5ugf - Revision history

OCA at 13:27, 4 October 2023

OCA — Wed, 04 Oct 2023 13:27:08 GMT

←Older revision		Revision as of 13:27, 4 October 2023
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	<StructureSection load='5ugf' size='340' side='right'caption='[[5ugf]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='5ugf' size='340' side='right'caption='[[5ugf]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ugf]] is a 6 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Human Human~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UGF OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5UGF FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ugf]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UGF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5UGF FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=IM5:2-AMINO-7-{[(3R,4R)-3-HYDROXY-4-(HYDROXYMETHYL)PYRROLIDIN-1-YL]METHYL}-3,5-DIHYDRO-4H-PYRROLO[3,2-D]PYRIMIDIN-4-ONE'>IM5</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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]] 2.2Å</td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PNP, NP ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=IM5:2-AMINO-7-{[(3R,4R)-3-HYDROXY-4-(HYDROXYMETHYL)PYRROLIDIN-1-YL]METHYL}-3,5-DIHYDRO-4H-PYRROLO[3,2-D]PYRIMIDIN-4-ONE'>IM5</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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=5ugf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ugf OCA], [https://pdbe.org/5ugf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ugf RCSB], [https://www.ebi.ac.uk/pdbsum/5ugf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ugf ProSAT]</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=5ugf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ugf OCA], [~~http~~://pdbe.org/5ugf PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5ugf RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5ugf PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5ugf ProSAT]</span></td></tr>	+
	</table>		</table>
	== Disease ==		== Disease ==
-	[~~[http~~://www.uniprot.org/uniprot/PNPH_HUMAN PNPH_HUMAN]] Defects in PNP are the cause of purine nucleoside phosphorylase deficiency (PNPD) [MIM:[~~http~~://omim.org/entry/613179 613179]]. It leads to a severe T-cell immunodeficiency with neurologic disorder in children.<ref>PMID:3029074</ref> <ref>PMID:1384322</ref> <ref>PMID:8931706</ref>	+	[https://www.uniprot.org/uniprot/PNPH_HUMAN PNPH_HUMAN] Defects in PNP are the cause of purine nucleoside phosphorylase deficiency (PNPD) [MIM:[https://omim.org/entry/613179 613179]. It leads to a severe T-cell immunodeficiency with neurologic disorder in children.<ref>PMID:3029074</ref> <ref>PMID:1384322</ref> <ref>PMID:8931706</ref>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/PNPH_HUMAN PNPH_HUMAN]] 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.<ref>PMID:2104852</ref>	+	[https://www.uniprot.org/uniprot/PNPH_HUMAN PNPH_HUMAN] 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.<ref>PMID:2104852</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	==See Also==		==See Also==
-	*[[Purine nucleoside phosphorylase\|Purine nucleoside phosphorylase]]	+	*[[Purine nucleoside phosphorylase 3D structures\|Purine nucleoside phosphorylase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Purine-nucleoside phosphorylase]]~~	+	[[Category: Almo SC]]
-	[[Category: Almo~~, S C~~]]	+	[[Category: Bonanno JB]]
-	[[Category: Bonanno~~, J B~~]]	+	[[Category: Cameron SA]]
-	[[Category: Cameron~~, S A~~]]	+	[[Category: Harijan RK]]
-	[[Category: Harijan~~, R K~~]]	+	[[Category: Schramm VL]]
-	[[Category: Schramm~~, V L]]~~	+
-	~~[[Category: Inhibitor]]~~	+
-	~~[[Category: Phosphorylase]]~~	+
-	~~[[Category: Purine salvage pathway]]~~	+
-	~~[[Category: Transferase-transferase inhibitor complex]]~~	+
-	~~[[Category: Transition state analogue~~]]	+

OCA at 07:58, 27 November 2019

OCA — Wed, 27 Nov 2019 07:58:46 GMT

←Older revision		Revision as of 07:58, 27 November 2019
Line 1:		Line 1:

	==Crystal structure of human purine nucleoside phosphorylase (F159Y) mutant complexed with DADMe-ImmG and phosphate==		==Crystal structure of human purine nucleoside phosphorylase (F159Y) mutant complexed with DADMe-ImmG and phosphate==
-	<StructureSection load='5ugf' size='340' side='right' caption='[[5ugf]], [[Resolution\|resolution]] 2.20Å' scene=''>	+	<StructureSection load='5ugf' size='340' side='right'caption='[[5ugf]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5ugf]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UGF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5UGF FirstGlance]. <br>		<table><tr><td colspan='2'>[[5ugf]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UGF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5UGF FirstGlance]. <br>
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	</div>		</div>
	<div class="pdbe-citations 5ugf" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5ugf" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Purine nucleoside phosphorylase\|Purine nucleoside phosphorylase]]
	== References ==		== References ==
	<references/>		<references/>
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	</StructureSection>		</StructureSection>
	[[Category: Human]]		[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Purine-nucleoside phosphorylase]]		[[Category: Purine-nucleoside phosphorylase]]
	[[Category: Almo, S C]]		[[Category: Almo, S C]]

OCA at 08:16, 16 November 2017

OCA — Thu, 16 Nov 2017 08:16:52 GMT

←Older revision		Revision as of 08:16, 16 November 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5ugf is ~~ON HOLD~~	+	==Crystal structure of human purine nucleoside phosphorylase (F159Y) mutant complexed with DADMe-ImmG and phosphate==
		+	<StructureSection load='5ugf' size='340' side='right' caption='[[5ugf]], [[Resolution\|resolution]] 2.20Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5ugf]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UGF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5UGF FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=IM5:2-AMINO-7-{[(3R,4R)-3-HYDROXY-4-(HYDROXYMETHYL)PYRROLIDIN-1-YL]METHYL}-3,5-DIHYDRO-4H-PYRROLO[3,2-D]PYRIMIDIN-4-ONE'>IM5</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PNP, NP ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=5ugf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ugf OCA], [http://pdbe.org/5ugf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ugf RCSB], [http://www.ebi.ac.uk/pdbsum/5ugf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ugf ProSAT]</span></td></tr>
		+	</table>
		+	== Disease ==
		+	[[http://www.uniprot.org/uniprot/PNPH_HUMAN PNPH_HUMAN]] Defects in PNP are the cause of purine nucleoside phosphorylase deficiency (PNPD) [MIM:[http://omim.org/entry/613179 613179]]. It leads to a severe T-cell immunodeficiency with neurologic disorder in children.<ref>PMID:3029074</ref> <ref>PMID:1384322</ref> <ref>PMID:8931706</ref>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/PNPH_HUMAN PNPH_HUMAN]] 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.<ref>PMID:2104852</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Heavy-enzyme isotope effects (15N-, 13C-, and 2H-labeled protein) explore mass-dependent vibrational modes linked to catalysis. Transition path-sampling (TPS) calculations have predicted femtosecond dynamic coupling at the catalytic site of human purine nucleoside phosphorylase (PNP). Coupling is observed in heavy PNPs, where slowed barrier crossing caused a normal heavy-enzyme isotope effect (kchemlight/kchemheavy > 1.0). We used TPS to design mutant F159Y PNP, predicted to improve barrier crossing for heavy F159Y PNP, an attempt to generate a rare inverse heavy-enzyme isotope effect (kchemlight/kchemheavy < 1.0). Steady-state kinetic comparison of light and heavy native PNPs to light and heavy F159Y PNPs revealed similar kinetic properties. Pre-steady-state chemistry was slowed 32-fold in F159Y PNP. Pre-steady-state chemistry compared heavy and light native and F159Y PNPs and found a normal heavy-enzyme isotope effect of 1.31 for native PNP and an inverse effect of 0.75 for F159Y PNP. Increased isotopic mass in F159Y PNP causes more efficient transition state formation. Independent validation of the inverse isotope effect for heavy F159Y PNP came from commitment to catalysis experiments. Most heavy enzymes demonstrate normal heavy-enzyme isotope effects, and F159Y PNP is a rare example of an inverse effect. Crystal structures and TPS dynamics of native and F159Y PNPs explore the catalytic-site geometry associated with these catalytic changes. Experimental validation of TPS predictions for barrier crossing establishes the connection of rapid protein dynamics and vibrational coupling to enzymatic transition state passage.

-	~~Authors:~~ Harijan, ~~R.K.~~, ~~Cameron~~, S.A.~~, Bonanno, J.B~~., ~~Almo, S~~.C.~~, Schramm, V~~.L.	+	Catalytic-site design for inverse heavy-enzyme isotope effects in human purine nucleoside phosphorylase.,Harijan RK, Zoi I, Antoniou D, Schwartz SD, Schramm VL Proc Natl Acad Sci U S A. 2017 Jun 20;114(25):6456-6461. doi:, 10.1073/pnas.1704786114. Epub 2017 Jun 5. PMID:28584087<ref>PMID:28584087</ref>

-	~~Description: Crystal structure~~ of ~~human purine nucleoside phosphorylase (F159Y) mutant complexed with DADMe~~-~~ImmG and phosphate~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
-	[[Category: Almo, S.C]]	+	<div class="pdbe-citations 5ugf" style="background-color:#fffaf0;"></div>
-	[[Category: ~~Schramm~~, ~~V.L~~]]	+	== References ==
-	[[Category: Harijan, R.K]]	+	<references/>
-	[[Category: ~~Cameron~~, ~~S.A~~]]	+	__TOC__
-	[[Category: ~~Bonanno, J.B~~]]	+	</StructureSection>
		+	[[Category: Human]]
		+	[[Category: Purine-nucleoside phosphorylase]]
		+	[[Category: Almo, S C]]
		+	[[Category: Bonanno, J B]]
		+	[[Category: Cameron, S A]]
		+	[[Category: Harijan, R K]]
		+	[[Category: Schramm, V L]]
		+	[[Category: Inhibitor]]
		+	[[Category: Phosphorylase]]
		+	[[Category: Purine salvage pathway]]
		+	[[Category: Transferase-transferase inhibitor complex]]
		+	[[Category: Transition state analogue]]

OCA at 10:36, 19 April 2017

OCA — Wed, 19 Apr 2017 10:36:31 GMT

←Older revision		Revision as of 10:36, 19 April 2017
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5ugf is ON HOLD ~~until Paper Publication~~	+	The entry 5ugf is ON HOLD

	Authors: Harijan, R.K., Cameron, S.A., Bonanno, J.B., Almo, S.C., Schramm, V.L.		Authors: Harijan, R.K., Cameron, S.A., Bonanno, J.B., Almo, S.C., Schramm, V.L.

OCA at 19:02, 15 March 2017

OCA — Wed, 15 Mar 2017 19:02:09 GMT

←Older revision		Revision as of 19:02, 15 March 2017
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	[[Category: Schramm, V.L]]		[[Category: Schramm, V.L]]
	[[Category: Harijan, R.K]]		[[Category: Harijan, R.K]]
-	[[Category: Bonanno, J.B]]
	[[Category: Cameron, S.A]]		[[Category: Cameron, S.A]]
		+	[[Category: Bonanno, J.B]]

OCA at 14:27, 9 March 2017

OCA — Thu, 09 Mar 2017 14:27:14 GMT

←Older revision		Revision as of 14:27, 9 March 2017
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5ugf is ON HOLD	+	The entry 5ugf is ON HOLD until Paper Publication

	Authors: Harijan, R.K., Cameron, S.A., Bonanno, J.B., Almo, S.C., Schramm, V.L.		Authors: Harijan, R.K., Cameron, S.A., Bonanno, J.B., Almo, S.C., Schramm, V.L.

OCA at 21:56, 25 January 2017

OCA — Wed, 25 Jan 2017 21:56:15 GMT

←Older revision		Revision as of 21:56, 25 January 2017
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	Authors: Harijan, R.K., Cameron, S.A., Bonanno, J.B., Almo, S.C., Schramm, V.L.		Authors: Harijan, R.K., Cameron, S.A., Bonanno, J.B., Almo, S.C., Schramm, V.L.

-	Description: Crystal structure of purine nucleoside phosphorylase (F159Y) mutant ~~from human~~ complexed with DADMe-ImmG and phosphate	+	Description: Crystal structure of human purine nucleoside phosphorylase (F159Y) mutant complexed with DADMe-ImmG and phosphate
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Almo, S.C]]		[[Category: Almo, S.C]]

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

OCA — Wed, 18 Jan 2017 14:57:25 GMT

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

←Older revision

Revision as of 14:57, 18 January 2017

OCA: New page: '''Unreleased structure''' The entry 5ugf is ON HOLD Authors: Harijan, R.K., Cameron, S.A., Bonanno, J.B., Almo, S.C., Schramm, V.L. Description: Crystal structure of purine nucleoside...

OCA — Wed, 18 Jan 2017 14:57:23 GMT

New page: '''Unreleased structure''' The entry 5ugf is ON HOLD Authors: Harijan, R.K., Cameron, S.A., Bonanno, J.B., Almo, S.C., Schramm, V.L. Description: Crystal structure of purine nucleoside...

New page

'''Unreleased structure'''

The entry 5ugf is ON HOLD

Authors: Harijan, R.K., Cameron, S.A., Bonanno, J.B., Almo, S.C., Schramm, V.L.

Description: Crystal structure of purine nucleoside phosphorylase (F159Y) mutant from human complexed with DADMe-ImmG and phosphate
[[Category: Unreleased Structures]]
[[Category: Almo, S.C]]
[[Category: Schramm, V.L]]
[[Category: Harijan, R.K]]
[[Category: Bonanno, J.B]]
[[Category: Cameron, S.A]]