OCA at 07:04, 7 April 2021

OCA — Wed, 07 Apr 2021 07:04:18 GMT

←Older revision		Revision as of 07:04, 7 April 2021
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	==Re-interpretation of ppGpp (G4P) electron density in the deposited crystal structure of Xanthine phosphoribosyltransferase (XPRT) (1Y0B).==		==Re-interpretation of ppGpp (G4P) electron density in the deposited crystal structure of Xanthine phosphoribosyltransferase (XPRT) (1Y0B).==
-	<StructureSection load='6w1i' size='340' side='right'caption='[[6w1i]]' scene=''>	+	<StructureSection load='6w1i' size='340' side='right'caption='[[6w1i]], [[Resolution\|resolution]] 1.80Å' 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=6W1I OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6W1I FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6w1i]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacsu Bacsu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6W1I OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6W1I FirstGlance]. <br>
-	</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=6w1i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6w1i OCA], [~~http~~://pdbe.org/6w1i PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6w1i RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6w1i PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6w1i 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=G4P:GUANOSINE-5,3-TETRAPHOSPHATE'>G4P</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1y0b\|1y0b]], [[6d9q\|6d9q]], [[6d9r\|6d9r]], [[6d9s\|6d9s]]</div></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">xpt, BSU22070 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=224308 BACSU])</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Xanthine_phosphoribosyltransferase Xanthine phosphoribosyltransferase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.2.22 2.4.2.22] </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=6w1i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6w1i OCA], [https://pdbe.org/6w1i PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6w1i RCSB], [https://www.ebi.ac.uk/pdbsum/6w1i PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6w1i ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[https://www.uniprot.org/uniprot/XPT_BACSU XPT_BACSU]] Converts the preformed base xanthine, a product of nucleic acid breakdown, to xanthosine 5'-monophosphate (XMP), so that it can be reused for RNA or DNA synthesis.[HAMAP-Rule:MF_01184]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The alarmones pppGpp and ppGpp mediate starvation response and maintain purine homeostasis to protect bacteria. In the bacterial phyla Firmicutes and Bacteroidetes, xanthine phosphoribosyltransferase (XPRT) is a purine salvage enzyme that produces the nucleotide XMP from PRPP and xanthine. Combining structural, biochemical, and genetic analyses, we show that pppGpp and ppGpp, as well as a third newly identified alarmone pGpp, all directly interact with XPRT from the Gram-positive bacterium Bacillus subtilis and inhibit XPRT activity by competing with its substrate PRPP. Structural analysis reveals that ppGpp binds the PRPP binding motif within the XPRT active site. This motif is present in another (p)ppGpp target, the purine salvage enzyme HPRT, suggesting evolutionary conservation in different enzymes. However, XPRT oligomeric interaction is distinct from HPRT in that XPRT forms a symmetric dimer with two (p)ppGpp binding sites at the dimer interface. (p)ppGpp's interaction with an XPRT bridging loop across the interface results in XPRT cooperatively binding (p)ppGpp. Also, XPRT displays differential regulation by the alarmones as it is potently inhibited by both ppGpp and pGpp, but only modestly by pppGpp. Lastly, we demonstrate that the alarmones are necessary for protecting GTP homeostasis against excess environmental xanthine in B. subtilis, suggesting that regulation of XPRT is key for regulating the purine salvage pathway.
		+
		+	Molecular Mechanism of Regulation of the Purine Salvage Enzyme XPRT by the Alarmones pppGpp, ppGpp, and pGpp.,Anderson BW, Hao A, Satyshur KA, Keck JL, Wang JD J Mol Biol. 2020 Jun 26;432(14):4108-4126. doi: 10.1016/j.jmb.2020.05.013. Epub, 2020 May 21. PMID:32446804<ref>PMID:32446804</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6w1i" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Phosphoribosyltransferase 3D structures\|Phosphoribosyltransferase 3D structures]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bacsu]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Anderson BW]]	+	[[Category: Xanthine phosphoribosyltransferase]]
-	[[Category: Keck JL]]	+	[[Category: Anderson, B W]]
-	[[Category: Satyshur KA]]	+	[[Category: Keck, J L]]
		+	[[Category: Structural genomic]]
		+	[[Category: Satyshur, K A]]
		+	[[Category: Gtp]]
		+	[[Category: Homeostasis]]
		+	[[Category: Mcsg]]
		+	[[Category: PSI, Protein structure initiative]]
		+	[[Category: Prpp]]
		+	[[Category: Purine]]
		+	[[Category: Salvage]]
		+	[[Category: Transferase]]
		+	[[Category: Xprt]]

OCA at 11:10, 29 July 2020

OCA — Wed, 29 Jul 2020 11:10:13 GMT

←Older revision		Revision as of 11:10, 29 July 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry 6w1i is ON HOLD~~	+	==Re-interpretation of ppGpp (G4P) electron density in the deposited crystal structure of Xanthine phosphoribosyltransferase (XPRT) (1Y0B).==
-		+	<StructureSection load='6w1i' size='340' side='right'caption='[[6w1i]]' scene=''>
-	~~Authors: Satyshur, K.A., Anderson, B.W., Keck, J.L., Midwest Center for Structural Genomics (MCSG)~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6W1I OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6W1I FirstGlance]. <br>
-	~~Description:~~ Re-interpretation of ppGpp (G4P) electron density in the deposited crystal structure of Xanthine phosphoribosyltransferase (XPRT) (1Y0B).	+	</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=6w1i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6w1i OCA], [http://pdbe.org/6w1i PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6w1i RCSB], [http://www.ebi.ac.uk/pdbsum/6w1i PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6w1i ProSAT]</span></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	</table>
-	[[~~Category~~: ~~Keck~~, J.L]]	+	__TOC__
-	[[Category: ~~Midwest Center For Structural Genomics (Mcsg)~~]]	+	</StructureSection>
-	[[Category: ~~Satyshur, K.A~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Anderson, B.W~~]]	+	[[Category: Anderson BW]]
		+	[[Category: Keck JL]]
		+	[[Category: Satyshur KA]]

OCA: Protected "6w1i" [edit=sysop:move=sysop]

OCA — Wed, 11 Mar 2020 06:09:36 GMT

Protected "6w1i" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:09, 11 March 2020

OCA: New page: '''Unreleased structure''' The entry 6w1i is ON HOLD Authors: Satyshur, K.A., Anderson, B.W., Keck, J.L., Midwest Center for Structural Genomics (MCSG) Description: Re-interpretation o...

OCA — Wed, 11 Mar 2020 06:09:34 GMT

New page: '''Unreleased structure''' The entry 6w1i is ON HOLD Authors: Satyshur, K.A., Anderson, B.W., Keck, J.L., Midwest Center for Structural Genomics (MCSG) Description: Re-interpretation o...

New page

'''Unreleased structure'''

The entry 6w1i is ON HOLD

Authors: Satyshur, K.A., Anderson, B.W., Keck, J.L., Midwest Center for Structural Genomics (MCSG)

Description: Re-interpretation of ppGpp (G4P) electron density in the deposited crystal structure of Xanthine phosphoribosyltransferase (XPRT) (1Y0B).
[[Category: Unreleased Structures]]
[[Category: Keck, J.L]]
[[Category: Midwest Center For Structural Genomics (Mcsg)]]
[[Category: Satyshur, K.A]]
[[Category: Anderson, B.W]]

6w1i - Revision history

OCA at 07:04, 7 April 2021

OCA at 11:10, 29 July 2020

OCA: Protected "6w1i" [edit=sysop:move=sysop]

OCA: New page: '''Unreleased structure''' The entry 6w1i is ON HOLD Authors: Satyshur, K.A., Anderson, B.W., Keck, J.L., Midwest Center for Structural Genomics (MCSG) Description: Re-interpretation o...