5tbt - Revision history

OCA at 12:57, 4 October 2023

OCA — Wed, 04 Oct 2023 12:57:31 GMT

←Older revision		Revision as of 12:57, 4 October 2023
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	<StructureSection load='5tbt' size='340' side='right'caption='[[5tbt]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='5tbt' size='340' side='right'caption='[[5tbt]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5tbt]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Blood_fluke Blood fluke~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TBT OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5TBT FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5tbt]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Schistosoma_mansoni Schistosoma mansoni]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TBT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5TBT FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=CTN:4-AMINO-1-BETA-D-RIBOFURANOSYL~~-2~~(1H)-PYRIMIDINONE'>CTN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 2.101Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~>[[5cxq\|5cxq]], [[5cxs\|5cxs]], [[5ko5\|5ko5]], [[5ko6\|5ko6]], [[5tbs\|5tbs]], [[5tbu\|5tbu]], [[5tbv\|5tbv]]</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CTN:4-AMINO-1-BETA-D-RIBOFURANOSYL-2(1H)-PYRIMIDINONE'>CTN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=5tbt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5tbt OCA], [https://pdbe.org/5tbt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5tbt RCSB], [https://www.ebi.ac.uk/pdbsum/5tbt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5tbt 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=5tbt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5tbt OCA], [~~http~~://pdbe.org/5tbt PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5tbt RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5tbt PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5tbt ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/A0A0U3AGT1_SCHMA A0A0U3AGT1_SCHMA]] 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/A0A0U3AGT1_SCHMA A0A0U3AGT1_SCHMA] 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 ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Blood fluke]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Purine-nucleoside phosphorylase~~]]	+	[[Category: Schistosoma mansoni]]
-	[[Category: Brandao-Neto, J]]	+	[[Category: Brandao-Neto J]]
-	[[Category: Faheem, M]]	+	[[Category: Faheem M]]
-	[[Category: Pereira~~, H M~~]]	+	[[Category: Pereira HM]]
-	[[Category: Romanello, L]]	+	[[Category: Romanello L]]
-	[[Category: Torini~~, J R]]~~	+	[[Category: Torini JR]]
-	~~[[Category: Transferase~~]]	+

OCA at 09:03, 1 January 2020

OCA — Wed, 01 Jan 2020 09:03:17 GMT

←Older revision		Revision as of 09:03, 1 January 2020
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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/>

OCA at 06:25, 17 April 2019

OCA — Wed, 17 Apr 2019 06:25:47 GMT

←Older revision		Revision as of 06:25, 17 April 2019
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	==Crystal Structure of Isoform 2 of Purine Nucleoside Phosphorylase complexed with Cytidine==		==Crystal Structure of Isoform 2 of Purine Nucleoside Phosphorylase complexed with Cytidine==
-	<StructureSection load='5tbt' size='340' side='right' caption='[[5tbt]], [[Resolution\|resolution]] 2.10Å' scene=''>	+	<StructureSection load='5tbt' size='340' side='right'caption='[[5tbt]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5tbt]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Blood_fluke Blood fluke]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TBT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5TBT FirstGlance]. <br>		<table><tr><td colspan='2'>[[5tbt]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Blood_fluke Blood fluke]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TBT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5TBT FirstGlance]. <br>
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	</StructureSection>		</StructureSection>
	[[Category: Blood fluke]]		[[Category: Blood fluke]]
		+	[[Category: Large Structures]]
	[[Category: Purine-nucleoside phosphorylase]]		[[Category: Purine-nucleoside phosphorylase]]
	[[Category: Brandao-Neto, J]]		[[Category: Brandao-Neto, J]]

OCA at 08:34, 26 September 2018

OCA — Wed, 26 Sep 2018 08:34:19 GMT

←Older revision		Revision as of 08:34, 26 September 2018
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-	'''Unreleased structure'''

-	~~The entry~~ 5tbt is ~~ON HOLD until Paper~~ Publication	+	==Crystal Structure of Isoform 2 of Purine Nucleoside Phosphorylase complexed with Cytidine==
		+	<StructureSection load='5tbt' size='340' side='right' caption='[[5tbt]], [[Resolution\|resolution]] 2.10Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5tbt]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Blood_fluke Blood fluke]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TBT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5TBT FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CTN:4-AMINO-1-BETA-D-RIBOFURANOSYL-2(1H)-PYRIMIDINONE'>CTN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5cxq\|5cxq]], [[5cxs\|5cxs]], [[5ko5\|5ko5]], [[5ko6\|5ko6]], [[5tbs\|5tbs]], [[5tbu\|5tbu]], [[5tbv\|5tbv]]</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=5tbt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5tbt OCA], [http://pdbe.org/5tbt PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5tbt RCSB], [http://www.ebi.ac.uk/pdbsum/5tbt PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5tbt ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/A0A0U3AGT1_SCHMA A0A0U3AGT1_SCHMA]] 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 ==
		+	Purine nucleoside phosphorylases (PNPs) play an important role in the blood fluke parasite Schistosoma mansoni as a key enzyme of the purine salvage pathway. Here we present the structural and kinetic characterization of a new PNP isoform from S. mansoni, SmPNP2. Thermofluorescence screening of different ligands suggested cytidine and cytosine are potential ligands. The binding of cytosine and cytidine were confirmed by isothermal titration calorimetry, with a KD of 27 muM for cytosine, and a KM of 76.3 muM for cytidine. SmPNP2 also displays catalytic activity against inosine and adenosine, making it the first described PNP with robust catalytic activity towards both pyrimidines and purines. Crystal structures of SmPNP2 with different ligands were obtained and comparison of these structures with the previously described S. mansoni PNP (SmPNP1) provided clues for the unique capacity of SmPNP2 to bind pyrimidines. When compared with the structure of SmPNP1, substitutions in the vicinity of SmPNP2 active site alter the architecture of the nucleoside base binding site thus permitting an alternative binding mode for nucleosides, with a 180 degrees rotation from the canonical binding mode. The remarkable plasticity of this binding site enhances our understanding of the correlation between structure and nucleotide selectivity, thus suggesting new ways to analyse PNP activity.

-	~~Authors: Faheem, M~~., Torini, J.R., ~~Romanello~~, L., Brandao-Neto, J., Pereira~~, H~~.M.	+	The molecular structure of Schistosoma mansoni PNP isoform 2 provides insights into the nucleoside selectivity of PNPs.,Torini JR, Romanello L, Batista FAH, Serrao VHB, Faheem M, Zeraik AE, Bird L, Nettleship J, Reddivari Y, Owens R, DeMarco R, Borges JC, Brandao-Neto J, Pereira HD PLoS One. 2018 Sep 7;13(9):e0203532. doi: 10.1371/journal.pone.0203532., eCollection 2018. PMID:30192840<ref>PMID:30192840</ref>

-	~~Description: Crystal Structure~~ of ~~Isoform 2~~ of Purine ~~Nucleoside Phosphorylase complexed with Cytidine~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5tbt" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Purine nucleoside phosphorylase\|Purine nucleoside phosphorylase]]
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Blood fluke]]
		+	[[Category: Purine-nucleoside phosphorylase]]
	[[Category: Brandao-Neto, J]]		[[Category: Brandao-Neto, J]]
-	[[Category: Pereira, H.M]]
-	[[Category: Torini, J.R]]
-	[[Category: Romanello, L]]
	[[Category: Faheem, M]]		[[Category: Faheem, M]]
		+	[[Category: Pereira, H M]]
		+	[[Category: Romanello, L]]
		+	[[Category: Torini, J R]]
		+	[[Category: Transferase]]

OCA at 13:21, 27 September 2017

OCA — Wed, 27 Sep 2017 13:21:09 GMT

←Older revision		Revision as of 13:21, 27 September 2017
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	Description: Crystal Structure of Isoform 2 of Purine Nucleoside Phosphorylase complexed with Cytidine		Description: Crystal Structure of Isoform 2 of Purine Nucleoside Phosphorylase complexed with Cytidine
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Torini, J.R]]
	[[Category: Brandao-Neto, J]]		[[Category: Brandao-Neto, J]]
	[[Category: Pereira, H.M]]		[[Category: Pereira, H.M]]
		+	[[Category: Torini, J.R]]
	[[Category: Romanello, L]]		[[Category: Romanello, L]]
	[[Category: Faheem, M]]		[[Category: Faheem, M]]

OCA at 13:27, 9 March 2017

OCA — Thu, 09 Mar 2017 13:27:18 GMT

←Older revision		Revision as of 13:27, 9 March 2017
Line 7:		Line 7:
	Description: Crystal Structure of Isoform 2 of Purine Nucleoside Phosphorylase complexed with Cytidine		Description: Crystal Structure of Isoform 2 of Purine Nucleoside Phosphorylase complexed with Cytidine
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
		+	[[Category: Torini, J.R]]
	[[Category: Brandao-Neto, J]]		[[Category: Brandao-Neto, J]]
	[[Category: Pereira, H.M]]		[[Category: Pereira, H.M]]
-	[[Category: Torini, J.R]]
	[[Category: Romanello, L]]		[[Category: Romanello, L]]
	[[Category: Faheem, M]]		[[Category: Faheem, M]]

OCA at 15:25, 3 October 2016

OCA — Mon, 03 Oct 2016 15:25:40 GMT

←Older revision		Revision as of 15:25, 3 October 2016
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	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Faheem, M., Torini, J.R., Romanello, L., Brandao-Neto, J., Pereira, H.M.		Authors: Faheem, M., Torini, J.R., Romanello, L., Brandao-Neto, J., Pereira, H.M.

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

OCA — Wed, 21 Sep 2016 12:28:16 GMT

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

←Older revision

Revision as of 12:28, 21 September 2016

OCA: New page: '''Unreleased structure''' The entry 5tbt is ON HOLD Authors: Faheem, M., Torini, J.R., Romanello, L., Brandao-Neto, J., Pereira, H.M. Description: Crystal Structure of Isoform 2 of Pu...

OCA — Wed, 21 Sep 2016 12:28:15 GMT

New page: '''Unreleased structure''' The entry 5tbt is ON HOLD Authors: Faheem, M., Torini, J.R., Romanello, L., Brandao-Neto, J., Pereira, H.M. Description: Crystal Structure of Isoform 2 of Pu...

New page

'''Unreleased structure'''

The entry 5tbt is ON HOLD

Authors: Faheem, M., Torini, J.R., Romanello, L., Brandao-Neto, J., Pereira, H.M.

Description: Crystal Structure of Isoform 2 of Purine Nucleoside Phosphorylase complexed with Cytidine
[[Category: Unreleased Structures]]
[[Category: Brandao-Neto, J]]
[[Category: Pereira, H.M]]
[[Category: Torini, J.R]]
[[Category: Romanello, L]]
[[Category: Faheem, M]]