4yjk - Revision history

OCA at 10:55, 10 January 2024

OCA — Wed, 10 Jan 2024 10:55:32 GMT

←Older revision		Revision as of 10:55, 10 January 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4yjk]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Shewanella_oneidensis_MR-1 Shewanella oneidensis MR-1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YJK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4YJK FirstGlance]. <br>		<table><tr><td colspan='2'>[[4yjk]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Shewanella_oneidensis_MR-1 Shewanella oneidensis MR-1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YJK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4YJK FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=URA:URACIL'>URA</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]] 1.68Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=URA:URACIL'>URA</scene></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=4yjk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4yjk OCA], [https://pdbe.org/4yjk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4yjk RCSB], [https://www.ebi.ac.uk/pdbsum/4yjk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4yjk 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=4yjk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4yjk OCA], [https://pdbe.org/4yjk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4yjk RCSB], [https://www.ebi.ac.uk/pdbsum/4yjk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4yjk ProSAT]</span></td></tr>
	</table>		</table>

OCA at 08:16, 3 May 2023

OCA — Wed, 03 May 2023 08:16:08 GMT

←Older revision		Revision as of 08:16, 3 May 2023
Line 1:		Line 1:

	==Crystal structure of C212S mutant of Shewanella oneidensis MR-1 uridine phosphorylase==		==Crystal structure of C212S mutant of Shewanella oneidensis MR-1 uridine phosphorylase==
-	<StructureSection load='4yjk' size='340' side='right' caption='[[4yjk]], [[Resolution\|resolution]] 1.68Å' scene=''>	+	<StructureSection load='4yjk' size='340' side='right'caption='[[4yjk]], [[Resolution\|resolution]] 1.68Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4yjk]] is a 6 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Sheon Sheon~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YJK OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4YJK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4yjk]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Shewanella_oneidensis_MR-1 Shewanella oneidensis MR-1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YJK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4YJK FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=URA:URACIL'>URA</scene~~></td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=URA:URACIL'>URA</scene></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4r2x\|4r2x]], [[4r2w\|4r2w]]</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=4yjk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4yjk OCA], [https://pdbe.org/4yjk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4yjk RCSB], [https://www.ebi.ac.uk/pdbsum/4yjk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4yjk ProSAT]</span></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">udp, SO_4133 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=211586 SHEON])</td></tr>	+
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Uridine_phosphorylase Uridine phosphorylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.2.3 2.4.2.3] </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=4yjk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4yjk OCA], [~~http~~://pdbe.org/4yjk PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4yjk RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4yjk PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4yjk ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q8E9X9_SHEON Q8E9X9_SHEON]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 19:		Line 18:
	</div>		</div>
	<div class="pdbe-citations 4yjk" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 4yjk" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Uridine phosphorylase 3D structures\|Uridine phosphorylase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Sheon~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Uridine phosphorylase~~]]	+	[[Category: Shewanella oneidensis MR-1]]
-	[[Category: Dorovatovsky~~, P V~~]]	+	[[Category: Dorovatovsky PV]]
-	[[Category: Manuvera~~, V A~~]]	+	[[Category: Manuvera VA]]
-	[[Category: Mordkovich~~, N N~~]]	+	[[Category: Mordkovich NN]]
-	[[Category: Polyakov~~, K M~~]]	+	[[Category: Polyakov KM]]
-	[[Category: Popov~~, V O~~]]	+	[[Category: Popov VO]]
-	[[Category: Safonova~~, T N~~]]	+	[[Category: Safonova TN]]
-	[[Category: Veiko~~, V P]]~~	+	[[Category: Veiko VP]]
-	~~[[Category: S212c mutant]]~~	+
-	~~[[Category: Transferase]]~~	+
-	~~[[Category: Uracil~~]]	+

OCA at 09:39, 22 November 2017

OCA — Wed, 22 Nov 2017 09:39:55 GMT

←Older revision		Revision as of 09:39, 22 November 2017
Line 3:		Line 3:
	<StructureSection load='4yjk' size='340' side='right' caption='[[4yjk]], [[Resolution\|resolution]] 1.68Å' scene=''>		<StructureSection load='4yjk' size='340' side='right' caption='[[4yjk]], [[Resolution\|resolution]] 1.68Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4yjk]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YJK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4YJK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4yjk]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Sheon Sheon]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YJK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4YJK FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=URA:URACIL'>URA</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=URA:URACIL'>URA</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4r2x\|4r2x]], [[4r2w\|4r2w]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">udp, SO_4133 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=211586 SHEON])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Uridine_phosphorylase Uridine phosphorylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.2.3 2.4.2.3] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Uridine_phosphorylase Uridine phosphorylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.2.3 2.4.2.3] </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=4yjk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4yjk OCA], [http://pdbe.org/4yjk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4yjk RCSB], [http://www.ebi.ac.uk/pdbsum/4yjk 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=4yjk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4yjk OCA], [http://pdbe.org/4yjk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4yjk RCSB], [http://www.ebi.ac.uk/pdbsum/4yjk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4yjk ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 17:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 4yjk" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 4yjk" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Uridine phosphorylase\|Uridine phosphorylase]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Sheon]]
	[[Category: Uridine phosphorylase]]		[[Category: Uridine phosphorylase]]
	[[Category: Dorovatovsky, P V]]		[[Category: Dorovatovsky, P V]]

OCA at 06:50, 2 March 2016

OCA — Wed, 02 Mar 2016 06:50:00 GMT

←Older revision		Revision as of 06:50, 2 March 2016
Line 1:		Line 1:
		+
	==Crystal structure of C212S mutant of Shewanella oneidensis MR-1 uridine phosphorylase==		==Crystal structure of C212S mutant of Shewanella oneidensis MR-1 uridine phosphorylase==
	<StructureSection load='4yjk' size='340' side='right' caption='[[4yjk]], [[Resolution\|resolution]] 1.68Å' scene=''>		<StructureSection load='4yjk' size='340' side='right' caption='[[4yjk]], [[Resolution\|resolution]] 1.68Å' scene=''>
Line 7:		Line 8:
	<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=4yjk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4yjk OCA], [http://pdbe.org/4yjk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4yjk RCSB], [http://www.ebi.ac.uk/pdbsum/4yjk 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=4yjk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4yjk OCA], [http://pdbe.org/4yjk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4yjk RCSB], [http://www.ebi.ac.uk/pdbsum/4yjk PDBsum]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Uridine phosphorylase (UP; EC 2.4.2.3), a key enzyme in the pyrimidine-salvage pathway, catalyzes the reversible phosphorolysis of uridine to uracil and ribose 1-phosphate. The structure of the C212S mutant of uridine phosphorylase from the facultatively aerobic Gram-negative gamma-proteobacterium Shewanella oneidensis MR-1 (SoUP) was determined at 1.68 A resolution. A comparison of the structures of the mutant and the wild-type enzyme showed that one dimer in the mutant hexamer differs from all other dimers in the mutant and wild-type SoUP (both in the free form and in complex with uridine). The key difference is the `maximum open' state of one of the subunits comprising this dimer, which has not been observed previously for uridine phosphorylases. Some conformational features of the SoUP dimer that provide access of the substrate into the active site are revealed. The binding of the substrate was shown to require the concerted action of two subunits of the dimer. The changes in the three-dimensional structure induced by the C212S mutation account for the lower affinity of the mutant for inorganic phosphate, while the affinity for uridine remains unchanged.
		+
		+	Concerted action of two subunits of the functional dimer of Shewanella oneidensis MR-1 uridine phosphorylase derived from a comparison of the C212S mutant and the wild-type enzyme.,Safonova TN, Mordkovich NN, Veiko VP, Okorokova NA, Manuvera VA, Dorovatovskii PV, Popov VO, Polyakov KM Acta Crystallogr D Struct Biol. 2016 Feb;72(Pt 2):203-10. doi:, 10.1107/S2059798315024353. Epub 2016 Jan 22. PMID:26894668<ref>PMID:26894668</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 4yjk" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Uridine phosphorylase\|Uridine phosphorylase]]		*[[Uridine phosphorylase\|Uridine phosphorylase]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 08:58, 10 February 2016

OCA — Wed, 10 Feb 2016 08:58:14 GMT

←Older revision		Revision as of 08:58, 10 February 2016
Line 5:		Line 5:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=URA:URACIL'>URA</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=URA:URACIL'>URA</scene></td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Uridine_phosphorylase Uridine phosphorylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.2.3 2.4.2.3] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Uridine_phosphorylase Uridine phosphorylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.2.3 2.4.2.3] </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=4yjk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4yjk OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4yjk RCSB], [http://www.ebi.ac.uk/pdbsum/4yjk 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=4yjk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4yjk OCA], [http://pdbe.org/4yjk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4yjk RCSB], [http://www.ebi.ac.uk/pdbsum/4yjk PDBsum]</span></td></tr>
	</table>		</table>
		+
		+	==See Also==
		+	*[[Uridine phosphorylase\|Uridine phosphorylase]]
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

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

OCA — Wed, 11 Mar 2015 12:02:28 GMT

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

←Older revision

Revision as of 12:02, 11 March 2015

OCA: New page: ==Crystal structure of C212S mutant of Shewanella oneidensis MR-1 uridine phosphorylase== == Structural highlights ==
<table><tr><td colspan='2'>[[4yjk]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YJK OCA]. For a guided tour on the structure components use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4YJK FirstGlance]. 
</td></tr><tr id='ligand'><td class="sblockLbl">[[Ligand|Ligands:]]</td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=URA:URACIL'>URA</scene></td></tr>
<tr id='activity'><td class="sblockLbl">Activity:</td><td class="sblockDat">[http://en.wikipedia.org/wiki/Uridine_phosphorylase Uridine phosphorylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.2.3 2.4.2.3] </td></tr>
<tr id='resources'><td class="sblockLbl">Resources:</td><td class="sblockDat">[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4yjk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4yjk OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4yjk RCSB], [http://www.ebi.ac.uk/pdbsum/4yjk PDBsum]</td></tr>
</table>
TOC
</StructureSection>
[[Category: Uridine phosphorylase]]
[[Category: Dorovatovsky, P V]]
[[Category: Manuvera, V A]]
[[Category: Mordkovich, N N]]
[[Category: Polyakov, K M]]
[[Category: Popov, V O]]
[[Category: Safonova, T N]]
[[Category: Veiko, V P]]
[[Category: S212c mutant]]
[[Category: Transferase]]
[[Category: Uracil]]