OCA at 05:19, 15 May 2024

OCA — Wed, 15 May 2024 05:19:22 GMT

←Older revision		Revision as of 05:19, 15 May 2024
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 8k06 is ~~ON HOLD until Paper~~ Publication	+	==Pseudouridine 5'-monophosphate glycosylase from Arabidopsis thaliana -- PSU, R5P bound K185A mutant==
		+	<StructureSection load='8k06' size='340' side='right'caption='[[8k06]], [[Resolution\|resolution]] 1.84Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[8k06]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8K06 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8K06 FirstGlance]. <br>
		+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 1.845Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=PSU:PSEUDOURIDINE-5-MONOPHOSPHATE'>PSU</scene>, <scene name='pdbligand=RP5:5-O-PHOSPHONO-BETA-D-RIBOFURANOSE'>RP5</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=8k06 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8k06 OCA], [https://pdbe.org/8k06 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8k06 RCSB], [https://www.ebi.ac.uk/pdbsum/8k06 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8k06 ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/PUMY_ARATH PUMY_ARATH] Catalyzes the reversible cleavage of pseudouridine 5'-phosphate (PsiMP) to ribose 5-phosphate and uracil (PubMed:31907295). Functions biologically in the cleavage direction, as part of a pseudouridine degradation pathway (PubMed:31907295). Acts together with the pseudouridine kinase PUKI in the peroxisome to prevent toxic pseudouridine monophosphate accumulation (PubMed:31907295). Can catalyze the formation of pseudouridine 5'-phosphate (reverse reaction) in vitro, with a catalytic efficiency 4 times lower than the hydrolysis reaction (PubMed:31907295).<ref>PMID:31907295</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Pseudouridine is a noncanonical C-nucleoside containing a C-C glycosidic linkage between uracil and ribose. In the two-step degradation of pseudouridine, pseudouridine 5'-monophosphate glycosylase (PUMY) is responsible for the second step and catalyses the cleavage of the C-C glycosidic bond in pseudouridine 5'-monophosphate (PsiMP) into uridine and ribose 5'-phosphate, which are recycled via other metabolic pathways. Structural features of Escherichia coli PUMY have been reported, but the details of the substrate specificity of PsiMP were unknown. Here, we present three crystal structures of Arabidopsis thaliana PUMY in different ligation states and a kinetic analysis of PsiMP degradation. The results indicate that Thr149 and Asn308, which are conserved in the PUMY family, are structural determinants for recognizing the nucleobase of PsiMP. The distinct binding modes of PsiMP and ribose 5'-phosphate also suggest that the nucleobase, rather than the phosphate group, of PsiMP dictates the substrate-binding mode. An open-to-close transition of the active site is essential for catalysis, which is mediated by two alpha-helices, alpha11 and alpha12, near the active site. Mutational analysis validates the proposed roles of the active site residues in catalysis. Our structural and functional analyses provide further insight into the enzymatic features of PUMY towards PsiMP.

-	~~Authors: Lee~~, J~~.Y.~~, Kim, S.H.~~, Rhee, S~~.K.	+	Structure and function of the pseudouridine 5'-monophosphate glycosylase PUMY from Arabidopsis thaliana.,Lee J, Kim SH, Rhee S RNA Biol. 2024 Jan;21(1):1-10. doi: 10.1080/15476286.2023.2293340. Epub 2023 Dec , 20. PMID:38117089<ref>PMID:38117089</ref>

-	~~Description: Pseudouridine 5''~~-~~monophosphate glycosylase from~~ Arabidopsis thaliana ~~--PSU, R5P bound K185A mutant~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
-	[[Category: Kim~~, S.H~~]]	+	<div class="pdbe-citations 8k06" style="background-color:#fffaf0;"></div>
-	[[Category: Lee~~, J.Y~~]]	+	== References ==
-	[[Category: Rhee~~, S.K~~]]	+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Arabidopsis thaliana]]
		+	[[Category: Large Structures]]
		+	[[Category: Kim SH]]
		+	[[Category: Lee JY]]
		+	[[Category: Rhee SK]]

OCA at 08:55, 2 August 2023

OCA — Wed, 02 Aug 2023 08:55:25 GMT

←Older revision		Revision as of 08:55, 2 August 2023
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 8k06 is ON HOLD	+	The entry 8k06 is ON HOLD until Paper Publication

	Authors: Lee, J.Y., Kim, S.H., Rhee, S.K.		Authors: Lee, J.Y., Kim, S.H., Rhee, S.K.

-	Description: ~~Structure of pseudouridine~~ 5''-monophosphate glycosylase ~~PUMY~~ from Arabidopsis thaliana	+	Description: Pseudouridine 5''-monophosphate glycosylase from Arabidopsis thaliana --PSU, R5P bound K185A mutant
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Kim, S.H]]		[[Category: Kim, S.H]]
-	[[Category: Rhee, S.K]]
	[[Category: Lee, J.Y]]		[[Category: Lee, J.Y]]
		+	[[Category: Rhee, S.K]]

OCA: Protected "8k06" [edit=sysop:move=sysop]

OCA — Wed, 12 Jul 2023 04:09:56 GMT

Protected "8k06" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:09, 12 July 2023

OCA: New page: '''Unreleased structure''' The entry 8k06 is ON HOLD Authors: Lee, J.Y., Kim, S.H., Rhee, S.K. Description: Structure of pseudouridine 5''-monophosphate glycosylase PUMY from Arabidops...

OCA — Wed, 12 Jul 2023 04:09:54 GMT

New page: '''Unreleased structure''' The entry 8k06 is ON HOLD Authors: Lee, J.Y., Kim, S.H., Rhee, S.K. Description: Structure of pseudouridine 5''-monophosphate glycosylase PUMY from Arabidops...

New page

'''Unreleased structure'''

The entry 8k06 is ON HOLD

Authors: Lee, J.Y., Kim, S.H., Rhee, S.K.

Description: Structure of pseudouridine 5''-monophosphate glycosylase PUMY from Arabidopsis thaliana
[[Category: Unreleased Structures]]
[[Category: Kim, S.H]]
[[Category: Rhee, S.K]]
[[Category: Lee, J.Y]]

8k06 - Revision history

OCA at 05:19, 15 May 2024

OCA at 08:55, 2 August 2023

OCA: Protected "8k06" [edit=sysop:move=sysop]

OCA: New page: '''Unreleased structure''' The entry 8k06 is ON HOLD Authors: Lee, J.Y., Kim, S.H., Rhee, S.K. Description: Structure of pseudouridine 5''-monophosphate glycosylase PUMY from Arabidops...