4i5w - Revision history

OCA at 08:43, 9 November 2022

OCA — Wed, 09 Nov 2022 08:43:23 GMT

←Older revision		Revision as of 08:43, 9 November 2022
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	==Crystal structure of yeast Ap4A phosphorylase Apa2 in complex with AMP==		==Crystal structure of yeast Ap4A phosphorylase Apa2 in complex with AMP==
-	<StructureSection load='4i5w' size='340' side='right' caption='[[4i5w]], [[Resolution\|resolution]] 2.79Å' scene=''>	+	<StructureSection load='4i5w' size='340' side='right'caption='[[4i5w]], [[Resolution\|resolution]] 2.79Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4i5w]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Baker's_yeast Baker's yeast~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4I5W OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4I5W FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4i5w]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_S288C Saccharomyces cerevisiae S288C]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4I5W OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4I5W FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</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=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</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">[[4i5t\|4i5t]], [[4i5v\|4i5v]]</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=4i5w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4i5w OCA], [https://pdbe.org/4i5w PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4i5w RCSB], [https://www.ebi.ac.uk/pdbsum/4i5w PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4i5w 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=559292 Baker's yeast])</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=4i5w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4i5w OCA], [~~http~~://pdbe.org/4i5w PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4i5w RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4i5w PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4i5w 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: ~~Baker's yeast~~]]	+	[[Category: Saccharomyces cerevisiae S288C]]
-	[[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 17:51, 4 August 2016

OCA — Thu, 04 Aug 2016 17:51:24 GMT

←Older revision		Revision as of 17:51, 4 August 2016
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		+
	==Crystal structure of yeast Ap4A phosphorylase Apa2 in complex with AMP==		==Crystal structure of yeast Ap4A phosphorylase Apa2 in complex with AMP==
	<StructureSection load='4i5w' size='340' side='right' caption='[[4i5w]], [[Resolution\|resolution]] 2.79Å' scene=''>		<StructureSection load='4i5w' size='340' side='right' caption='[[4i5w]], [[Resolution\|resolution]] 2.79Å' scene=''>
Line 7:		Line 8:
	<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=559292 Baker's yeast])</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=559292 Baker's yeast])</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=4i5w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4i5w OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4i5w RCSB], [http://www.ebi.ac.uk/pdbsum/4i5w 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=4i5w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4i5w OCA], [http://pdbe.org/4i5w PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4i5w RCSB], [http://www.ebi.ac.uk/pdbsum/4i5w PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4i5w 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 4i5w" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 11:36, 25 December 2014

OCA — Thu, 25 Dec 2014 11:36:15 GMT

←Older revision		Revision as of 11:36, 25 December 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_4i5w\| PDB=4i5w \| SCENE= }}~~	+	==Crystal structure of yeast Ap4A phosphorylase Apa2 in complex with AMP==
-	===Crystal structure of yeast Ap4A phosphorylase Apa2 in complex with AMP===	+	<StructureSection load='4i5w' size='340' side='right' caption='[[4i5w]], [[Resolution\|resolution]] 2.79Å' scene=''>
-	~~{{ABSTRACT_PUBMED_23628156}}~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[4i5w]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Baker's_yeast Baker's yeast]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4I5W OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4I5W FirstGlance]. <br>
-	==Function==	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</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">[[4i5t\|4i5t]], [[4i5v\|4i5v]]</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=559292 Baker's yeast])</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=4i5w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4i5w OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4i5w RCSB], [http://www.ebi.ac.uk/pdbsum/4i5w 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>
-	~~[[4i5w]] is~~ a ~~2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Baker's_yeast Baker's yeast]~~. ~~Full crystallographic information is available from [http~~:/~~/oca~~.~~weizmann~~.ac.il/~~oca-bin/ocashort?id=4I5W 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: Baker's yeast]]		[[Category: Baker's yeast]]
-	[[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 09:19, 5 February 2014

OCA — Wed, 05 Feb 2014 09:19:01 GMT

←Older revision		Revision as of 09:19, 5 February 2014
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	{{STRUCTURE_4i5w\| PDB=4i5w \| SCENE= }}		{{STRUCTURE_4i5w\| PDB=4i5w \| SCENE= }}
	===Crystal structure of yeast Ap4A phosphorylase Apa2 in complex with AMP===		===Crystal structure of yeast Ap4A phosphorylase Apa2 in complex with AMP===
		+	{{ABSTRACT_PUBMED_23628156}}

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

	==About this Structure==		==About this Structure==
-	[[4i5w]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Saccharomyces_cerevisiae_s288c Saccharomyces cerevisiae s288c~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4I5W OCA].	+	[[4i5w]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Baker's_yeast Baker's yeast]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4I5W OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:023628156</ref><references group="xtra"/><references/>
	[[Category: ATP adenylyltransferase]]		[[Category: ATP adenylyltransferase]]
-	[[Category: ~~Saccharomyces cerevisiae s288c~~]]	+	[[Category: Baker's yeast]]
	[[Category: Chen, Y.]]		[[Category: Chen, Y.]]
	[[Category: Hou, W T.]]		[[Category: Hou, W T.]]

OCA at 07:54, 8 May 2013

OCA — Wed, 08 May 2013 07:54:56 GMT

←Older revision		Revision as of 07:54, 8 May 2013
Line 1:		Line 1:
-	~~'''Unreleased~~ structure~~'''~~	+	{{STRUCTURE_4i5w\| PDB=4i5w \| SCENE= }}
		+	===Crystal structure of yeast Ap4A phosphorylase Apa2 in complex with AMP===

-	~~The entry 4i5w 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==
-		+	[[4i5w]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_s288c Saccharomyces cerevisiae s288c]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4I5W OCA].
-	~~Description~~: ~~Crystal structure of yeast Ap4A~~ phosphorylase ~~Apa2 in complex with AMP~~	+	[[Category: ATP adenylyltransferase]]
		+	[[Category: Saccharomyces cerevisiae s288c]]
		+	[[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

OCA — Wed, 19 Dec 2012 11:03:47 GMT

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

-	The entry 4i5w is ON HOLD	+	The entry 4i5w 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 AMP		Description: Crystal structure of yeast Ap4A phosphorylase Apa2 in complex with AMP

OCA at 20:48, 12 December 2012

OCA — Wed, 12 Dec 2012 20:48:19 GMT

←Older revision		Revision as of 20:48, 12 December 2012
Line 3:		Line 3:
	The entry 4i5w is ON HOLD		The entry 4i5w is ON HOLD

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

OCA: Protected "4i5w" [edit=sysop:move=sysop]

OCA — Wed, 05 Dec 2012 10:35:32 GMT

Protected "4i5w" [edit=sysop:move=sysop]

←Older revision

Revision as of 10:35, 5 December 2012

OCA: New page: '''Unreleased structure''' The entry 4i5w 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 w...

OCA — Wed, 05 Dec 2012 10:35:31 GMT

New page: '''Unreleased structure''' The entry 4i5w 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 w...

New page

'''Unreleased structure'''

The entry 4i5w 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 AMP