6ni7 - Revision history

OCA at 06:54, 11 October 2023

OCA — Wed, 11 Oct 2023 06:54:12 GMT

←Older revision		Revision as of 06:54, 11 October 2023
Line 3:		Line 3:
	<StructureSection load='6ni7' size='340' side='right'caption='[[6ni7]], [[Resolution\|resolution]] 1.15Å' scene=''>		<StructureSection load='6ni7' size='340' side='right'caption='[[6ni7]], [[Resolution\|resolution]] 1.15Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6ni7]] 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=6NI7 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6NI7 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6ni7]] 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=6NI7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6NI7 FirstGlance]. <br>
-	</td></tr><tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=CSO:S~~-~~HYDROXYCYSTEINE'>CSO</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]] 1.15Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~>[[6ni6\|6ni6]]</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</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'>[https://proteopedia.org/fgij/fg.htm?mol=6ni7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ni7 OCA], [https://pdbe.org/6ni7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6ni7 RCSB], [https://www.ebi.ac.uk/pdbsum/6ni7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6ni7 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=6ni7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ni7 OCA], [~~http~~://pdbe.org/6ni7 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6ni7 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6ni7 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6ni7 ProSAT]</span></td></tr>	+
	</table>		</table>
-	~~<div style~~=~~"background-color:#fffaf0;">~~	+	== Function ==
-	=~~= Publication Abstract from PubMed~~ ==	+	[https://www.uniprot.org/uniprot/Q4K977_PSEF5 Q4K977_PSEF5]
-	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 6ni7" style="background-color:#fffaf0;"></div>~~	+
-	~~== References ==~~	+
-	~~<references~~/>	+
	__TOC__		__TOC__
	</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: ~~Dj-1 superfamily]]~~	+
-	~~[[Category: Lyase]]~~	+
-	~~[[Category: Thij/pfpi~~]]	+

OCA at 11:40, 1 January 2020

OCA — Wed, 01 Jan 2020 11:40:59 GMT

←Older revision		Revision as of 11:40, 1 January 2020
Line 3:		Line 3:
	<StructureSection load='6ni7' size='340' side='right'caption='[[6ni7]], [[Resolution\|resolution]] 1.15Å' scene=''>		<StructureSection load='6ni7' size='340' side='right'caption='[[6ni7]], [[Resolution\|resolution]] 1.15Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6ni7]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6NI7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6NI7 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6ni7]] 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=6NI7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6NI7 FirstGlance]. <br>
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</scene></td></tr>		</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6ni6\|6ni6]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6ni6\|6ni6]]</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=6ni7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ni7 OCA], [http://pdbe.org/6ni7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ni7 RCSB], [http://www.ebi.ac.uk/pdbsum/6ni7 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ni7 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=6ni7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ni7 OCA], [http://pdbe.org/6ni7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ni7 RCSB], [http://www.ebi.ac.uk/pdbsum/6ni7 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ni7 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 6ni7" 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 15:27, 20 November 2019

OCA — Wed, 20 Nov 2019 15:27:01 GMT

←Older revision		Revision as of 15:27, 20 November 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6ni7 is ~~ON HOLD until Paper Publication~~	+	==Pseudomonas fluorescens isocyanide hydratase at 277 K==
-		+	<StructureSection load='6ni7' size='340' side='right'caption='[[6ni7]], [[Resolution\|resolution]] 1.15Å' scene=''>
-	~~Authors~~: ~~Wilson~~, M.A., ~~Dasgupta~~, M., ~~van den Bedem~~, H.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6ni7]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6NI7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6NI7 FirstGlance]. <br>
-	~~Description: Pseudomonas fluorescens isocyanide hydratase at 277 K~~	+	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</scene></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6ni6\|6ni6]]</td></tr>
-	[[Category: ~~Van Den~~ Bedem, H]]	+	<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=6ni7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ni7 OCA], [http://pdbe.org/6ni7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ni7 RCSB], [http://www.ebi.ac.uk/pdbsum/6ni7 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ni7 ProSAT]</span></td></tr>
		+	</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: Dj-1 superfamily]]
		+	[[Category: Lyase]]
		+	[[Category: Thij/pfpi]]

OCA at 05:04, 21 February 2019

OCA — Thu, 21 Feb 2019 05:04:43 GMT

←Older revision		Revision as of 05:04, 21 February 2019
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6ni7 is ON HOLD	+	The entry 6ni7 is ON HOLD until Paper Publication

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

OCA: Protected "6ni7" [edit=sysop:move=sysop]

OCA — Wed, 02 Jan 2019 04:59:33 GMT

Protected "6ni7" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:59, 2 January 2019

OCA: New page: '''Unreleased structure''' The entry 6ni7 is ON HOLD Authors: Wilson, M.A., Dasgupta, M., van den Bedem, H. Description: Pseudomonas fluorescens isocyanide hydratase at 277 K [[Categor...

OCA — Wed, 02 Jan 2019 04:59:32 GMT

New page: '''Unreleased structure''' The entry 6ni7 is ON HOLD Authors: Wilson, M.A., Dasgupta, M., van den Bedem, H. Description: Pseudomonas fluorescens isocyanide hydratase at 277 K [[Categor...

New page

'''Unreleased structure'''

The entry 6ni7 is ON HOLD

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

Description: Pseudomonas fluorescens isocyanide hydratase at 277 K
[[Category: Unreleased Structures]]
[[Category: Van Den Bedem, H]]
[[Category: Dasgupta, M]]
[[Category: Wilson, M.A]]