4i5v - Revision history

OCA at 08:43, 9 November 2022

2022-11-09T08:43:21Z

←Older revision		Revision as of 08:43, 9 November 2022
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	==Crystal structure of yeast Ap4A phosphorylase Apa2 in complex with Ap4A==		==Crystal structure of yeast Ap4A phosphorylase Apa2 in complex with Ap4A==
-	<StructureSection load='4i5v' size='340' side='right' caption='[[4i5v]], [[Resolution\|resolution]] 2.70Å' scene=''>	+	<StructureSection load='4i5v' size='340' side='right'caption='[[4i5v]], [[Resolution\|resolution]] 2.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4i5v]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Atcc_18824 Atcc 18824~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4I5V OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4I5V FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4i5v]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4I5V OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4I5V FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=B4P:BIS(ADENOSINE)-5-TETRAPHOSPHATE'>B4P</scene~~></td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=B4P:BIS(ADENOSINE)-5-TETRAPHOSPHATE'>B4P</scene></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4i5t\|4i5t]], [[4i5w\|4i5w]]</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=4i5v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4i5v OCA], [https://pdbe.org/4i5v PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4i5v RCSB], [https://www.ebi.ac.uk/pdbsum/4i5v PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4i5v ProSAT]</span></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">APA2, YDR530C, D9719.33 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824])</td></tr>	+
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/ATP_adenylyltransferase ATP adenylyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.53 2.7.7.53] </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=4i5v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4i5v OCA], [~~http~~://pdbe.org/4i5v PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4i5v RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4i5v PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4i5v ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/APA2_YEAST APA2_YEAST]] Sustains the catabolism of Np-4-N' nucleotides, rather than their synthesis.	+	[https://www.uniprot.org/uniprot/APA2_YEAST APA2_YEAST] Sustains the catabolism of Np-4-N' nucleotides, rather than their synthesis.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 25:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~ATP adenylyltransferase~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Atcc 18824~~]]	+	[[Category: Saccharomyces cerevisiae]]
-	[[Category: Chen, Y]]	+	[[Category: Chen Y]]
-	[[Category: Hou~~, W T~~]]	+	[[Category: Hou WT]]
-	[[Category: Jiang~~, Y L~~]]	+	[[Category: Jiang YL]]
-	[[Category: Zhou~~, C Z]]~~	+	[[Category: Zhou CZ]]
-	~~[[Category: Alpha/beta fold]]~~	+
-	~~[[Category: Ap4a]]~~	+
-	~~[[Category: Ap4a phosphorylase]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 09:08, 4 August 2016

2016-08-04T09:08:42Z

←Older revision		Revision as of 09:08, 4 August 2016
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		+
	==Crystal structure of yeast Ap4A phosphorylase Apa2 in complex with Ap4A==		==Crystal structure of yeast Ap4A phosphorylase Apa2 in complex with Ap4A==
	<StructureSection load='4i5v' size='340' side='right' caption='[[4i5v]], [[Resolution\|resolution]] 2.70Å' scene=''>		<StructureSection load='4i5v' size='340' side='right' caption='[[4i5v]], [[Resolution\|resolution]] 2.70Å' scene=''>
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	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">APA2, YDR530C, D9719.33 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">APA2, YDR530C, D9719.33 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/ATP_adenylyltransferase ATP adenylyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.53 2.7.7.53] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/ATP_adenylyltransferase ATP adenylyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.53 2.7.7.53] </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=4i5v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4i5v OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4i5v RCSB], [http://www.ebi.ac.uk/pdbsum/4i5v 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=4i5v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4i5v OCA], [http://pdbe.org/4i5v PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4i5v RCSB], [http://www.ebi.ac.uk/pdbsum/4i5v PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4i5v ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 19:		Line 20:
	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 4i5v" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 08:02, 24 December 2014

2014-12-24T08:02:37Z

←Older revision		Revision as of 08:02, 24 December 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_4i5v\| PDB=4i5v \| SCENE= }}~~	+	==Crystal structure of yeast Ap4A phosphorylase Apa2 in complex with Ap4A==
-	===Crystal structure of yeast Ap4A phosphorylase Apa2 in complex with Ap4A===	+	<StructureSection load='4i5v' size='340' side='right' caption='[[4i5v]], [[Resolution\|resolution]] 2.70Å' scene=''>
-	~~{{ABSTRACT_PUBMED_23628156}}~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[4i5v]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4I5V OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4I5V FirstGlance]. <br>
-	==Function==	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=B4P:BIS(ADENOSINE)-5-TETRAPHOSPHATE'>B4P</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4i5t\|4i5t]], [[4i5w\|4i5w]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">APA2, YDR530C, D9719.33 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824])</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/ATP_adenylyltransferase ATP adenylyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.53 2.7.7.53] </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=4i5v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4i5v OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4i5v RCSB], [http://www.ebi.ac.uk/pdbsum/4i5v PDBsum]</span></td></tr>
		+	</table>
		+	== Function ==
	[[http://www.uniprot.org/uniprot/APA2_YEAST APA2_YEAST]] Sustains the catabolism of Np-4-N' nucleotides, rather than their synthesis.		[[http://www.uniprot.org/uniprot/APA2_YEAST APA2_YEAST]] Sustains the catabolism of Np-4-N' nucleotides, rather than their synthesis.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The homeostasis of intracellular diadenosine 5',5'''-P(1),P(4)-tetraphosphate (Ap4A) in the yeast Saccharomyces cerevisiae is maintained by two 60% sequence-identical paralogs of Ap4A phosphorylases (Apa1 and Apa2). Enzymatic assays show that, compared to Apa1, Apa2 has a relatively higher phosphorylase activity towards Ap3A (5',5'''-P(1),P(3)-tetraphosphate), Ap4A, and Ap5A (5',5'''-P(1),P(5)-tetraphosphate), and Ap4A is the favorable substrate for both enzymes. To decipher the catalytic insights, we determined the crystal structures of Apa2 in the apo-, AMP-, and Ap4A-complexed forms at 2.30, 2.80, and 2.70A resolution, respectively. Apa2 is an alpha/beta protein with a core domain of a twisted eight-stranded antiparallel beta-sheet flanked by several alpha-helices, similar to the galactose-1-phosphate uridylyltransferase (GalT) members of the histidine triad (HIT) superfamily. However, a unique auxiliary domain enables an individual Apa2 monomer to possess an intact substrate-binding cleft, which is distinct from previously reported dimeric GalT proteins. This cleft is perfectly complementary to the favorable substrate Ap4A, the AMP and ATP moieties of which are perpendicular to each other, leaving the alpha-phosphate group exposed at the sharp turn against the catalytic residue His161. Structural comparisons combined with site-directed mutagenesis and activity assays enable us to define the key residues for catalysis. Furthermore, multiple-sequence alignment reveals that Apa2 and homologs represent canonical Ap4A phosphorylases, which could be grouped as a unique branch in the GalT family.

-	~~==About this Structure==~~	+	Structures of yeast Apa2 reveal catalytic insights into a canonical AP(4)A phosphorylase of the histidine triad superfamily.,Hou WT, Li WZ, Chen Y, Jiang YL, Zhou CZ J Mol Biol. 2013 Aug 9;425(15):2687-98. doi: 10.1016/j.jmb.2013.04.018. Epub 2013, Apr 26. PMID:23628156<ref>PMID:23628156</ref>
-	~~[[4i5v]] is~~ a ~~2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Atcc_18824 Atcc 18824]~~. ~~Full crystallographic information is available from [http~~:/~~/oca~~.~~weizmann~~.ac.il/~~oca-bin/ocashort?id=4I5V OCA].~~	+

-	==~~Reference~~==	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~<ref group="xtra">PMID:023628156</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	</div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: ATP adenylyltransferase]]		[[Category: ATP adenylyltransferase]]
	[[Category: Atcc 18824]]		[[Category: Atcc 18824]]
-	[[Category: Chen, Y.]]	+	[[Category: Chen, Y]]
-	[[Category: Hou, W T.]]	+	[[Category: Hou, W T]]
-	[[Category: Jiang, Y L.]]	+	[[Category: Jiang, Y L]]
-	[[Category: Zhou, C Z.]]	+	[[Category: Zhou, C Z]]
	[[Category: Alpha/beta fold]]		[[Category: Alpha/beta fold]]
	[[Category: Ap4a]]		[[Category: Ap4a]]
	[[Category: Ap4a phosphorylase]]		[[Category: Ap4a phosphorylase]]
	[[Category: Transferase]]		[[Category: Transferase]]

OCA at 07:39, 5 February 2014

2014-02-05T07:39:18Z

←Older revision		Revision as of 07:39, 5 February 2014
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	{{STRUCTURE_4i5v\| PDB=4i5v \| SCENE= }}		{{STRUCTURE_4i5v\| PDB=4i5v \| SCENE= }}
	===Crystal structure of yeast Ap4A phosphorylase Apa2 in complex with Ap4A===		===Crystal structure of yeast Ap4A phosphorylase Apa2 in complex with Ap4A===
		+	{{ABSTRACT_PUBMED_23628156}}

	==Function==		==Function==
Line 6:		Line 7:

	==About this Structure==		==About this Structure==
-	[[4i5v]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Saccharomyces_cerevisiae Saccharomyces cerevisiae~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4I5V OCA].	+	[[4i5v]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4I5V OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:023628156</ref><references group="xtra"/><references/>
	[[Category: ATP adenylyltransferase]]		[[Category: ATP adenylyltransferase]]
-	[[Category: ~~Saccharomyces cerevisiae~~]]	+	[[Category: Atcc 18824]]
	[[Category: Chen, Y.]]		[[Category: Chen, Y.]]
	[[Category: Hou, W T.]]		[[Category: Hou, W T.]]

OCA at 07:54, 8 May 2013

2013-05-08T07:54:41Z

←Older revision		Revision as of 07:54, 8 May 2013
Line 1:		Line 1:
-	~~'''Unreleased~~ structure~~'''~~	+	{{STRUCTURE_4i5v\| PDB=4i5v \| SCENE= }}
		+	===Crystal structure of yeast Ap4A phosphorylase Apa2 in complex with Ap4A===

-	~~The entry 4i5v is ON HOLD until Paper Publication~~	+	==Function==
		+	[[http://www.uniprot.org/uniprot/APA2_YEAST APA2_YEAST]] Sustains the catabolism of Np-4-N' nucleotides, rather than their synthesis.

-	~~Authors~~: ~~Jiang, Y~~.L., Hou, W.T.~~, Chen~~, Y., Zhou, C.Z.	+	==About this Structure==
-		+	[[4i5v]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4I5V OCA].
-	~~Description~~: ~~Crystal structure of yeast Ap4A~~ phosphorylase ~~Apa2 in complex with Ap4A~~	+	[[Category: ATP adenylyltransferase]]
		+	[[Category: Saccharomyces cerevisiae]]
		+	[[Category: Chen, Y.]]
		+	[[Category: Hou, W T.]]
		+	[[Category: Jiang, Y L.]]
		+	[[Category: Zhou, C Z.]]
		+	[[Category: Alpha/beta fold]]
		+	[[Category: Ap4a]]
		+	[[Category: Ap4a phosphorylase]]
		+	[[Category: Transferase]]

OCA at 11:03, 19 December 2012

2012-12-19T11:03:46Z

←Older revision		Revision as of 11:03, 19 December 2012
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4i5v is ON HOLD	+	The entry 4i5v is ON HOLD until Paper Publication

	Authors: Jiang, Y.L., Hou, W.T., Chen, Y., Zhou, C.Z.		Authors: Jiang, Y.L., Hou, W.T., Chen, Y., Zhou, C.Z.

	Description: Crystal structure of yeast Ap4A phosphorylase Apa2 in complex with Ap4A		Description: Crystal structure of yeast Ap4A phosphorylase Apa2 in complex with Ap4A

OCA: Protected "4i5v" [edit=sysop:move=sysop]

2012-12-05T10:35:30Z

Protected "4i5v" [edit=sysop:move=sysop]

←Older revision

Revision as of 10:35, 5 December 2012

OCA: New page: '''Unreleased structure''' The entry 4i5v is ON HOLD Authors: Jiang, Y.L., Hou, W.T., Chen, Y., Zhou, C.Z. Description: Crystal structure of yeast Ap4A phosphorylase Apa2 in complex wi...

2012-12-05T10:35:29Z

New page: '''Unreleased structure''' The entry 4i5v is ON HOLD Authors: Jiang, Y.L., Hou, W.T., Chen, Y., Zhou, C.Z. Description: Crystal structure of yeast Ap4A phosphorylase Apa2 in complex wi...

New page

'''Unreleased structure'''

The entry 4i5v is ON HOLD

Authors: Jiang, Y.L., Hou, W.T., Chen, Y., Zhou, C.Z.

Description: Crystal structure of yeast Ap4A phosphorylase Apa2 in complex with Ap4A