: Wilson, M.A]]