2isc - Revision history

OCA at 09:04, 21 February 2024

2024-02-21T09:04:14Z

←Older revision		Revision as of 09:04, 21 February 2024
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	<StructureSection load='2isc' size='340' side='right'caption='[[2isc]], [[Resolution\|resolution]] 2.70Å' scene=''>		<StructureSection load='2isc' size='340' side='right'caption='[[2isc]], [[Resolution\|resolution]] 2.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2isc]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Triva Triva~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ISC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2ISC FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2isc]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Trichomonas_vaginalis Trichomonas vaginalis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ISC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2ISC FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=223:(3R,4R)-1-[(4-AMINO-5H-PYRROLO[3,2-D]PYRIMIDIN-7-YL)METHYL]-4-(HYDROXYMETHYL)PYRROLIDIN-3-OL'>223</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]] 2.7Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2i4t\|2i4t]]</div></td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=223:(3R,4R)-1-[(4-AMINO-5H-PYRROLO[3,2-D]PYRIMIDIN-7-YL)METHYL]-4-(HYDROXYMETHYL)PYRROLIDIN-3-OL'>223</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'>[https://en.wikipedia.org/wiki/Purine-nucleoside_phosphorylase Purine-nucleoside phosphorylase], with EC number [https://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=2isc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2isc OCA], [https://pdbe.org/2isc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2isc RCSB], [https://www.ebi.ac.uk/pdbsum/2isc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2isc ProSAT]</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=2isc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2isc OCA], [https://pdbe.org/2isc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2isc RCSB], [https://www.ebi.ac.uk/pdbsum/2isc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2isc ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A2E7Y6_TRIV3 A2E7Y6_TRIV3]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2isc ConSurf].		</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2isc ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Trichomonas vaginalis is a parasitic protozoan purine auxotroph possessing a unique purine salvage pathway consisting of a bacterial type purine nucleoside phosphorylase (PNP) and a purine nucleoside kinase. Thus, T. vaginalis PNP (TvPNP) functions in the reverse direction relative to the PNPs in other organisms. Immucillin-A (ImmA) and DADMe-Immucillin-A (DADMe-ImmA) are transition state mimics of adenosine with geometric and electrostatic features that resemble early and late transition states of adenosine at the transition state stabilized by TvPNP. ImmA demonstrates slow-onset tight-binding inhibition with TvPNP, to give an equilibrium dissociation constant of 87 pM, an inhibitor release half-time of 17.2 min, and a Km/Kd ratio of 70,100. DADMe-ImmA resembles a late ribooxacarbenium ion transition state for TvPNP to give a dissociation constant of 30 pM, an inhibitor release half-time of 64 min, and a Km/Kd ratio of 203,300. The tight binding of DADMe-ImmA supports a late SN1 transition state. Despite their tight binding to TvPNP, ImmA and DADMe-ImmA are weak inhibitors of human and P. falciparum PNPs. The crystal structures of the TvPNP x ImmA x PO4 and TvPNP x DADMe-ImmA x PO4 ternary complexes differ from previous structures with substrate analogues. The tight binding with DADMe-ImmA is in part due to a 2.7 A ionic interaction between a PO4 oxygen and the N1' cation of the hydroxypyrrolidine and is weaker in the TvPNP x ImmA x PO4 structure at 3.5 A. However, the TvPNP x ImmA x PO4 structure includes hydrogen bonds between the 2'-hydroxyl and the protein that are not present in TvPNP x DADMe-ImmA x PO4. These structures explain why DADMe-ImmA binds tighter than ImmA. Immucillin-H is a 12 nM inhibitor of TvPNP but a 56 pM inhibitor of human PNP. And this difference is explained by isotope-edited difference infrared spectroscopy with [6-18O]ImmH to establish that O6 is the keto tautomer in TvPNP x ImmH x PO4, causing an unfavorable leaving-group interaction.
-
-	Inhibition and structure of Trichomonas vaginalis purine nucleoside phosphorylase with picomolar transition state analogues.,Rinaldo-Matthis A, Wing C, Ghanem M, Deng H, Wu P, Gupta A, Tyler PC, Evans GB, Furneaux RH, Almo SC, Wang CC, Schramm VL Biochemistry. 2007 Jan 23;46(3):659-68. PMID:17223688<ref>PMID:17223688</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 2isc" 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>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Purine-nucleoside phosphorylase]]~~	+	[[Category: Trichomonas vaginalis]]
-	~~[[Category: Triva~~]]	+	[[Category: Almo SC]]
-	[[Category: Almo~~, S C~~]]	+	[[Category: Rinaldo-Matthis A]]
-	[[Category: Rinaldo-Matthis, A]]	+	[[Category: Schramm VL]]
-	[[Category: Schramm~~, V L]]~~	+
-	~~[[Category: Purine nucleoside phosphorylase]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 10:05, 12 May 2021

2021-05-12T10:05:43Z

←Older revision		Revision as of 10:05, 12 May 2021
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	<StructureSection load='2isc' size='340' side='right'caption='[[2isc]], [[Resolution\|resolution]] 2.70Å' scene=''>		<StructureSection load='2isc' size='340' side='right'caption='[[2isc]], [[Resolution\|resolution]] 2.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2isc]] is a 6 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Triva Triva]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ISC OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2ISC FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2isc]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Triva Triva]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ISC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2ISC FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=223:(3R,4R)-1-[(4-AMINO-5H-PYRROLO[3,2-D]PYRIMIDIN-7-YL)METHYL]-4-(HYDROXYMETHYL)PYRROLIDIN-3-OL'>223</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=223:(3R,4R)-1-[(4-AMINO-5H-PYRROLO[3,2-D]PYRIMIDIN-7-YL)METHYL]-4-(HYDROXYMETHYL)PYRROLIDIN-3-OL'>223</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2i4t\|2i4t]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2i4t\|2i4t]]</div></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'>[https://en.wikipedia.org/wiki/Purine-nucleoside_phosphorylase Purine-nucleoside phosphorylase], with EC number [https://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=2isc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2isc OCA], [~~http~~://pdbe.org/2isc PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2isc RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2isc PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2isc ProSAT]</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=2isc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2isc OCA], [https://pdbe.org/2isc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2isc RCSB], [https://www.ebi.ac.uk/pdbsum/2isc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2isc ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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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 09:07, 24 July 2019

2019-07-24T09:07:30Z

←Older revision		Revision as of 09:07, 24 July 2019
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	==Crystal structure of Purine Nucleoside Phosphorylase from Trichomonas vaginalis with DADMe-Imm-A==		==Crystal structure of Purine Nucleoside Phosphorylase from Trichomonas vaginalis with DADMe-Imm-A==
-	<StructureSection load='2isc' size='340' side='right' caption='[[2isc]], [[Resolution\|resolution]] 2.70Å' scene=''>	+	<StructureSection load='2isc' size='340' side='right'caption='[[2isc]], [[Resolution\|resolution]] 2.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2isc]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Triva Triva]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ISC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ISC FirstGlance]. <br>		<table><tr><td colspan='2'>[[2isc]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Triva Triva]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ISC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ISC FirstGlance]. <br>
Line 13:		Line 13:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/is/2isc_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/is/2isc_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
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	</div>		</div>
	<div class="pdbe-citations 2isc" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 2isc" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Purine nucleoside phosphorylase\|Purine nucleoside phosphorylase]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Purine-nucleoside phosphorylase]]		[[Category: Purine-nucleoside phosphorylase]]
	[[Category: Triva]]		[[Category: Triva]]

OCA at 08:34, 18 October 2017

2017-10-18T08:34:58Z

←Older revision		Revision as of 08:34, 18 October 2017
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	<StructureSection load='2isc' size='340' side='right' caption='[[2isc]], [[Resolution\|resolution]] 2.70Å' scene=''>		<StructureSection load='2isc' size='340' side='right' caption='[[2isc]], [[Resolution\|resolution]] 2.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2isc]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ISC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ISC FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2isc]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Triva Triva]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ISC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ISC FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=223:(3R,4R)-1-[(4-AMINO-5H-PYRROLO[3,2-D]PYRIMIDIN-7-YL)METHYL]-4-(HYDROXYMETHYL)PYRROLIDIN-3-OL'>223</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=223:(3R,4R)-1-[(4-AMINO-5H-PYRROLO[3,2-D]PYRIMIDIN-7-YL)METHYL]-4-(HYDROXYMETHYL)PYRROLIDIN-3-OL'>223</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2i4t\|2i4t]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2i4t\|2i4t]]</td></tr>
Line 28:		Line 28:
	</div>		</div>
	<div class="pdbe-citations 2isc" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 2isc" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Purine nucleoside phosphorylase\|Purine nucleoside phosphorylase]]
	== References ==		== References ==
	<references/>		<references/>
Line 36:		Line 33:
	</StructureSection>		</StructureSection>
	[[Category: Purine-nucleoside phosphorylase]]		[[Category: Purine-nucleoside phosphorylase]]
		+	[[Category: Triva]]
	[[Category: Almo, S C]]		[[Category: Almo, S C]]
	[[Category: Rinaldo-Matthis, A]]		[[Category: Rinaldo-Matthis, A]]

OCA at 01:25, 10 March 2017

2017-03-10T01:25:49Z

←Older revision		Revision as of 01:25, 10 March 2017
Line 28:		Line 28:
	</div>		</div>
	<div class="pdbe-citations 2isc" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 2isc" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Purine nucleoside phosphorylase\|Purine nucleoside phosphorylase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 11:06, 1 February 2017

2017-02-01T11:06:29Z

←Older revision		Revision as of 11:06, 1 February 2017
Line 1:		Line 1:
-	==Crystal ~~stucture~~ of Purine Nucleoside Phosphorylase from Trichomonas vaginalis with DADMe-Imm-A==	+
		+	==Crystal structure of Purine Nucleoside Phosphorylase from Trichomonas vaginalis with DADMe-Imm-A==
	<StructureSection load='2isc' size='340' side='right' caption='[[2isc]], [[Resolution\|resolution]] 2.70Å' scene=''>		<StructureSection load='2isc' size='340' side='right' caption='[[2isc]], [[Resolution\|resolution]] 2.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2isc]] is a 6 chain structure ~~with sequence from [http://en.wikipedia.org/wiki/Triva Triva]~~. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ISC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ISC FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2isc]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ISC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ISC FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=223:(3R,4R)-1-[(4-AMINO-5H-PYRROLO[3,2-D]PYRIMIDIN-7-YL)METHYL]-4-(HYDROXYMETHYL)PYRROLIDIN-3-OL'>223</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=223:(3R,4R)-1-[(4-AMINO-5H-PYRROLO[3,2-D]PYRIMIDIN-7-YL)METHYL]-4-(HYDROXYMETHYL)PYRROLIDIN-3-OL'>223</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2i4t\|2i4t]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2i4t\|2i4t]]</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=2isc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2isc OCA], [http://pdbe.org/2isc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2isc RCSB], [http://www.ebi.ac.uk/pdbsum/2isc PDBsum]</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=2isc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2isc OCA], [http://pdbe.org/2isc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2isc RCSB], [http://www.ebi.ac.uk/pdbsum/2isc PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2isc ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 27:		Line 28:
	</div>		</div>
	<div class="pdbe-citations 2isc" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 2isc" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Purine nucleoside phosphorylase\|Purine nucleoside phosphorylase]]
	== References ==		== References ==
	<references/>		<references/>
Line 35:		Line 33:
	</StructureSection>		</StructureSection>
	[[Category: Purine-nucleoside phosphorylase]]		[[Category: Purine-nucleoside phosphorylase]]
-	[[Category: Triva]]
	[[Category: Almo, S C]]		[[Category: Almo, S C]]
	[[Category: Rinaldo-Matthis, A]]		[[Category: Rinaldo-Matthis, A]]

OCA at 05:53, 9 February 2016

2016-02-09T05:53:04Z

←Older revision		Revision as of 05:53, 9 February 2016
Line 16:		Line 16:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2isc ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 19:15, 10 September 2015

2015-09-10T19:15:59Z

←Older revision		Revision as of 19:15, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='2isc' size='340' side='right' caption='[[2isc]], [[Resolution\|resolution]] 2.70Å' scene=''>		<StructureSection load='2isc' size='340' side='right' caption='[[2isc]], [[Resolution\|resolution]] 2.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2isc]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Trichomonas_vaginalis Trichomonas vaginalis~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ISC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ISC FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2isc]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Triva Triva]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ISC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ISC FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=223:(3R,4R)-1-[(4-AMINO-5H-PYRROLO[3,2-D]PYRIMIDIN-7-YL)METHYL]-4-(HYDROXYMETHYL)PYRROLIDIN-3-OL'>223</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=223:(3R,4R)-1-[(4-AMINO-5H-PYRROLO[3,2-D]PYRIMIDIN-7-YL)METHYL]-4-(HYDROXYMETHYL)PYRROLIDIN-3-OL'>223</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2i4t\|2i4t]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2i4t\|2i4t]]</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=2isc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2isc OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2isc RCSB], [http://www.ebi.ac.uk/pdbsum/2isc PDBsum]</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=2isc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2isc OCA], [http://pdbe.org/2isc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2isc RCSB], [http://www.ebi.ac.uk/pdbsum/2isc PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 26:		Line 26:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 2isc" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 34:		Line 35:
	</StructureSection>		</StructureSection>
	[[Category: Purine-nucleoside phosphorylase]]		[[Category: Purine-nucleoside phosphorylase]]
-	[[Category: ~~Trichomonas vaginalis~~]]	+	[[Category: Triva]]
	[[Category: Almo, S C]]		[[Category: Almo, S C]]
	[[Category: Rinaldo-Matthis, A]]		[[Category: Rinaldo-Matthis, A]]

OCA at 08:10, 16 January 2015

2015-01-16T08:10:14Z

←Older revision		Revision as of 08:10, 16 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2isc]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Trichomonas_vaginalis Trichomonas vaginalis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ISC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ISC FirstGlance]. <br>		<table><tr><td colspan='2'>[[2isc]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Trichomonas_vaginalis Trichomonas vaginalis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ISC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ISC FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=223:(3R,4R)-1-[(4-AMINO-5H-PYRROLO[3,2-D]PYRIMIDIN-7-YL)METHYL]-4-(HYDROXYMETHYL)PYRROLIDIN-3-OL'>223</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=223:(3R,4R)-1-[(4-AMINO-5H-PYRROLO[3,2-D]PYRIMIDIN-7-YL)METHYL]-4-(HYDROXYMETHYL)PYRROLIDIN-3-OL'>223</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2i4t\|2i4t]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2i4t\|2i4t]]</td></tr>
-	<tr><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><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2isc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2isc OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2isc RCSB], [http://www.ebi.ac.uk/pdbsum/2isc PDBsum]</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=2isc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2isc OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2isc RCSB], [http://www.ebi.ac.uk/pdbsum/2isc PDBsum]</span></td></tr>
-	<table>	+	</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 35:		Line 35:
	[[Category: Purine-nucleoside phosphorylase]]		[[Category: Purine-nucleoside phosphorylase]]
	[[Category: Trichomonas vaginalis]]		[[Category: Trichomonas vaginalis]]
-	[[Category: Almo, S C.]]	+	[[Category: Almo, S C]]
-	[[Category: Rinaldo-Matthis, A.]]	+	[[Category: Rinaldo-Matthis, A]]
-	[[Category: Schramm, V L.]]	+	[[Category: Schramm, V L]]
	[[Category: Purine nucleoside phosphorylase]]		[[Category: Purine nucleoside phosphorylase]]
	[[Category: Transferase]]		[[Category: Transferase]]

OCA at 07:51, 30 September 2014

2014-09-30T07:51:35Z

←Older revision		Revision as of 07:51, 30 September 2014
Line 1:		Line 1:
-	[[~~Image:~~2isc.~~png~~\|~~left~~\|200px]]	+	==Crystal stucture of Purine Nucleoside Phosphorylase from Trichomonas vaginalis with DADMe-Imm-A==
		+	<StructureSection load='2isc' size='340' side='right' caption='[[2isc]], [[Resolution\|resolution]] 2.70Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2isc]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Trichomonas_vaginalis Trichomonas vaginalis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ISC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ISC FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=223:(3R,4R)-1-[(4-AMINO-5H-PYRROLO[3,2-D]PYRIMIDIN-7-YL)METHYL]-4-(HYDROXYMETHYL)PYRROLIDIN-3-OL'>223</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2i4t\|2i4t]]</td></tr>
		+	<tr><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><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2isc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2isc OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2isc RCSB], [http://www.ebi.ac.uk/pdbsum/2isc PDBsum]</span></td></tr>
		+	<table>
		+	== Evolutionary Conservation ==
		+	[[Image:Consurf_key_small.gif\|200px\|right]]
		+	Check<jmol>
		+	<jmolCheckbox>
		+	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/is/2isc_consurf.spt"</scriptWhenChecked>
		+	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
		+	<text>to colour the structure by Evolutionary Conservation</text>
		+	</jmolCheckbox>
		+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Trichomonas vaginalis is a parasitic protozoan purine auxotroph possessing a unique purine salvage pathway consisting of a bacterial type purine nucleoside phosphorylase (PNP) and a purine nucleoside kinase. Thus, T. vaginalis PNP (TvPNP) functions in the reverse direction relative to the PNPs in other organisms. Immucillin-A (ImmA) and DADMe-Immucillin-A (DADMe-ImmA) are transition state mimics of adenosine with geometric and electrostatic features that resemble early and late transition states of adenosine at the transition state stabilized by TvPNP. ImmA demonstrates slow-onset tight-binding inhibition with TvPNP, to give an equilibrium dissociation constant of 87 pM, an inhibitor release half-time of 17.2 min, and a Km/Kd ratio of 70,100. DADMe-ImmA resembles a late ribooxacarbenium ion transition state for TvPNP to give a dissociation constant of 30 pM, an inhibitor release half-time of 64 min, and a Km/Kd ratio of 203,300. The tight binding of DADMe-ImmA supports a late SN1 transition state. Despite their tight binding to TvPNP, ImmA and DADMe-ImmA are weak inhibitors of human and P. falciparum PNPs. The crystal structures of the TvPNP x ImmA x PO4 and TvPNP x DADMe-ImmA x PO4 ternary complexes differ from previous structures with substrate analogues. The tight binding with DADMe-ImmA is in part due to a 2.7 A ionic interaction between a PO4 oxygen and the N1' cation of the hydroxypyrrolidine and is weaker in the TvPNP x ImmA x PO4 structure at 3.5 A. However, the TvPNP x ImmA x PO4 structure includes hydrogen bonds between the 2'-hydroxyl and the protein that are not present in TvPNP x DADMe-ImmA x PO4. These structures explain why DADMe-ImmA binds tighter than ImmA. Immucillin-H is a 12 nM inhibitor of TvPNP but a 56 pM inhibitor of human PNP. And this difference is explained by isotope-edited difference infrared spectroscopy with [6-18O]ImmH to establish that O6 is the keto tautomer in TvPNP x ImmH x PO4, causing an unfavorable leaving-group interaction.

-	~~{{STRUCTURE_2isc\| PDB=2isc \| SCENE= }}~~	+	Inhibition and structure of Trichomonas vaginalis purine nucleoside phosphorylase with picomolar transition state analogues.,Rinaldo-Matthis A, Wing C, Ghanem M, Deng H, Wu P, Gupta A, Tyler PC, Evans GB, Furneaux RH, Almo SC, Wang CC, Schramm VL Biochemistry. 2007 Jan 23;46(3):659-68. PMID:17223688<ref>PMID:17223688</ref>

-	~~===Crystal stucture~~ of ~~Purine Nucleoside Phosphorylase from Trichomonas vaginalis with DADMe-Imm-A===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>

-	~~{{ABSTRACT_PUBMED_17223688}}~~	+	==See Also==
-		+	*[[Purine nucleoside phosphorylase\|Purine nucleoside phosphorylase]]
-	==~~About this Structure~~==	+	== References ==
-	[[~~2isc~~]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Trichomonas_vaginalis Trichomonas vaginalis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ISC OCA].	+	<references/>
-		+	__TOC__
-	==~~Reference~~==	+	</StructureSection>
-	<~~ref group="xtra">PMID:017223688<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Purine-nucleoside phosphorylase]]		[[Category: Purine-nucleoside phosphorylase]]
	[[Category: Trichomonas vaginalis]]		[[Category: Trichomonas vaginalis]]