7vtg - Revision history

OCA at 17:32, 29 November 2023

OCA — Wed, 29 Nov 2023 17:32:28 GMT

←Older revision		Revision as of 17:32, 29 November 2023
Line 1:		Line 1:

	==Pseudouridine bound structure of Pseudouridine kinase (PUKI) S30A mutant from Escherichia coli strain B==		==Pseudouridine bound structure of Pseudouridine kinase (PUKI) S30A mutant from Escherichia coli strain B==
-	<StructureSection load='7vtg' size='340' side='right'caption='[[7vtg]]' scene=''>	+	<StructureSection load='7vtg' size='340' side='right'caption='[[7vtg]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7VTG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7VTG FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7vtg]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7VTG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7VTG FirstGlance]. <br>
-	</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=7vtg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7vtg OCA], [https://pdbe.org/7vtg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7vtg RCSB], [https://www.ebi.ac.uk/pdbsum/7vtg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7vtg ProSAT]</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]] 1.8985913Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FJF:5-[(2~{S},3~{R},4~{S},5~{R})-5-(hydroxymethyl)-3,4-bis(oxidanyl)oxolan-2-yl]-1~{H}-pyrimidine-2,4-dione'>FJF</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=7vtg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7vtg OCA], [https://pdbe.org/7vtg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7vtg RCSB], [https://www.ebi.ac.uk/pdbsum/7vtg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7vtg ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/PSUK_ECOLI PSUK_ECOLI] Catalyzes the phosphorylation of pseudouridine to pseudouridine 5'-phosphate (PsiMP).<ref>PMID:18591240</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Pseudouridine, one major RNA modification, is catabolized into uracil and ribose-5'-phosphate by two sequential enzymatic reactions. In the first step, pseudouridine kinase (PUKI) phosphorylates pseudouridine to pseudouridine 5'-monophosphate. High-fidelity catalysis of pseudouridine by PUKI prevents possible disturbance of in vivo pyrimidine homeostasis. However, the molecular basis of how PUKI selectively phosphorylates pseudouridine over uridine with >100-fold greater efficiency despite minor differences in their Km values has not been elucidated. To investigate this selectivity, in this study we determined the structures of PUKI from Escherichia coli strain B (EcPUKI) in various ligation states. The structure of EcPUKI was determined to be similar to PUKI from Arabidopsis thaliana, including an alpha/beta core domain and beta-stranded small domain, with dimerization occurring via the beta-stranded small domain. In a binary complex, we show that Ser30 in the substrate-binding loop of the small domain mediates interactions with the hallmark N1 atom of pseudouridine nucleobase, causing conformational changes in its quaternary structure. Kinetic and fluorescence spectroscopic analyses also showed that the Ser30-mediated interaction is a prerequisite for conformational changes and subsequent catalysis by EcPUKI. Furthermore, S30A mutation or EcPUKI complexed with other nucleosides homologous to pseudouridine but lacking the pseudouridine-specific N1 atom did not induce such conformational changes, demonstrating the catalytic significance of the proposed Ser30-mediated interaction. These analyses provide structural and functional evidence for a pseudouridine-dependent conformational change of EcPUKI and its functional linkage to catalysis.
		+
		+	Substrate-binding loop interactions with pseudouridine trigger conformational changes that promote catalytic efficiency of pseudouridine kinase PUKI.,Kim SH, Kim M, Park D, Byun S, Rhee S J Biol Chem. 2022 Mar 25:101869. doi: 10.1016/j.jbc.2022.101869. PMID:35346685<ref>PMID:35346685</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7vtg" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Escherichia coli]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Kim SH]]		[[Category: Kim SH]]
	[[Category: Rhee S]]		[[Category: Rhee S]]

OCA at 14:54, 31 August 2022

OCA — Wed, 31 Aug 2022 14:54:51 GMT

←Older revision		Revision as of 14:54, 31 August 2022
Line 1:		Line 1:

	==Pseudouridine bound structure of Pseudouridine kinase (PUKI) S30A mutant from Escherichia coli strain B==		==Pseudouridine bound structure of Pseudouridine kinase (PUKI) S30A mutant from Escherichia coli strain B==
-	<StructureSection load='7vtg' size='340' side='right'caption='[[7vtg]]~~, [[Resolution\|resolution]] 1.90Å~~' scene=''>	+	<StructureSection load='7vtg' size='340' side='right'caption='[[7vtg]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>~~[[7vtg]] is a 4 chain structure.~~ Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7VTG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7VTG FirstGlance]. <br>	+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7VTG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7VTG FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FJF:5-[(2~{S},3~{R},4~{S},5~{R})-5-(hydroxymethyl)-3,4-bis(oxidanyl)oxolan-2-yl]-1~{H}-pyrimidine-2,4-dione'>FJF</scene></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=7vtg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7vtg OCA], [https://pdbe.org/7vtg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7vtg RCSB], [https://www.ebi.ac.uk/pdbsum/7vtg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7vtg ProSAT]</span></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Pseudouridine_kinase Pseudouridine kinase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.83 2.7.1.83] </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=7vtg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7vtg OCA], [https://pdbe.org/7vtg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7vtg RCSB], [https://www.ebi.ac.uk/pdbsum/7vtg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7vtg ProSAT]</span></td></tr>	+
	</table>		</table>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Pseudouridine, one major RNA modification, is catabolized into uracil and ribose-5'-phosphate by two sequential enzymatic reactions. In the first step, pseudouridine kinase (PUKI) phosphorylates pseudouridine to pseudouridine 5'-monophosphate. High-fidelity catalysis of pseudouridine by PUKI prevents possible disturbance of in vivo pyrimidine homeostasis. However, the molecular basis of how PUKI selectively phosphorylates pseudouridine over uridine with >100-fold greater efficiency despite minor differences in their Km values has not been elucidated. To investigate this selectivity, in this study we determined the structures of PUKI from Escherichia coli strain B (EcPUKI) in various ligation states. The structure of EcPUKI was determined to be similar to PUKI from Arabidopsis thaliana, including an alpha/beta core domain and beta-stranded small domain, with dimerization occurring via the beta-stranded small domain. In a binary complex, we show that Ser30 in the substrate-binding loop of the small domain mediates interactions with the hallmark N1 atom of pseudouridine nucleobase, causing conformational changes in its quaternary structure. Kinetic and fluorescence spectroscopic analyses also showed that the Ser30-mediated interaction is a prerequisite for conformational changes and subsequent catalysis by EcPUKI. Furthermore, S30A mutation or EcPUKI complexed with other nucleosides homologous to pseudouridine but lacking the pseudouridine-specific N1 atom did not induce such conformational changes, demonstrating the catalytic significance of the proposed Ser30-mediated interaction. These analyses provide structural and functional evidence for a pseudouridine-dependent conformational change of EcPUKI and its functional linkage to catalysis.
-
-	Substrate-binding loop interactions with pseudouridine trigger conformational changes that promote catalytic efficiency of pseudouridine kinase PUKI.,Kim SH, Kim M, Park D, Byun S, Rhee S J Biol Chem. 2022 Mar 25:101869. doi: 10.1016/j.jbc.2022.101869. PMID:35346685<ref>PMID:35346685</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 7vtg" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Pseudouridine kinase]]~~	+	[[Category: Kim SH]]
-	[[Category: Kim~~, S H~~]]	+	[[Category: Rhee S]]
-	[[Category: Rhee, S]]	+
-	~~[[Category: Pfkb family]]~~	+
-	~~[[Category: Pseudourdine]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 10:25, 13 April 2022

OCA — Wed, 13 Apr 2022 10:25:08 GMT

←Older revision		Revision as of 10:25, 13 April 2022
Line 1:		Line 1:

	==Pseudouridine bound structure of Pseudouridine kinase (PUKI) S30A mutant from Escherichia coli strain B==		==Pseudouridine bound structure of Pseudouridine kinase (PUKI) S30A mutant from Escherichia coli strain B==
-	<StructureSection load='7vtg' size='340' side='right'caption='[[7vtg]]' scene=''>	+	<StructureSection load='7vtg' size='340' side='right'caption='[[7vtg]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7VTG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7VTG FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7vtg]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7VTG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7VTG FirstGlance]. <br>
-	</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=7vtg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7vtg OCA], [https://pdbe.org/7vtg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7vtg RCSB], [https://www.ebi.ac.uk/pdbsum/7vtg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7vtg 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=FJF:5-[(2~{S},3~{R},4~{S},5~{R})-5-(hydroxymethyl)-3,4-bis(oxidanyl)oxolan-2-yl]-1~{H}-pyrimidine-2,4-dione'>FJF</scene></td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Pseudouridine_kinase Pseudouridine kinase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.83 2.7.1.83] </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=7vtg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7vtg OCA], [https://pdbe.org/7vtg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7vtg RCSB], [https://www.ebi.ac.uk/pdbsum/7vtg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7vtg ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Pseudouridine, one major RNA modification, is catabolized into uracil and ribose-5'-phosphate by two sequential enzymatic reactions. In the first step, pseudouridine kinase (PUKI) phosphorylates pseudouridine to pseudouridine 5'-monophosphate. High-fidelity catalysis of pseudouridine by PUKI prevents possible disturbance of in vivo pyrimidine homeostasis. However, the molecular basis of how PUKI selectively phosphorylates pseudouridine over uridine with >100-fold greater efficiency despite minor differences in their Km values has not been elucidated. To investigate this selectivity, in this study we determined the structures of PUKI from Escherichia coli strain B (EcPUKI) in various ligation states. The structure of EcPUKI was determined to be similar to PUKI from Arabidopsis thaliana, including an alpha/beta core domain and beta-stranded small domain, with dimerization occurring via the beta-stranded small domain. In a binary complex, we show that Ser30 in the substrate-binding loop of the small domain mediates interactions with the hallmark N1 atom of pseudouridine nucleobase, causing conformational changes in its quaternary structure. Kinetic and fluorescence spectroscopic analyses also showed that the Ser30-mediated interaction is a prerequisite for conformational changes and subsequent catalysis by EcPUKI. Furthermore, S30A mutation or EcPUKI complexed with other nucleosides homologous to pseudouridine but lacking the pseudouridine-specific N1 atom did not induce such conformational changes, demonstrating the catalytic significance of the proposed Ser30-mediated interaction. These analyses provide structural and functional evidence for a pseudouridine-dependent conformational change of EcPUKI and its functional linkage to catalysis.
		+
		+	Substrate-binding loop interactions with pseudouridine trigger conformational changes that promote catalytic efficiency of pseudouridine kinase PUKI.,Kim SH, Kim M, Park D, Byun S, Rhee S J Biol Chem. 2022 Mar 25:101869. doi: 10.1016/j.jbc.2022.101869. PMID:35346685<ref>PMID:35346685</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7vtg" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Kim SH]]	+	[[Category: Pseudouridine kinase]]
-	[[Category: Rhee S]]	+	[[Category: Kim, S H]]
		+	[[Category: Rhee, S]]
		+	[[Category: Pfkb family]]
		+	[[Category: Pseudourdine]]
		+	[[Category: Transferase]]

OCA at 10:27, 6 April 2022

OCA — Wed, 06 Apr 2022 10:27:39 GMT

←Older revision		Revision as of 10:27, 6 April 2022
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry 7vtg is ON HOLD until Paper Publication~~	+	==Pseudouridine bound structure of Pseudouridine kinase (PUKI) S30A mutant from Escherichia coli strain B==
-		+	<StructureSection load='7vtg' size='340' side='right'caption='[[7vtg]]' scene=''>
-	~~Authors: Kim, S.H., Rhee, S.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7VTG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7VTG FirstGlance]. <br>
-	~~Description:~~ Pseudouridine bound structure of Pseudouridine kinase (PUKI) S30A mutant from Escherichia coli strain B	+	</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=7vtg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7vtg OCA], [https://pdbe.org/7vtg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7vtg RCSB], [https://www.ebi.ac.uk/pdbsum/7vtg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7vtg ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
-	[[Category: Kim~~, S.H~~]]	+	__TOC__
-	[[Category: Rhee, S]]	+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Kim SH]]
		+	[[Category: Rhee S]]

OCA at 12:29, 29 December 2021

OCA — Wed, 29 Dec 2021 12:29:12 GMT

←Older revision		Revision as of 12:29, 29 December 2021
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7vtg is ON HOLD	+	The entry 7vtg is ON HOLD until Paper Publication

	Authors: Kim, S.H., Rhee, S.		Authors: Kim, S.H., Rhee, S.

OCA: Protected "7vtg" [edit=sysop:move=sysop]

OCA — Wed, 03 Nov 2021 13:04:34 GMT

Protected "7vtg" [edit=sysop:move=sysop]

←Older revision

Revision as of 13:04, 3 November 2021

OCA: New page: '''Unreleased structure''' The entry 7vtg is ON HOLD Authors: Kim, S.H., Rhee, S. Description: Pseudouridine bound structure of Pseudouridine kinase (PUKI) S30A mutant from Escherichia...

OCA — Wed, 03 Nov 2021 13:04:33 GMT

New page: '''Unreleased structure''' The entry 7vtg is ON HOLD Authors: Kim, S.H., Rhee, S. Description: Pseudouridine bound structure of Pseudouridine kinase (PUKI) S30A mutant from Escherichia...

New page

'''Unreleased structure'''

The entry 7vtg is ON HOLD

Authors: Kim, S.H., Rhee, S.

Description: Pseudouridine bound structure of Pseudouridine kinase (PUKI) S30A mutant from Escherichia coli strain B
[[Category: Unreleased Structures]]
[[Category: Kim, S.H]]
[[Category: Rhee, S]]