OCA at 17:10, 18 October 2023

OCA — Wed, 18 Oct 2023 17:10:15 GMT

←Older revision		Revision as of 17:10, 18 October 2023
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-	'''Unreleased structure'''

-	~~The entry~~ 7u1x is ~~ON HOLD until Paper~~ Publication	+	==Structure of SPAC806.04c protein from fission yeast covalently bound to BeF3==
		+	<StructureSection load='7u1x' size='340' side='right'caption='[[7u1x]], [[Resolution\|resolution]] 2.12Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[7u1x]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Schizosaccharomyces_pombe Schizosaccharomyces pombe]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7U1X OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7U1X 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]] 2.12Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BFD:ASPARTATE+BERYLLIUM+TRIFLUORIDE'>BFD</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=7u1x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7u1x OCA], [https://pdbe.org/7u1x PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7u1x RCSB], [https://www.ebi.ac.uk/pdbsum/7u1x PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7u1x ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/ART1A_SCHPO ART1A_SCHPO] Metal-dependent phosphatase that shows phosphatase activity against several substrates, including fructose-1-phosphate and fructose-6-phosphate (By similarity). Its preference for fructose-1-phosphate, a strong glycating agent that causes DNA damage rather than a canonical yeast metabolite, suggests a damage-control function in hexose phosphate metabolism (By similarity).[UniProtKB:Q04371]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Domain of Unknown Function 89 (DUF89) proteins are metal-dependent phosphohydrolases. Exemplary DUF89 enzymes differ in their metal and phosphosubstrate preferences. Here, we interrogated the activities and structures of two DUF89 paralogs from fission yeast-Duf89 and Duf8901. We find that Duf89 and Duf8901 are cobalt/nickel-dependent phosphohydrolases adept at hydrolyzing p-nitrophenylphosphate and PP(i). Crystal structures of metal-free Duf89 and Co(2+)-bound Duf8901 disclosed two enzyme conformations that differed with respect to the position of a three-helix module, which is either oriented away from the active site in Duf89 or forms a lid over the active site in Duf8901. Lid closure results in a 16 A movement of Duf8901 Asp195, vis-a-vis Asp199 in Duf89, that brings Asp195 into contact with an octahedrally coordinated cobalt. Reaction of Duf8901 with BeCl(2) and NaF in the presence of divalent cations Co(2+), Ni(2+), or Zn(2+) generated covalent Duf8901-(Asp248)-beryllium trifluoride (BeF(3))Co(2+), Duf8901-(Asp248)-BeF(3)Ni(2+), or Duf8901-(Asp248)-BeF(3)Zn(2+) adducts, the structures of which suggest a two-step catalytic mechanism via formation and hydrolysis of an enzyme-(aspartyl)-phosphate intermediate. Alanine mutations of Duf8901 Asp248, Asn249, Lys401, Asp286, and Asp195 that interact with BeF(3)Co(2+) squelched p-nitrophenylphosphatase activity. A 1.8 A structure of a Duf8901-(Asp248)-AlF(4)-OH(2)*Co(2+) transition-state mimetic suggests an associative mechanism in which Asp195 and Asp363 orient and activate the water nucleophile. Whereas deletion of the duf89 gene elicited a phenotype in which expression of phosphate homeostasis gene pho1 was derepressed, deleting duf8901 did not, thereby hinting that the DUF89 paralogs have distinct functional repertoires in vivo.

-	~~Authors: Jacewicz, A~~., Sanchez, A~~.M.~~, Shuman, S.	+	Fission yeast Duf89 and Duf8901 are cobalt/nickel-dependent phosphatase-pyrophosphatases that act via a covalent aspartyl-phosphate intermediate.,Sanchez AM, Jacewicz A, Shuman S J Biol Chem. 2022 May;298(5):101851. doi: 10.1016/j.jbc.2022.101851. Epub 2022 , Mar 18. PMID:35314193<ref>PMID:35314193</ref>

-	~~Description: Structure~~ of ~~SPAC806~~.~~04c protein from fission yeast covalently bound to BeF3~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
-	[[Category: ~~Shuman, S~~]]	+	<div class="pdbe-citations 7u1x" style="background-color:#fffaf0;"></div>
-	[[Category: ~~Sanchez,~~ A.M]]	+	== References ==
-	[[Category: ~~Jacewicz, A~~]]	+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Schizosaccharomyces pombe]]
		+	[[Category: Jacewicz A]]
		+	[[Category: Sanchez AM]]
		+	[[Category: Shuman S]]

OCA: Protected "7u1x" [edit=sysop:move=sysop]

OCA — Wed, 02 Mar 2022 05:08:23 GMT

Protected "7u1x" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:08, 2 March 2022

OCA: New page: '''Unreleased structure''' The entry 7u1x is ON HOLD until Paper Publication Authors: Jacewicz, A., Sanchez, A.M., Shuman, S. Description: Structure of SPAC806.04c protein from fission...

OCA — Wed, 02 Mar 2022 05:08:22 GMT

New page: '''Unreleased structure''' The entry 7u1x is ON HOLD until Paper Publication Authors: Jacewicz, A., Sanchez, A.M., Shuman, S. Description: Structure of SPAC806.04c protein from fission...

New page

'''Unreleased structure'''

The entry 7u1x is ON HOLD until Paper Publication

Authors: Jacewicz, A., Sanchez, A.M., Shuman, S.

Description: Structure of SPAC806.04c protein from fission yeast covalently bound to BeF3
[[Category: Unreleased Structures]]
[[Category: Shuman, S]]
[[Category: Sanchez, A.M]]
[[Category: Jacewicz, A]]

7u1x - Revision history

OCA at 17:10, 18 October 2023

OCA: Protected "7u1x" [edit=sysop:move=sysop]

OCA: New page: '''Unreleased structure''' The entry 7u1x is ON HOLD until Paper Publication Authors: Jacewicz, A., Sanchez, A.M., Shuman, S. Description: Structure of SPAC806.04c protein from fission...