5ifk - Revision history

OCA at 09:16, 20 March 2024

OCA — Wed, 20 Mar 2024 09:16:45 GMT

←Older revision		Revision as of 09:16, 20 March 2024
Line 10:		Line 10:
	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/Q6CSZ6_KLULA Q6CSZ6_KLULA] The purine nucleoside phosphorylases catalyze the phosphorolytic breakdown of the N-glycosidic bond in the beta-(deoxy)ribonucleoside molecules, with the formation of the corresponding free purine bases and pentose-1-phosphate.[PIRNR:PIRNR000477]		[https://www.uniprot.org/uniprot/Q6CSZ6_KLULA Q6CSZ6_KLULA] The purine nucleoside phosphorylases catalyze the phosphorolytic breakdown of the N-glycosidic bond in the beta-(deoxy)ribonucleoside molecules, with the formation of the corresponding free purine bases and pentose-1-phosphate.[PIRNR:PIRNR000477]
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Consumption of foods and beverages with high purine content increases the risk of hyperuricemia, which causes gout and can lead to cardiovascular, renal, and other metabolic disorders. As patients often find dietary restrictions challenging, enzymatically lowering purine content in popular foods and beverages offers a safe and attractive strategy to control hyperuricemia. Here, we report structurally and functionally characterized purine nucleoside phosphorylase (PNP) from Kluyveromyces lactis (KlacPNP), a key enzyme involved in the purine degradation pathway. We report a 1.97 A resolution crystal structure of homotrimeric KlacPNP with an intrinsically bound hypoxanthine in the active site. KlacPNP belongs to the nucleoside phosphorylase-I (NP-I) family, and it specifically utilizes 6-oxopurine substrates in the following order: inosine > guanosine > xanthosine, but is inactive towards adenosine. To engineer enzymes with broad substrate specificity, we created two point variants, KlacPNPN256D and KlacPNPN256E, by replacing the catalytically active Asn256 with Asp and Glu, respectively, based on structural and comparative sequence analysis. KlacPNPN256D not only displayed broad substrate specificity by utilizing both 6-oxopurines and 6-aminopurines in the order adenosine > inosine > xanthosine > guanosine, but also displayed reversal of substrate specificity. In contrast, KlacPNPN256E was highly specific to inosine and could not utilize other tested substrates. Beer consumption is associated with increased risk of developing gout, owing to its high purine content. Here, we demonstrate that KlacPNP and KlacPNPN256D could be used to catalyze a key reaction involved in lowering beer purine content. Biochemical properties of these enzymes such as activity across a wide pH range, optimum activity at about 25 degrees C, and stability for months at about 8 degrees C, make them suitable candidates for food and beverage industries. Since KlacPNPN256D has broad substrate specificity, a combination of engineered KlacPNP and other enzymes involved in purine degradation could effectively lower the purine content in foods and beverages.
-
-	Functional and Structural Characterization of Purine Nucleoside Phosphorylase from Kluyveromyces lactis and Its Potential Applications in Reducing Purine Content in Food.,Mahor D, Priyanka A, Prasad GS, Thakur KG PLoS One. 2016 Oct 21;11(10):e0164279. doi: 10.1371/journal.pone.0164279., eCollection 2016. PMID:27768715<ref>PMID:27768715</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 5ifk" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Purine nucleoside phosphorylase 3D structures\|Purine nucleoside phosphorylase 3D structures]]		*[[Purine nucleoside phosphorylase 3D structures\|Purine nucleoside phosphorylase 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 13:49, 30 August 2023

OCA — Wed, 30 Aug 2023 13:49:33 GMT

←Older revision		Revision as of 13:49, 30 August 2023
Line 3:		Line 3:
	<StructureSection load='5ifk' size='340' side='right'caption='[[5ifk]], [[Resolution\|resolution]] 1.97Å' scene=''>		<StructureSection load='5ifk' size='340' side='right'caption='[[5ifk]], [[Resolution\|resolution]] 1.97Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ifk]] is a 3 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Candida_sphaerica Candida sphaerica~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5IFK OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5IFK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ifk]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Kluyveromyces_lactis_NRRL_Y-1140 Kluyveromyces lactis NRRL Y-1140]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5IFK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5IFK FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=HPA:HYPOXANTHINE'>HPA</scene>~~</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]] 1.967Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>KLLA0_C16621g ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~284590 Candida sphaerica])</td~~><~~/tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HPA:HYPOXANTHINE'>HPA</scene></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b></td><td class="sblockDat"><span class='plainlinks~~'>~~[http://en.wikipedia.org/wiki/Purine-nucleoside_phosphorylase Purine-nucleoside phosphorylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.2.1 2.4.2.1]~~ </~~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=5ifk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ifk OCA], [https://pdbe.org/5ifk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ifk RCSB], [https://www.ebi.ac.uk/pdbsum/5ifk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ifk ProSAT]</span></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=5ifk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ifk OCA], [~~http~~://pdbe.org/5ifk PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5ifk RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5ifk PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5ifk ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/Q6CSZ6_KLULA Q6CSZ6_KLULA]] The purine nucleoside phosphorylases catalyze the phosphorolytic breakdown of the N-glycosidic bond in the beta-(deoxy)ribonucleoside molecules, with the formation of the corresponding free purine bases and pentose-1-phosphate.[PIRNR:PIRNR000477]	+	[https://www.uniprot.org/uniprot/Q6CSZ6_KLULA Q6CSZ6_KLULA] The purine nucleoside phosphorylases catalyze the phosphorolytic breakdown of the N-glycosidic bond in the beta-(deoxy)ribonucleoside molecules, with the formation of the corresponding free purine bases and pentose-1-phosphate.[PIRNR:PIRNR000477]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 27:		Line 26:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Candida sphaerica~~]]	+	[[Category: Kluyveromyces lactis NRRL Y-1140]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Purine-nucleoside phosphorylase]]~~	+	[[Category: Priyanka A]]
-	[[Category: Priyanka, A]]	+	[[Category: Thakur KG]]
-	[[Category: Thakur~~, K G]]~~	+
-	~~[[Category: Purine nucleoside phosphorylase hypoxanthine np-i family kluyveromyces lacti]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 07:16, 3 June 2020

OCA — Wed, 03 Jun 2020 07:16:53 GMT

←Older revision		Revision as of 07:16, 3 June 2020
Line 1:		Line 1:

	==Purine nucleoside phosphorylase==		==Purine nucleoside phosphorylase==
-	<StructureSection load='5ifk' size='340' side='right' caption='[[5ifk]], [[Resolution\|resolution]] 1.97Å' scene=''>	+	<StructureSection load='5ifk' size='340' side='right'caption='[[5ifk]], [[Resolution\|resolution]] 1.97Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ifk]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5IFK OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5IFK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ifk]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Candida_sphaerica Candida sphaerica]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5IFK OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5IFK FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HPA:HYPOXANTHINE'>HPA</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HPA:HYPOXANTHINE'>HPA</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">KLLA0_C16621g ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=284590 Candida sphaerica])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Purine-nucleoside_phosphorylase Purine-nucleoside phosphorylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.2.1 2.4.2.1] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Purine-nucleoside_phosphorylase Purine-nucleoside phosphorylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.2.1 2.4.2.1] </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=5ifk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ifk OCA], [http://pdbe.org/5ifk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ifk RCSB], [http://www.ebi.ac.uk/pdbsum/5ifk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ifk ProSAT]</span></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=5ifk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ifk OCA], [http://pdbe.org/5ifk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ifk RCSB], [http://www.ebi.ac.uk/pdbsum/5ifk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ifk ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 19:		Line 20:
	</div>		</div>
	<div class="pdbe-citations 5ifk" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5ifk" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Purine nucleoside phosphorylase 3D structures\|Purine nucleoside phosphorylase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Candida sphaerica]]
		+	[[Category: Large Structures]]
	[[Category: Purine-nucleoside phosphorylase]]		[[Category: Purine-nucleoside phosphorylase]]
	[[Category: Priyanka, A]]		[[Category: Priyanka, A]]

OCA at 07:40, 27 April 2017

OCA — Thu, 27 Apr 2017 07:40:19 GMT

←Older revision		Revision as of 07:40, 27 April 2017
Line 10:		Line 10:
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/Q6CSZ6_KLULA Q6CSZ6_KLULA]] The purine nucleoside phosphorylases catalyze the phosphorolytic breakdown of the N-glycosidic bond in the beta-(deoxy)ribonucleoside molecules, with the formation of the corresponding free purine bases and pentose-1-phosphate.[PIRNR:PIRNR000477]		[[http://www.uniprot.org/uniprot/Q6CSZ6_KLULA Q6CSZ6_KLULA]] The purine nucleoside phosphorylases catalyze the phosphorolytic breakdown of the N-glycosidic bond in the beta-(deoxy)ribonucleoside molecules, with the formation of the corresponding free purine bases and pentose-1-phosphate.[PIRNR:PIRNR000477]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Consumption of foods and beverages with high purine content increases the risk of hyperuricemia, which causes gout and can lead to cardiovascular, renal, and other metabolic disorders. As patients often find dietary restrictions challenging, enzymatically lowering purine content in popular foods and beverages offers a safe and attractive strategy to control hyperuricemia. Here, we report structurally and functionally characterized purine nucleoside phosphorylase (PNP) from Kluyveromyces lactis (KlacPNP), a key enzyme involved in the purine degradation pathway. We report a 1.97 A resolution crystal structure of homotrimeric KlacPNP with an intrinsically bound hypoxanthine in the active site. KlacPNP belongs to the nucleoside phosphorylase-I (NP-I) family, and it specifically utilizes 6-oxopurine substrates in the following order: inosine > guanosine > xanthosine, but is inactive towards adenosine. To engineer enzymes with broad substrate specificity, we created two point variants, KlacPNPN256D and KlacPNPN256E, by replacing the catalytically active Asn256 with Asp and Glu, respectively, based on structural and comparative sequence analysis. KlacPNPN256D not only displayed broad substrate specificity by utilizing both 6-oxopurines and 6-aminopurines in the order adenosine > inosine > xanthosine > guanosine, but also displayed reversal of substrate specificity. In contrast, KlacPNPN256E was highly specific to inosine and could not utilize other tested substrates. Beer consumption is associated with increased risk of developing gout, owing to its high purine content. Here, we demonstrate that KlacPNP and KlacPNPN256D could be used to catalyze a key reaction involved in lowering beer purine content. Biochemical properties of these enzymes such as activity across a wide pH range, optimum activity at about 25 degrees C, and stability for months at about 8 degrees C, make them suitable candidates for food and beverage industries. Since KlacPNPN256D has broad substrate specificity, a combination of engineered KlacPNP and other enzymes involved in purine degradation could effectively lower the purine content in foods and beverages.
		+
		+	Functional and Structural Characterization of Purine Nucleoside Phosphorylase from Kluyveromyces lactis and Its Potential Applications in Reducing Purine Content in Food.,Mahor D, Priyanka A, Prasad GS, Thakur KG PLoS One. 2016 Oct 21;11(10):e0164279. doi: 10.1371/journal.pone.0164279., eCollection 2016. PMID:27768715<ref>PMID:27768715</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5ifk" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Purine-nucleoside phosphorylase]]		[[Category: Purine-nucleoside phosphorylase]]
	[[Category: Priyanka, A]]		[[Category: Priyanka, A]]
-	[[Category: Thakur, K]]	+	[[Category: Thakur, K G]]
	[[Category: Purine nucleoside phosphorylase hypoxanthine np-i family kluyveromyces lacti]]		[[Category: Purine nucleoside phosphorylase hypoxanthine np-i family kluyveromyces lacti]]
	[[Category: Transferase]]		[[Category: Transferase]]

OCA at 09:33, 11 March 2017

OCA — Sat, 11 Mar 2017 09:33:51 GMT

←Older revision		Revision as of 09:33, 11 March 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5ifk is ~~ON HOLD~~	+	==Purine nucleoside phosphorylase==
-		+	<StructureSection load='5ifk' size='340' side='right' caption='[[5ifk]], [[Resolution\|resolution]] 1.97Å' scene=''>
-	~~Authors~~: ~~Thakur~~, K., ~~Priyanka~~, A.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5ifk]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5IFK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5IFK FirstGlance]. <br>
-	~~Description~~: ~~Purine~~ nucleoside ~~phosphorylase~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HPA:HYPOXANTHINE'>HPA</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Purine-nucleoside_phosphorylase Purine-nucleoside phosphorylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.2.1 2.4.2.1] </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=5ifk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ifk OCA], [http://pdbe.org/5ifk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ifk RCSB], [http://www.ebi.ac.uk/pdbsum/5ifk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ifk ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/Q6CSZ6_KLULA Q6CSZ6_KLULA]] The purine nucleoside phosphorylases catalyze the phosphorolytic breakdown of the N-glycosidic bond in the beta-(deoxy)ribonucleoside molecules, with the formation of the corresponding free purine bases and pentose-1-phosphate.[PIRNR:PIRNR000477]
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Purine-nucleoside phosphorylase]]
	[[Category: Priyanka, A]]		[[Category: Priyanka, A]]
	[[Category: Thakur, K]]		[[Category: Thakur, K]]
		+	[[Category: Purine nucleoside phosphorylase hypoxanthine np-i family kluyveromyces lacti]]
		+	[[Category: Transferase]]

OCA at 00:27, 11 May 2016

OCA — Wed, 11 May 2016 00:27:42 GMT

←Older revision		Revision as of 00:27, 11 May 2016
Line 3:		Line 3:
	The entry 5ifk is ON HOLD		The entry 5ifk is ON HOLD

-	Authors: ~~KrishanG~~ Thakur, ~~Anupriyanka~~	+	Authors: Thakur, K., Priyanka, A.

	Description: Purine nucleoside phosphorylase		Description: Purine nucleoside phosphorylase
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: ~~Krishang~~ Thakur, ~~Anupriyanka~~]]	+	[[Category: Priyanka, A]]
		+	[[Category: Thakur, K]]

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

OCA — Wed, 02 Mar 2016 13:54:12 GMT

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

←Older revision

Revision as of 13:54, 2 March 2016

OCA: New page: '''Unreleased structure''' The entry 5ifk is ON HOLD Authors: KrishanG Thakur, Anupriyanka Description: Purine nucleoside phosphorylase Category: Unreleased Structures [[Category: ...

OCA — Wed, 02 Mar 2016 13:54:10 GMT

New page: '''Unreleased structure''' The entry 5ifk is ON HOLD Authors: KrishanG Thakur, Anupriyanka Description: Purine nucleoside phosphorylase Category: Unreleased Structures [[Category: ...

New page

'''Unreleased structure'''

The entry 5ifk is ON HOLD

Authors: KrishanG Thakur, Anupriyanka

Description: Purine nucleoside phosphorylase
[[Category: Unreleased Structures]]
[[Category: Krishang Thakur, Anupriyanka]]