6wup - Revision history

OCA at 14:36, 18 October 2023

2023-10-18T14:36:25Z

← Older revision		Revision as of 14:36, 18 October 2023
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	<StructureSection load='6wup' size='340' side='right'caption='[[6wup]], [[Resolution\|resolution]] 1.49Å' scene=''>		<StructureSection load='6wup' size='340' side='right'caption='[[6wup]], [[Resolution\|resolution]] 1.49Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6wup]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Synthetic_construct_sequences~~ Synthetic construct ~~sequences~~]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=6oki 6oki]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6WUP OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6WUP FirstGlance]. <br>		<table><tr><td colspan='2'>[[6wup]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=6oki 6oki]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6WUP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6WUP FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</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]] 1.49Å</td></tr>
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=6wup FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6wup OCA], [~~http~~://pdbe.org/6wup PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6wup RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6wup PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6wup ProSAT]</span></td></tr>		<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</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=6wup FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6wup OCA], [https://pdbe.org/6wup PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6wup RCSB], [https://www.ebi.ac.uk/pdbsum/6wup PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6wup ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Synthetic construct ~~sequences~~]]		[[Category: Synthetic construct]]
	[[Category: Kaczmarski~~, J A~~]]		[[Category: Kaczmarski JA]]
	[[Category: Mahawaththa~~, M C]]~~		[[Category: Mahawaththa MC]]
	~~[[Category: Cyclohexadienyl dehydratase ancestral protein reconstruction]]~~
	~~[[Category: Lyase~~]]

OCA at 06:50, 9 December 2020

2020-12-09T06:50:33Z

← Older revision		Revision as of 06:50, 9 December 2020
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	==Crystal structure of an ancestral cyclohexadienyl dehydratase, AncCDT-5==		==Crystal structure of an ancestral cyclohexadienyl dehydratase, AncCDT-5==
	<StructureSection load='6wup' size='340' side='right'caption='[[6wup]]' scene=''>		<StructureSection load='6wup' size='340' side='right'caption='[[6wup]], [[Resolution\|resolution]] 1.49Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=6oki 6oki]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6WUP OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6WUP FirstGlance]. <br>		<table><tr><td colspan='2'>[[6wup]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Synthetic_construct_sequences Synthetic construct sequences]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=6oki 6oki]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6WUP OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6WUP FirstGlance]. <br>
	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6wup FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6wup OCA], [http://pdbe.org/6wup PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6wup RCSB], [http://www.ebi.ac.uk/pdbsum/6wup PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6wup ProSAT]</span></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene></td></tr>
			<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6wup FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6wup OCA], [http://pdbe.org/6wup PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6wup RCSB], [http://www.ebi.ac.uk/pdbsum/6wup PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6wup ProSAT]</span></td></tr>
	</table>		</table>
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			Several enzymes are known to have evolved from non-catalytic proteins such as solute-binding proteins (SBPs). Although attention has been focused on how a binding site can evolve to become catalytic, an equally important question is: how do the structural dynamics of a binding protein change as it becomes an efficient enzyme? Here we performed a variety of experiments, including propargyl-DO3A-Gd(III) tagging and double electron-electron resonance (DEER) to study the rigid body protein dynamics of reconstructed evolutionary intermediates to determine how the conformational sampling of a protein changes along an evolutionary trajectory linking an arginine SBP to a cyclohexadienyl dehydratase (CDT). We observed that primitive dehydratases predominantly populate catalytically unproductive conformations that are vestiges of their ancestral SBP function. Non-productive conformational states, including a wide-open state, are frozen out of the conformational landscape via remote mutations, eventually leading to extant CDT that exclusively samples catalytically relevant compact states. These results show that remote mutations can reshape the global conformational landscape of an enzyme as a mechanism for increasing catalytic activity.

			Altered conformational sampling along an evolutionary trajectory changes the catalytic activity of an enzyme.,Kaczmarski JA, Mahawaththa MC, Feintuch A, Clifton BE, Adams LA, Goldfarb D, Otting G, Jackson CJ Nat Commun. 2020 Nov 23;11(1):5945. doi: 10.1038/s41467-020-19695-9. PMID:33230119<ref>PMID:33230119</ref>

			From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
			<div class="pdbe-citations 6wup" style="background-color:#fffaf0;"></div>
			== References ==
			<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Kaczmarski JA]]		[[Category: Synthetic construct sequences]]
	[[Category: Mahawaththa MC]]		[[Category: Kaczmarski, J A]]
			[[Category: Mahawaththa, M C]]
			[[Category: Cyclohexadienyl dehydratase ancestral protein reconstruction]]
			[[Category: Lyase]]

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

2020-05-13T05:21:34Z

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

← Older revision	Revision as of 05:21, 13 May 2020
(No difference)

OCA: New page: ==Crystal structure of an ancestral cyclohexadienyl dehydratase, AncCDT-5== == Structural highlights == <...

2020-05-13T05:21:33Z

New page: ==Crystal structure of an ancestral cyclohexadienyl dehydratase, AncCDT-5== <StructureSection load='6wup' size='340' side='right'caption='6wup' scene=''> == Structural highlights == <...

New page

==Crystal structure of an ancestral cyclohexadienyl dehydratase, AncCDT-5==
<StructureSection load='6wup' size='340' side='right'caption='[[6wup]]' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=6oki 6oki]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6WUP OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6WUP FirstGlance]. <br>
</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6wup FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6wup OCA], [http://pdbe.org/6wup PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6wup RCSB], [http://www.ebi.ac.uk/pdbsum/6wup PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6wup ProSAT]</span></td></tr>
</table>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Kaczmarski JA]]
[[Category: Mahawaththa MC]]