5g2i - Revision history

OCA at 13:36, 26 July 2023

2023-07-26T13:36:11Z

←Older revision		Revision as of 13:36, 26 July 2023
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	<StructureSection load='5g2i' size='340' side='right'caption='[[5g2i]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='5g2i' size='340' side='right'caption='[[5g2i]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5g2i]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"bacillus_cholerae-suis"_smith_1894 "bacillus cholerae-suis" smith 1894~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5G2I OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5G2I FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5g2i]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Salmonella_enterica Salmonella enterica]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5G2I OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5G2I FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=NA:SODIUM+ION'>NA</scene>~~, ~~<scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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]] 1.601Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~>[[5g2h\|5g2h]]</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-	~~<tr~~ id~~='activity'><td class~~="~~sblockLbl~~"><~~b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks~~'>[http://en.wikipedia.org/wiki/1-(5-phosphoribosyl)-5-_((5-phosphoribosylamino)methylideneamino)imidazole-4-carboxamide_isomerase 1-(5-phosphoribosyl)-5- ((5-phosphoribosylamino)methylideneamino)imidazole-4-carboxamide isomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.3.1.16 5.3.1.16] </~~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=5g2i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5g2i OCA], [https://pdbe.org/5g2i PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5g2i RCSB], [https://www.ebi.ac.uk/pdbsum/5g2i PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5g2i ProSAT]</span></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=5g2i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5g2i OCA], [~~http~~://pdbe.org/5g2i PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5g2i RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5g2i PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5g2i ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/HIS4_SALTY HIS4_SALTY]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 22:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Bacillus cholerae-suis smith 1894]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Andersson, D]]	+	[[Category: Salmonella enterica]]
-	[[Category: Duarte, F]]	+	[[Category: Andersson D]]
-	[[Category: Guo, X]]	+	[[Category: Duarte F]]
-	[[Category: Nasvall, J]]	+	[[Category: Guo X]]
-	[[Category: Newton, M]]	+	[[Category: Nasvall J]]
-	[[Category: Patrick, W]]	+	[[Category: Newton M]]
-	[[Category: Selmer, M]]	+	[[Category: Patrick W]]
-	[[Category: Soderholm, A]]	+	[[Category: Selmer M]]
-	~~[[Category: Hisa]]~~	+	[[Category: Soderholm A]]
-	~~[[Category: Iad model]]~~	+
-	~~[[Category: Isomerase]]~~	+
-	~~[[Category: Protein evolution]]~~	+
-	~~[[Category: Trpf~~]]	+

OCA at 06:36, 13 May 2020

2020-05-13T06:36:23Z

←Older revision		Revision as of 06:36, 13 May 2020
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	==S. enterica HisA mutant Dup13-15(VVR)==		==S. enterica HisA mutant Dup13-15(VVR)==
-	<StructureSection load='5g2i' size='340' side='right' caption='[[5g2i]], [[Resolution\|resolution]] 1.60Å' scene=''>	+	<StructureSection load='5g2i' size='340' side='right'caption='[[5g2i]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5g2i]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_cholerae-suis"_smith_1894 "bacillus cholerae-suis" smith 1894]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5G2I OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5G2I FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5g2i]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_cholerae-suis"_smith_1894 "bacillus cholerae-suis" smith 1894]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5G2I OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5G2I FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5g2h\|5g2h]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5g2h\|5g2h]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/1-(5-phosphoribosyl)-5-_((5-phosphoribosylamino)methylideneamino)imidazole-4-carboxamide_isomerase 1-(5-phosphoribosyl)-5- ((5-phosphoribosylamino)methylideneamino)imidazole-4-carboxamide isomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.3.1.16 5.3.1.16] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/1-(5-phosphoribosyl)-5-_((5-phosphoribosylamino)methylideneamino)imidazole-4-carboxamide_isomerase 1-(5-phosphoribosyl)-5- ((5-phosphoribosylamino)methylideneamino)imidazole-4-carboxamide isomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.3.1.16 5.3.1.16] </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=5g2i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5g2i OCA], [http://pdbe.org/5g2i PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5g2i RCSB], [http://www.ebi.ac.uk/pdbsum/5g2i PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5g2i ProSAT]</span></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=5g2i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5g2i OCA], [http://pdbe.org/5g2i PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5g2i RCSB], [http://www.ebi.ac.uk/pdbsum/5g2i PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5g2i ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 23:		Line 23:
	</StructureSection>		</StructureSection>
	[[Category: Bacillus cholerae-suis smith 1894]]		[[Category: Bacillus cholerae-suis smith 1894]]
		+	[[Category: Large Structures]]
	[[Category: Andersson, D]]		[[Category: Andersson, D]]
	[[Category: Duarte, F]]		[[Category: Duarte, F]]

OCA at 23:07, 15 November 2017

2017-11-15T23:07:59Z

←Older revision		Revision as of 23:07, 15 November 2017
Line 3:		Line 3:
	<StructureSection load='5g2i' size='340' side='right' caption='[[5g2i]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='5g2i' size='340' side='right' caption='[[5g2i]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5g2i]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5G2I OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5G2I FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5g2i]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_cholerae-suis"_smith_1894 "bacillus cholerae-suis" smith 1894]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5G2I OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5G2I FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5g2h\|5g2h]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5g2h\|5g2h]]</td></tr>
Line 22:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bacillus cholerae-suis smith 1894]]
	[[Category: Andersson, D]]		[[Category: Andersson, D]]
	[[Category: Duarte, F]]		[[Category: Duarte, F]]

OCA at 07:41, 27 April 2017

2017-04-27T07:41:25Z

←Older revision		Revision as of 07:41, 27 April 2017
Line 9:		Line 9:
	<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=5g2i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5g2i OCA], [http://pdbe.org/5g2i PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5g2i RCSB], [http://www.ebi.ac.uk/pdbsum/5g2i PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5g2i 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=5g2i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5g2i OCA], [http://pdbe.org/5g2i PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5g2i RCSB], [http://www.ebi.ac.uk/pdbsum/5g2i PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5g2i ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	New genes can arise by duplication and divergence, but there is a fundamental gap in our understanding of the relationship between these genes, the evolving proteins they encode, and the fitness of the organism. Here we used crystallography, NMR dynamics, kinetics, and mass spectrometry to explain the molecular innovations that arose during a previous real-time evolution experiment. In that experiment, the (betaalpha)8 barrel enzyme HisA was under selection for two functions (HisA and TrpF), resulting in duplication and divergence of the hisA gene to encode TrpF specialists, HisA specialists, and bifunctional generalists. We found that selection affects enzyme structure and dynamics, and thus substrate preference, simultaneously and sequentially. Bifunctionality is associated with two distinct sets of loop conformations, each essential for one function. We observed two mechanisms for functional specialization: structural stabilization of each loop conformation and substrate-specific adaptation of the active site. Intracellular enzyme performance, calculated as the product of catalytic efficiency and relative expression level, was not linearly related to fitness. Instead, we observed thresholds for each activity above which further improvements in catalytic efficiency had little if any effect on growth rate. Overall, we have shown how beneficial substitutions selected during real-time evolution can lead to manifold changes in enzyme function and bacterial fitness. This work emphasizes the speed at which adaptive evolution can yield enzymes with sufficiently high activities such that they no longer limit the growth of their host organism, and confirms the (betaalpha)8 barrel as an inherently evolvable protein scaffold.
		+
		+	Structural and functional innovations in the real-time evolution of new (betaalpha)8 barrel enzymes.,Newton MS, Guo X, Soderholm A, Nasvall J, Lundstrom P, Andersson DI, Selmer M, Patrick WM Proc Natl Acad Sci U S A. 2017 Apr 17. pii: 201618552. doi:, 10.1073/pnas.1618552114. PMID:28416687<ref>PMID:28416687</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5g2i" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 12:56, 19 April 2017

2017-04-19T12:56:12Z

←Older revision		Revision as of 12:56, 19 April 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5g2i ~~is ON HOLD until Paper Publication~~	+	==S. enterica HisA mutant Dup13-15(VVR)==
-		+	<StructureSection load='5g2i' size='340' side='right' caption='[[5g2i]], [[Resolution\|resolution]] 1.60Å' scene=''>
-	~~Authors~~: ~~Guo, X~~.~~, Soderholm, A~~., ~~Newton~~, M., ~~Nasvall, J~~., ~~Duarte, F~~., ~~Andersson, D~~., ~~Patrick, W~~., ~~Selmer, M~~.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5g2i]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5G2I OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5G2I FirstGlance]. <br>
-	~~Description~~: ~~S. enterica HisA mutant Dup13-15(VVR)~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5g2h\|5g2h]]</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/1-(5-phosphoribosyl)-5-_((5-phosphoribosylamino)methylideneamino)imidazole-4-carboxamide_isomerase 1-(5-phosphoribosyl)-5- ((5-phosphoribosylamino)methylideneamino)imidazole-4-carboxamide isomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.3.1.16 5.3.1.16] </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=5g2i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5g2i OCA], [http://pdbe.org/5g2i PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5g2i RCSB], [http://www.ebi.ac.uk/pdbsum/5g2i PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5g2i ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Andersson, D]]
		+	[[Category: Duarte, F]]
		+	[[Category: Guo, X]]
	[[Category: Nasvall, J]]		[[Category: Nasvall, J]]
-	[[Category: Guo, X]]
-	[[Category: Soderholm, A]]
	[[Category: Newton, M]]		[[Category: Newton, M]]
		+	[[Category: Patrick, W]]
	[[Category: Selmer, M]]		[[Category: Selmer, M]]
-	[[Category: ~~Patrick~~, W]]	+	[[Category: Soderholm, A]]
-	[[Category: ~~Duarte, F~~]]	+	[[Category: Hisa]]
-	[[Category: ~~Andersson, D~~]]	+	[[Category: Iad model]]
		+	[[Category: Isomerase]]
		+	[[Category: Protein evolution]]
		+	[[Category: Trpf]]

OCA at 08:46, 9 March 2017

2017-03-09T08:46:52Z

←Older revision		Revision as of 08:46, 9 March 2017
Line 9:		Line 9:
	[[Category: Nasvall, J]]		[[Category: Nasvall, J]]
	[[Category: Guo, X]]		[[Category: Guo, X]]
-	[[Category: Selmer, M]]
-	[[Category: Patrick, W]]
-	[[Category: Andersson, D]]
	[[Category: Soderholm, A]]		[[Category: Soderholm, A]]
	[[Category: Newton, M]]		[[Category: Newton, M]]
		+	[[Category: Selmer, M]]
		+	[[Category: Patrick, W]]
	[[Category: Duarte, F]]		[[Category: Duarte, F]]
		+	[[Category: Andersson, D]]

OCA: Protected "5g2i" [edit=sysop:move=sysop]

2016-05-10T23:24:52Z

Protected "5g2i" [edit=sysop:move=sysop]

←Older revision

Revision as of 23:24, 10 May 2016

OCA: New page: '''Unreleased structure''' The entry 5g2i is ON HOLD until Paper Publication Authors: Guo, X., Soderholm, A., Newton, M., Nasvall, J., Duarte, F., Andersson, D., Patrick, W., Selmer, M....

2016-05-10T23:24:51Z

New page: '''Unreleased structure''' The entry 5g2i is ON HOLD until Paper Publication Authors: Guo, X., Soderholm, A., Newton, M., Nasvall, J., Duarte, F., Andersson, D., Patrick, W., Selmer, M....

New page

'''Unreleased structure'''

The entry 5g2i is ON HOLD until Paper Publication

Authors: Guo, X., Soderholm, A., Newton, M., Nasvall, J., Duarte, F., Andersson, D., Patrick, W., Selmer, M.

Description: S. enterica HisA mutant Dup13-15(VVR)
[[Category: Unreleased Structures]]
[[Category: Nasvall, J]]
[[Category: Guo, X]]
[[Category: Selmer, M]]
[[Category: Patrick, W]]
[[Category: Andersson, D]]
[[Category: Soderholm, A]]
[[Category: Newton, M]]
[[Category: Duarte, F]]