5xv9 - Revision history

OCA at 10:32, 14 June 2023

2023-06-14T10:32:14Z

←Older revision		Revision as of 10:32, 14 June 2023
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	==Solution Structure of Cold Shock Protein from Colwellia psychrerythraea==		==Solution Structure of Cold Shock Protein from Colwellia psychrerythraea==
-	<StructureSection load='5xv9' size='340' side='right'caption='[[5xv9~~]], [[NMR_Ensembles_of_Models \| 20 NMR models~~]]' scene=''>	+	<StructureSection load='5xv9' size='340' side='right'caption='[[5xv9]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5xv9]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Colp3 Colp3~~]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XV9 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5XV9 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5xv9]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Colwellia_psychrerythraea_34H Colwellia psychrerythraea 34H]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XV9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5XV9 FirstGlance]. <br>
-	</td></tr>~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CPS_0718 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=167879 COLP3])</td></tr>~~	+	</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=5xv9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xv9 OCA], [https://pdbe.org/5xv9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5xv9 RCSB], [https://www.ebi.ac.uk/pdbsum/5xv9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5xv9 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=5xv9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xv9 OCA], [~~http~~://pdbe.org/5xv9 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5xv9 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5xv9 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5xv9 ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q488P6_COLP3 Q488P6_COLP3]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 20:		Line 21:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Colp3~~]]	+	[[Category: Colwellia psychrerythraea 34H]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Kim, Y]]	+	[[Category: Kim Y]]
-	[[Category: Lee, Y]]	+	[[Category: Lee Y]]
-	~~[[Category: Cold-shock protein]]~~	+
-	~~[[Category: Nmr spectroscopy]]~~	+
-	~~[[Category: Psychrophile]]~~	+
-	~~[[Category: Rna binding protein]]~~	+
-	~~[[Category: Solution structure~~]]	+

OCA at 06:42, 31 July 2019

2019-07-31T06:42:10Z

←Older revision		Revision as of 06:42, 31 July 2019
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	==Solution Structure of Cold Shock Protein from Colwellia psychrerythraea==		==Solution Structure of Cold Shock Protein from Colwellia psychrerythraea==
-	<StructureSection load='5xv9' size='340' side='right' caption='[[5xv9]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>	+	<StructureSection load='5xv9' size='340' side='right'caption='[[5xv9]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5xv9]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XV9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5XV9 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5xv9]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Colp3 Colp3]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XV9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5XV9 FirstGlance]. <br>
-	</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=5xv9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xv9 OCA], [http://pdbe.org/5xv9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xv9 RCSB], [http://www.ebi.ac.uk/pdbsum/5xv9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xv9 ProSAT]</span></td></tr>	+	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CPS_0718 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=167879 COLP3])</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=5xv9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xv9 OCA], [http://pdbe.org/5xv9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xv9 RCSB], [http://www.ebi.ac.uk/pdbsum/5xv9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xv9 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
-	~~The thermophilic bacterium Thermus aquaticus is a well~~-~~known source of Taq polymerase~~. Here, we ~~studied~~ the structure and dynamics of the ~~T. aquaticus cold-shock protein~~ (Ta-Csp) ~~to better understand its thermostability using NMR spectroscopy~~. ~~We found that Ta~~-Csp ~~has~~ a five~~-stranded~~ beta-barrel ~~structure~~ with ~~five salt bridges which are important for more rigid structure and a higher melting temperature~~ (76 degrees C) of Ta-Csp ~~compared~~ to ~~mesophilic and psychrophilic Csps~~. ~~Microsecond to millisecond time scale exchange processes occur~~ only at the ~~beta1~~-~~beta2~~ surface ~~region~~ of the ~~nucleic acid binding site with an average conformational exchange rate constant~~ of ~~674s~~-1. ~~The results imply that thermophilic Ta~~-Csp has a ~~more rigid structure~~ and ~~may not need high structural~~ flexibility ~~to accommodate~~ nucleic acids ~~upon cold shock compared to its mesophile~~ and ~~psychrophile counterparts~~.	+	Cold-shock proteins (Csps) are expressed at lower-than-optimum temperatures, and they function as RNA chaperones; however, no structural studies on psychrophilic Csps have been reported. Here, we aimed to investigate the structure and dynamics of the Csp of psychrophile Colwellia psychrerythraea 34H, ( Cp-Csp). Although Cp-Csp shares sequence homology, common folding patterns, and motifs, including a five beta-stranded barrel, with its thermophilic counterparts, its thermostability (37 degrees C) was markedly lower than those of other Csps. Cp-Csp binds heptathymidine with an affinity of 10(-7) M, thereby increasing its thermostability to 50 degrees C. Nuclear magnetic resonance spectroscopic analysis of the Cp-Csp structure and backbone dynamics revealed a flexible structure with only one salt bridge and 10 residues in the hydrophobic cavity. Notably, Cp-Csp contains Tyr51 instead of the conserved Phe in the hydrophobic core, and its phenolic hydroxyl group projects toward the surface. The Y51F mutation increased the stability of hydrophobic packing and may have allowed for the formation of a K3-E21 salt bridge, thereby increasing its thermostability to 43 degrees C. Cp-Csp exhibited conformational exchanges in its ribonucleoprotein motifs 1 and 2 (754 and 642 s(-1)), and heptathymidine binding markedly decreased these motions. Cp-Csp lacks salt bridges and has longer flexible loops and a less compact hydrophobic cavity resulting from Tyr51 compared to mesophilic and thermophilic Csps. These might explain the low thermostability of Cp-Csp. The conformational flexibility of Cp-Csp facilitates its accommodation of nucleic acids at low temperatures in polar oceans and its function as an RNA chaperone for cold adaptation.

-	~~Structure and flexibility~~ of the ~~thermophilic cold-shock protein~~ of ~~Thermus aquaticus~~.,~~Jin B~~, Jeong KW, Kim Y ~~Biochem Biophys Res Commun~~. ~~2014 Aug 4. pii: S0006-291X~~(14)~~01377~~-1. doi:, 10.~~1016~~/j.~~bbrc~~.~~2014~~.~~07.127~~. PMID:~~25101648~~<ref>PMID:~~25101648~~</ref>	+	Tyr51: Key Determinant of the Low Thermostability of the Colwellia psychrerythraea Cold-Shock Protein.,Lee Y, Kwak C, Jeong KW, Durai P, Ryu KS, Kim EH, Cheong C, Ahn HC, Kim HJ, Kim Y Biochemistry. 2018 Jul 3;57(26):3625-3640. doi: 10.1021/acs.biochem.8b00144. Epub, 2018 May 18. PMID:29737840<ref>PMID:29737840</ref>

	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Colp3]]
		+	[[Category: Large Structures]]
	[[Category: Kim, Y]]		[[Category: Kim, Y]]
	[[Category: Lee, Y]]		[[Category: Lee, Y]]

OCA at 07:07, 4 July 2018

2018-07-04T07:07:36Z

←Older revision		Revision as of 07:07, 4 July 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5xv9 is ~~ON HOLD until Paper~~ Publication	+	==Solution Structure of Cold Shock Protein from Colwellia psychrerythraea==
		+	<StructureSection load='5xv9' size='340' side='right' caption='[[5xv9]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5xv9]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XV9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5XV9 FirstGlance]. <br>
		+	</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=5xv9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xv9 OCA], [http://pdbe.org/5xv9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xv9 RCSB], [http://www.ebi.ac.uk/pdbsum/5xv9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xv9 ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The thermophilic bacterium Thermus aquaticus is a well-known source of Taq polymerase. Here, we studied the structure and dynamics of the T. aquaticus cold-shock protein (Ta-Csp) to better understand its thermostability using NMR spectroscopy. We found that Ta-Csp has a five-stranded beta-barrel structure with five salt bridges which are important for more rigid structure and a higher melting temperature (76 degrees C) of Ta-Csp compared to mesophilic and psychrophilic Csps. Microsecond to millisecond time scale exchange processes occur only at the beta1-beta2 surface region of the nucleic acid binding site with an average conformational exchange rate constant of 674s-1. The results imply that thermophilic Ta-Csp has a more rigid structure and may not need high structural flexibility to accommodate nucleic acids upon cold shock compared to its mesophile and psychrophile counterparts.

-	~~Authors: Lee, Y~~., ~~Kim~~, Y.	+	Structure and flexibility of the thermophilic cold-shock protein of Thermus aquaticus.,Jin B, Jeong KW, Kim Y Biochem Biophys Res Commun. 2014 Aug 4. pii: S0006-291X(14)01377-1. doi:, 10.1016/j.bbrc.2014.07.127. PMID:25101648<ref>PMID:25101648</ref>

-	~~Description: Solution Structure~~ of ~~Cold Shock Protein from Colwellia psychrerythraea~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category: Unreleased Structures]]~~	+	</div>
-	~~[[Category~~: ~~Lee, Y]]~~	+	<div class="pdbe-citations 5xv9" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Kim, Y]]		[[Category: Kim, Y]]
		+	[[Category: Lee, Y]]
		+	[[Category: Cold-shock protein]]
		+	[[Category: Nmr spectroscopy]]
		+	[[Category: Psychrophile]]
		+	[[Category: Rna binding protein]]
		+	[[Category: Solution structure]]

OCA at 04:00, 18 April 2018

2018-04-18T04:00:33Z

←Older revision		Revision as of 04:00, 18 April 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5xv9 is ON HOLD	+	The entry 5xv9 is ON HOLD until Paper Publication

	Authors: Lee, Y., Kim, Y.		Authors: Lee, Y., Kim, Y.

OCA at 12:14, 11 April 2018

2018-04-11T12:14:05Z

←Older revision		Revision as of 12:14, 11 April 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5xv9 is ON HOLD ~~until Paper Publication~~	+	The entry 5xv9 is ON HOLD

	Authors: Lee, Y., Kim, Y.		Authors: Lee, Y., Kim, Y.

OCA: Protected "5xv9" [edit=sysop:move=sysop]

2017-09-27T15:49:06Z

Protected "5xv9" [edit=sysop:move=sysop]

←Older revision

Revision as of 15:49, 27 September 2017

OCA: New page: '''Unreleased structure''' The entry 5xv9 is ON HOLD until Paper Publication Authors: Lee, Y., Kim, Y. Description: Solution Structure of Cold Shock Protein from Colwellia psychrerythr...

2017-09-27T15:49:05Z

New page: '''Unreleased structure''' The entry 5xv9 is ON HOLD until Paper Publication Authors: Lee, Y., Kim, Y. Description: Solution Structure of Cold Shock Protein from Colwellia psychrerythr...

New page

'''Unreleased structure'''

The entry 5xv9 is ON HOLD until Paper Publication

Authors: Lee, Y., Kim, Y.

Description: Solution Structure of Cold Shock Protein from Colwellia psychrerythraea
[[Category: Unreleased Structures]]
[[Category: Lee, Y]]
[[Category: Kim, Y]]