5yzv - Revision history

OCA at 10:25, 27 March 2024

OCA — Wed, 27 Mar 2024 10:25:58 GMT

←Older revision		Revision as of 10:25, 27 March 2024
Line 3:		Line 3:
	<StructureSection load='5yzv' size='340' side='right'caption='[[5yzv]], [[Resolution\|resolution]] 2.60Å' scene=''>		<StructureSection load='5yzv' size='340' side='right'caption='[[5yzv]], [[Resolution\|resolution]] 2.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5yzv]] is a 5 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YZV OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5YZV FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5yzv]] is a 5 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermomonospora_curvata Thermomonospora curvata]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YZV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5YZV FirstGlance]. <br>
-	</td></tr><tr id='~~activity~~'><td class="sblockLbl"><b>~~Activity~~:</b></td><td class="sblockDat"~~><span class~~=~~'plainlinks'~~>~~[http://en.wikipedia.org/wiki/Non~~-~~specific_serine/threonine_protein_kinase Non-specific serine/threonine protein kinase]~~, ~~with EC number~~ [~~http://www.brenda-enzymes.info/php/result_flat.php4?ecno=~~2.~~7.11.1 2.7.11.1] </span>~~</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]] 2.6Å</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=5yzv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yzv OCA], [~~http~~://pdbe.org/5yzv PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5yzv RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5yzv PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5yzv 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=5yzv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yzv OCA], [https://pdbe.org/5yzv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5yzv RCSB], [https://www.ebi.ac.uk/pdbsum/5yzv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5yzv ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/PKWA_THECU PKWA_THECU]] May play a regulatory role during the complex growth cycle and in secondary metabolite production.	+	[https://www.uniprot.org/uniprot/PKWA_THECU PKWA_THECU] May play a regulatory role during the complex growth cycle and in secondary metabolite production.
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	WD40 proteins belong to a big protein family with members identified in every eukaryotic proteome. However, WD40 proteins were only reported in a few prokaryotic proteomes. Using WDSP ( http://wu.scbb.pkusz.edu.cn/wdsp/ ), a prediction tool, we identified thousands of prokaryotic WD40 proteins, among which few proteins have been biochemically characterized. As shown in our previous bioinformatics study, a large proportion of prokaryotic WD40 proteins have higher intramolecular sequence identity among repeats and more hydrogen networks, which may indicate better stability than eukaryotic WD40s. Here we report our biophysical and structural study on the WD40 domain of PkwA from Thermomonospora curvata (referred as tPkwA-C). We demonstrated that the stability of thermophilic tPkwA-C correlated to ionic strength and tPkwA-C exhibited fully reversible unfolding under different denaturing conditions. Therefore, the folding kinetics was also studied through stopped-flow circular dichroism spectra. The crystal structure of tPkwA-C was further resolved and shed light on the key factors that stabilize its beta-propeller structure. Like other WD40 proteins, DHSW tetrad has a significant impact on the stability of tPkwA-C. Considering its unique features, we proposed that tPkwA-C should be a great structural template for protein engineering to study key residues involved in protein-protein interaction of a WD40 protein.	+
-		+
-	Biophysical and structural characterization of the thermostable WD40 domain of a prokaryotic protein, Thermomonospora curvata PkwA.,Shen C, Du Y, Qiao F, Kong T, Yuan L, Zhang D, Wu X, Li D, Wu YD Sci Rep. 2018 Aug 28;8(1):12965. doi: 10.1038/s41598-018-31140-y. PMID:30154510<ref>PMID:30154510</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 5yzv" style="background-color:#fffaf0;"></div>~~	+
-	~~== References ==~~	+
-	~~<references/>~~	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Non-specific serine/threonine protein kinase~~]]	+	[[Category: Thermomonospora curvata]]
-	[[Category: Du, Y]]	+	[[Category: Du Y]]
-	[[Category: Kong, T]]	+	[[Category: Kong T]]
-	[[Category: Li~~, D Y~~]]	+	[[Category: Li DY]]
-	[[Category: Qiao~~, F F~~]]	+	[[Category: Qiao FF]]
-	[[Category: Shen, C]]	+	[[Category: Shen C]]
-	[[Category: Wu~~, X H~~]]	+	[[Category: Wu XH]]
-	[[Category: Wu~~, Y D~~]]	+	[[Category: Wu YD]]
-	[[Category: Yuan~~, L R~~]]	+	[[Category: Yuan LR]]
-	[[Category: Zhang~~, D L]]~~	+	[[Category: Zhang DL]]
-	~~[[Category: Prokaryotic]]~~	+
-	~~[[Category: Protein binding]]~~	+
-	~~[[Category: Reversible folding]]~~	+
-	~~[[Category: Thermostable~~]]	+

OCA at 09:32, 21 October 2020

OCA — Wed, 21 Oct 2020 09:32:15 GMT

←Older revision		Revision as of 09:32, 21 October 2020
Line 1:		Line 1:

	==Biophysical and structural characterization of the thermostable WD40 domain of a prokaryotic protein, Thermomonospora curvata PkwA==		==Biophysical and structural characterization of the thermostable WD40 domain of a prokaryotic protein, Thermomonospora curvata PkwA==
-	<StructureSection load='5yzv' size='340' side='right' caption='[[5yzv]], [[Resolution\|resolution]] 2.60Å' scene=''>	+	<StructureSection load='5yzv' size='340' side='right'caption='[[5yzv]], [[Resolution\|resolution]] 2.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5yzv]] is a 5 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YZV OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5YZV FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5yzv]] is a 5 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YZV OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5YZV FirstGlance]. <br>
	</td></tr><tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Non-specific_serine/threonine_protein_kinase Non-specific serine/threonine protein kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.11.1 2.7.11.1] </span></td></tr>		</td></tr><tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Non-specific_serine/threonine_protein_kinase Non-specific serine/threonine protein kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.11.1 2.7.11.1] </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=5yzv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yzv OCA], [http://pdbe.org/5yzv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yzv RCSB], [http://www.ebi.ac.uk/pdbsum/5yzv PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yzv 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=5yzv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yzv OCA], [http://pdbe.org/5yzv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yzv RCSB], [http://www.ebi.ac.uk/pdbsum/5yzv PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yzv ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 22:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Non-specific serine/threonine protein kinase]]		[[Category: Non-specific serine/threonine protein kinase]]
	[[Category: Du, Y]]		[[Category: Du, Y]]

OCA at 07:38, 3 October 2018

OCA — Wed, 03 Oct 2018 07:38:31 GMT

←Older revision		Revision as of 07:38, 3 October 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5yzv is ~~ON HOLD until Paper~~ Publication	+	==Biophysical and structural characterization of the thermostable WD40 domain of a prokaryotic protein, Thermomonospora curvata PkwA==
		+	<StructureSection load='5yzv' size='340' side='right' caption='[[5yzv]], [[Resolution\|resolution]] 2.60Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5yzv]] is a 5 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YZV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YZV FirstGlance]. <br>
		+	</td></tr><tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Non-specific_serine/threonine_protein_kinase Non-specific serine/threonine protein kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.11.1 2.7.11.1] </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=5yzv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yzv OCA], [http://pdbe.org/5yzv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yzv RCSB], [http://www.ebi.ac.uk/pdbsum/5yzv PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yzv ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/PKWA_THECU PKWA_THECU]] May play a regulatory role during the complex growth cycle and in secondary metabolite production.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	WD40 proteins belong to a big protein family with members identified in every eukaryotic proteome. However, WD40 proteins were only reported in a few prokaryotic proteomes. Using WDSP ( http://wu.scbb.pkusz.edu.cn/wdsp/ ), a prediction tool, we identified thousands of prokaryotic WD40 proteins, among which few proteins have been biochemically characterized. As shown in our previous bioinformatics study, a large proportion of prokaryotic WD40 proteins have higher intramolecular sequence identity among repeats and more hydrogen networks, which may indicate better stability than eukaryotic WD40s. Here we report our biophysical and structural study on the WD40 domain of PkwA from Thermomonospora curvata (referred as tPkwA-C). We demonstrated that the stability of thermophilic tPkwA-C correlated to ionic strength and tPkwA-C exhibited fully reversible unfolding under different denaturing conditions. Therefore, the folding kinetics was also studied through stopped-flow circular dichroism spectra. The crystal structure of tPkwA-C was further resolved and shed light on the key factors that stabilize its beta-propeller structure. Like other WD40 proteins, DHSW tetrad has a significant impact on the stability of tPkwA-C. Considering its unique features, we proposed that tPkwA-C should be a great structural template for protein engineering to study key residues involved in protein-protein interaction of a WD40 protein.

-	~~Authors: Li~~, ~~D.Y~~., Shen, C., Du, Y., Qiao, F~~.F.~~, Kong, T., Yuan, L~~.R.~~, Zhang, D~~.L.~~, Wu, X~~.H.~~, Wu~~, Y~~.D.	+	Biophysical and structural characterization of the thermostable WD40 domain of a prokaryotic protein, Thermomonospora curvata PkwA.,Shen C, Du Y, Qiao F, Kong T, Yuan L, Zhang D, Wu X, Li D, Wu YD Sci Rep. 2018 Aug 28;8(1):12965. doi: 10.1038/s41598-018-31140-y. PMID:30154510<ref>PMID:30154510</ref>

-	~~Description: Biophysical and structural characterization~~ of the ~~thermostable WD40 domain~~ of ~~a prokaryotic protein, Thermomonospora curvata PkwA~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category: Unreleased Structures]]~~	+	</div>
-	~~[[Category~~: ~~Li, D.Y]]~~	+	<div class="pdbe-citations 5yzv" style="background-color:#fffaf0;"></div>
-	~~[[Category: Qiao, F.F]]~~	+	== References ==
-	~~[[Category: Zhang, D.L]]~~	+	<references/>
-	~~[[Category: Wu, Y.D]]~~	+	__TOC__
-	[[Category: ~~Kong, T~~]]	+	</StructureSection>
		+	[[Category: Non-specific serine/threonine protein kinase]]
	[[Category: Du, Y]]		[[Category: Du, Y]]
-	[[Category: Wu, ~~X.H~~]]	+	[[Category: Kong, T]]
		+	[[Category: Li, D Y]]
		+	[[Category: Qiao, F F]]
	[[Category: Shen, C]]		[[Category: Shen, C]]
-	[[Category: Yuan, L.R]]	+	[[Category: Wu, X H]]
		+	[[Category: Wu, Y D]]
		+	[[Category: Yuan, L R]]
		+	[[Category: Zhang, D L]]
		+	[[Category: Prokaryotic]]
		+	[[Category: Protein binding]]
		+	[[Category: Reversible folding]]
		+	[[Category: Thermostable]]

OCA at 06:03, 26 September 2018

OCA — Wed, 26 Sep 2018 06:03:18 GMT

←Older revision		Revision as of 06:03, 26 September 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5yzv is ON HOLD	+	The entry 5yzv is ON HOLD until Paper Publication

	Authors: Li, D.Y., Shen, C., Du, Y., Qiao, F.F., Kong, T., Yuan, L.R., Zhang, D.L., Wu, X.H., Wu, Y.D.		Authors: Li, D.Y., Shen, C., Du, Y., Qiao, F.F., Kong, T., Yuan, L.R., Zhang, D.L., Wu, X.H., Wu, Y.D.
Line 8:		Line 8:
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Li, D.Y]]		[[Category: Li, D.Y]]
-	[[Category: Zhang, D.L]]
	[[Category: Qiao, F.F]]		[[Category: Qiao, F.F]]
		+	[[Category: Zhang, D.L]]
	[[Category: Wu, Y.D]]		[[Category: Wu, Y.D]]
	[[Category: Kong, T]]		[[Category: Kong, T]]
-	[[Category: Wu, X.H]]
	[[Category: Du, Y]]		[[Category: Du, Y]]
-	[[Category: ~~Yuan~~, L.R]]	+	[[Category: Wu, X.H]]
	[[Category: Shen, C]]		[[Category: Shen, C]]
		+	[[Category: Yuan, L.R]]

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

OCA — Wed, 27 Dec 2017 07:12:12 GMT

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

←Older revision

Revision as of 07:12, 27 December 2017

OCA: New page: '''Unreleased structure''' The entry 5yzv is ON HOLD Authors: Li, D.Y., Shen, C., Du, Y., Qiao, F.F., Kong, T., Yuan, L.R., Zhang, D.L., Wu, X.H., Wu, Y.D. Description: Biophysical and...

OCA — Wed, 27 Dec 2017 07:12:11 GMT

New page: '''Unreleased structure''' The entry 5yzv is ON HOLD Authors: Li, D.Y., Shen, C., Du, Y., Qiao, F.F., Kong, T., Yuan, L.R., Zhang, D.L., Wu, X.H., Wu, Y.D. Description: Biophysical and...

New page

'''Unreleased structure'''

The entry 5yzv is ON HOLD

Authors: Li, D.Y., Shen, C., Du, Y., Qiao, F.F., Kong, T., Yuan, L.R., Zhang, D.L., Wu, X.H., Wu, Y.D.

Description: Biophysical and structural characterization of the thermostable WD40 domain of a prokaryotic protein, Thermomonospora curvata PkwA
[[Category: Unreleased Structures]]
[[Category: Li, D.Y]]
[[Category: Zhang, D.L]]
[[Category: Qiao, F.F]]
[[Category: Wu, Y.D]]
[[Category: Kong, T]]
[[Category: Wu, X.H]]
[[Category: Du, Y]]
[[Category: Yuan, L.R]]
[[Category: Shen, C]]