5yw5 - Revision history

OCA at 08:39, 22 November 2023

OCA — Wed, 22 Nov 2023 08:39:15 GMT

←Older revision		Revision as of 08:39, 22 November 2023
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	==Crystal structure of Adenine phosphoribosyltransferase from Francisella tularensis in complex with adenine==		==Crystal structure of Adenine phosphoribosyltransferase from Francisella tularensis in complex with adenine==
-	<StructureSection load='5yw5' size='340' side='right' caption='[[5yw5]], [[Resolution\|resolution]] 1.90Å' scene=''>	+	<StructureSection load='5yw5' size='340' side='right'caption='[[5yw5]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5yw5]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"bacterium_tularense"_mccoy_and_chapin_1912 "bacterium tularense" mccoy and chapin 1912~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YW5 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5YW5 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5yw5]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Francisella_tularensis Francisella tularensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YW5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5YW5 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=ADE:ADENINE'>ADE</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]] 1.9Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>apt ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~263~~ "~~Bacterium tularense~~" ~~McCoy and Chapin 1912])</td~~><~~/tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADE:ADENINE'>ADE</scene></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b></td><td class="sblockDat"><span class='plainlinks~~'>~~[http://en.wikipedia.org/wiki/Adenine_phosphoribosyltransferase Adenine phosphoribosyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.2.7 2.4.2.7]~~ </~~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=5yw5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yw5 OCA], [https://pdbe.org/5yw5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5yw5 RCSB], [https://www.ebi.ac.uk/pdbsum/5yw5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5yw5 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=5yw5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yw5 OCA], [~~http~~://pdbe.org/5yw5 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5yw5 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5yw5 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5yw5 ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/~~A0A0E2ZLA9_FRATU A0A0E2ZLA9_FRATU]~~] Catalyzes a salvage reaction resulting in the formation of AMP, that is energically less costly than de novo synthesis.[HAMAP-Rule:MF_00004~~][SAAS:SAAS00766748~~]	+	[https://www.uniprot.org/uniprot/APT_FRATT APT_FRATT] Catalyzes a salvage reaction resulting in the formation of AMP, that is energically less costly than de novo synthesis.[HAMAP-Rule:MF_00004]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 20:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 5yw5" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5yw5" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Phosphoribosyltransferase 3D structures\|Phosphoribosyltransferase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacterium tularense mccoy and chapin 1912~~]]	+	[[Category: Francisella tularensis]]
-	[[Category: ~~Adenine phosphoribosyltransferase~~]]	+	[[Category: Large Structures]]
-	[[Category: Pavithra~~, G C~~]]	+	[[Category: Pavithra GC]]
-	[[Category: Ramagopal~~, U A]]~~	+	[[Category: Ramagopal UA]]
-	~~[[Category: Transferase~~]]	+

OCA at 07:36, 4 July 2018

OCA — Wed, 04 Jul 2018 07:36:53 GMT

←Older revision		Revision as of 07:36, 4 July 2018
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	<StructureSection load='5yw5' size='340' side='right' caption='[[5yw5]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='5yw5' size='340' side='right' caption='[[5yw5]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5yw5]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YW5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YW5 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5yw5]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacterium_tularense"_mccoy_and_chapin_1912 "bacterium tularense" mccoy and chapin 1912]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YW5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YW5 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADE:ADENINE'>ADE</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADE:ADENINE'>ADE</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">apt ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=263 "Bacterium tularense" McCoy and Chapin 1912])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Adenine_phosphoribosyltransferase Adenine phosphoribosyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.2.7 2.4.2.7] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Adenine_phosphoribosyltransferase Adenine phosphoribosyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.2.7 2.4.2.7] </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=5yw5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yw5 OCA], [http://pdbe.org/5yw5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yw5 RCSB], [http://www.ebi.ac.uk/pdbsum/5yw5 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yw5 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=5yw5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yw5 OCA], [http://pdbe.org/5yw5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yw5 RCSB], [http://www.ebi.ac.uk/pdbsum/5yw5 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yw5 ProSAT]</span></td></tr>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bacterium tularense mccoy and chapin 1912]]
	[[Category: Adenine phosphoribosyltransferase]]		[[Category: Adenine phosphoribosyltransferase]]
	[[Category: Pavithra, G C]]		[[Category: Pavithra, G C]]
	[[Category: Ramagopal, U A]]		[[Category: Ramagopal, U A]]
	[[Category: Transferase]]		[[Category: Transferase]]

OCA at 06:29, 9 May 2018

OCA — Wed, 09 May 2018 06:29:20 GMT

←Older revision		Revision as of 06:29, 9 May 2018
Line 10:		Line 10:
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/A0A0E2ZLA9_FRATU A0A0E2ZLA9_FRATU]] Catalyzes a salvage reaction resulting in the formation of AMP, that is energically less costly than de novo synthesis.[HAMAP-Rule:MF_00004][SAAS:SAAS00766748]		[[http://www.uniprot.org/uniprot/A0A0E2ZLA9_FRATU A0A0E2ZLA9_FRATU]] Catalyzes a salvage reaction resulting in the formation of AMP, that is energically less costly than de novo synthesis.[HAMAP-Rule:MF_00004][SAAS:SAAS00766748]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Francisella tularensis is classified as a category A bioterrorism agent, which also causes tularemia. Here, we present the crystal structure of apo and adenine bound form of the adenine phosphoribosyltransferase (APRT) from Francisella tularensis.. APRT is an enzyme involved in the salvage of adenine (a 6-aminopurine) to adenosine monophosphate (AMP). The purine salvage pathway relies on two essential and distinct enzymes to convert 6-aminopurine and 6-oxopurines into corresponding nucleotides. The mechanism by which these enzymes differentiate different purines is not clearly understood. Analysis of structures of apo and adenine bound APRT from F. tularensis, together with all other available structures of APRTs, suggests that (1) the base-binding loop is stabilized by a cluster of aromatic and conformation restricting proline residues and (2) an N-H N hydrogen bond between the base-binding loop and N1 atom of adenine is the key interaction that differentiates adenine from 6-oxopurines. These observations were corroborated by bioinformatics analysis of ~4000 sequences of APRTs (with 80% identity cutoff) which confirms that the residues conferring rigidity to the base-binding loop are highly conserved. Furthermore, F23A mutation on the base-binding loop severely affects the efficiency of the enzyme. We extend our analysis to the structure and sequences of APRTs from Trypanosomatidae family with a destabilizing insertion on the base-binding loop and propose the mechanism by which these evolutionarily deviated enzymes achieve base specificity. Our results suggest that the base-binding loop not only confers appropriate affinity, but also provides defined specificity for adenine. This article is protected by copyright. All rights reserved.
		+
		+	Crystal structures of APRT from Francisella tularensis: An N-H N hydrogen bond imparts adenine specificity in adenine phosporibosyltransferases.,Pavithra GC, Ramagopal UA FEBS J. 2018 Apr 25. doi: 10.1111/febs.14481. PMID:29694705<ref>PMID:29694705</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5yw5" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 05:50, 3 January 2018

OCA — Wed, 03 Jan 2018 05:50:32 GMT

←Older revision		Revision as of 05:50, 3 January 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5yw5 is ~~ON HOLD until Paper Publication~~	+	==Crystal structure of Adenine phosphoribosyltransferase from Francisella tularensis in complex with adenine==
-		+	<StructureSection load='5yw5' size='340' side='right' caption='[[5yw5]], [[Resolution\|resolution]] 1.90Å' scene=''>
-	~~Authors~~: ~~Pavithra~~, G.C., ~~Ramagopal~~, U.A.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5yw5]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YW5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YW5 FirstGlance]. <br>
-	~~Description~~: ~~Crystal structure of Adenine phosphoribosyltransferase from Francisella tularensis~~ in ~~complex with adenine~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADE:ADENINE'>ADE</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/Adenine_phosphoribosyltransferase Adenine phosphoribosyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.2.7 2.4.2.7] </span></td></tr>
-	[[Category: Pavithra, G.C]]	+	<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=5yw5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yw5 OCA], [http://pdbe.org/5yw5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yw5 RCSB], [http://www.ebi.ac.uk/pdbsum/5yw5 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yw5 ProSAT]</span></td></tr>
-	[[Category: Ramagopal, U.A]]	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/A0A0E2ZLA9_FRATU A0A0E2ZLA9_FRATU]] Catalyzes a salvage reaction resulting in the formation of AMP, that is energically less costly than de novo synthesis.[HAMAP-Rule:MF_00004][SAAS:SAAS00766748]
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Adenine phosphoribosyltransferase]]
		+	[[Category: Pavithra, G C]]
		+	[[Category: Ramagopal, U A]]
		+	[[Category: Transferase]]

OCA at 04:49, 20 December 2017

OCA — Wed, 20 Dec 2017 04:49:17 GMT

←Older revision		Revision as of 04:49, 20 December 2017
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5yw5 is ON HOLD	+	The entry 5yw5 is ON HOLD until Paper Publication

	Authors: Pavithra, G.C., Ramagopal, U.A.		Authors: Pavithra, G.C., Ramagopal, U.A.

OCA: Protected "5yw5" [edit=sysop:move=sysop]

OCA — Wed, 06 Dec 2017 05:59:38 GMT

Protected "5yw5" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:59, 6 December 2017

OCA: New page: '''Unreleased structure''' The entry 5yw5 is ON HOLD Authors: Pavithra, G.C., Ramagopal, U.A. Description: Crystal structure of Adenine phosphoribosyltransferase from Francisella tular...

OCA — Wed, 06 Dec 2017 05:59:37 GMT

New page: '''Unreleased structure''' The entry 5yw5 is ON HOLD Authors: Pavithra, G.C., Ramagopal, U.A. Description: Crystal structure of Adenine phosphoribosyltransferase from Francisella tular...

New page

'''Unreleased structure'''

The entry 5yw5 is ON HOLD

Authors: Pavithra, G.C., Ramagopal, U.A.

Description: Crystal structure of Adenine phosphoribosyltransferase from Francisella tularensis in complex with adenine
[[Category: Unreleased Structures]]
[[Category: Pavithra, G.C]]
[[Category: Ramagopal, U.A]]