6n54 - Revision history

OCA at 06:45, 11 October 2023

OCA — Wed, 11 Oct 2023 06:45:11 GMT

←Older revision		Revision as of 06:45, 11 October 2023
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	<StructureSection load='6n54' size='340' side='right'caption='[[6n54]], [[Resolution\|resolution]] 2.42Å' scene=''>		<StructureSection load='6n54' size='340' side='right'caption='[[6n54]], [[Resolution\|resolution]] 2.42Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6n54]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Human Human~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6N54 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6N54 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6n54]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6N54 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6N54 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=KEA:2-azido-2-deoxycytidine+5-(dihydrogen+phosphate)'>KEA</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 2.424Å</td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">UCK2, UMPK ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=KEA:2-azido-2-deoxycytidine+5-(dihydrogen+phosphate)'>KEA</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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'>[http://en.wikipedia.org/wiki/Uridine_kinase Uridine kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.48 2.7.1.48] </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=6n54 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6n54 OCA], [https://pdbe.org/6n54 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6n54 RCSB], [https://www.ebi.ac.uk/pdbsum/6n54 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6n54 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=6n54 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6n54 OCA], [~~http~~://pdbe.org/6n54 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6n54 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6n54 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6n54 ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/UCK2_HUMAN UCK2_HUMAN]] Phosphorylates uridine and cytidine to uridine monophosphate and cytidine monophosphate. Does not phosphorylate deoxyribonucleosides or purine ribonucleosides. Can use ATP or GTP as a phosphate donor. Can also phosphorylate cytidine and uridine nucleoside analogs such as 6-azauridine, 5-fluorouridine, 4-thiouridine, 5-bromouridine, N(4)-acetylcytidine, N(4)-benzoylcytidine, 5-fluorocytidine, 2-thiocytidine, 5-methylcytidine, and N(4)-anisoylcytidine.	+	[https://www.uniprot.org/uniprot/UCK2_HUMAN UCK2_HUMAN] Phosphorylates uridine and cytidine to uridine monophosphate and cytidine monophosphate. Does not phosphorylate deoxyribonucleosides or purine ribonucleosides. Can use ATP or GTP as a phosphate donor. Can also phosphorylate cytidine and uridine nucleoside analogs such as 6-azauridine, 5-fluorouridine, 4-thiouridine, 5-bromouridine, N(4)-acetylcytidine, N(4)-benzoylcytidine, 5-fluorocytidine, 2-thiocytidine, 5-methylcytidine, and N(4)-anisoylcytidine.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Uridine kinase]]~~	+	[[Category: Cuthbert BJ]]
-	[[Category: Cuthbert~~, B J~~]]	+	[[Category: Goulding CW]]
-	[[Category: Goulding~~, C W~~]]	+	[[Category: Nainar S]]
-	[[Category: Nainar, S]]	+	[[Category: Spitale RC]]
-	[[Category: Spitale~~, R C]]~~	+
-	~~[[Category: Azide]]~~	+
-	~~[[Category: Complex]]~~	+
-	~~[[Category: Cytosolic protein]]~~	+
-	~~[[Category: Kinase]]~~	+
-	~~[[Category: Uck2]]~~	+
-	~~[[Category: Uridine-cytidine kinase 2~~]]	+

OCA at 07:24, 19 February 2020

OCA — Wed, 19 Feb 2020 07:24:17 GMT

←Older revision		Revision as of 07:24, 19 February 2020
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	<StructureSection load='6n54' size='340' side='right'caption='[[6n54]], [[Resolution\|resolution]] 2.42Å' scene=''>		<StructureSection load='6n54' size='340' side='right'caption='[[6n54]], [[Resolution\|resolution]] 2.42Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6n54]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6N54 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6N54 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6n54]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6N54 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6N54 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=KEA:2-azido-2-deoxycytidine+5-(dihydrogen+phosphate)'>KEA</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=KEA:2-azido-2-deoxycytidine+5-(dihydrogen+phosphate)'>KEA</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">UCK2, UMPK ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Uridine_kinase Uridine kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.48 2.7.1.48] </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_kinase Uridine kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.48 2.7.1.48] </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=6n54 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6n54 OCA], [http://pdbe.org/6n54 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6n54 RCSB], [http://www.ebi.ac.uk/pdbsum/6n54 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6n54 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=6n54 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6n54 OCA], [http://pdbe.org/6n54 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6n54 RCSB], [http://www.ebi.ac.uk/pdbsum/6n54 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6n54 ProSAT]</span></td></tr>
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	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/UCK2_HUMAN UCK2_HUMAN]] Phosphorylates uridine and cytidine to uridine monophosphate and cytidine monophosphate. Does not phosphorylate deoxyribonucleosides or purine ribonucleosides. Can use ATP or GTP as a phosphate donor. Can also phosphorylate cytidine and uridine nucleoside analogs such as 6-azauridine, 5-fluorouridine, 4-thiouridine, 5-bromouridine, N(4)-acetylcytidine, N(4)-benzoylcytidine, 5-fluorocytidine, 2-thiocytidine, 5-methylcytidine, and N(4)-anisoylcytidine.		[[http://www.uniprot.org/uniprot/UCK2_HUMAN UCK2_HUMAN]] Phosphorylates uridine and cytidine to uridine monophosphate and cytidine monophosphate. Does not phosphorylate deoxyribonucleosides or purine ribonucleosides. Can use ATP or GTP as a phosphate donor. Can also phosphorylate cytidine and uridine nucleoside analogs such as 6-azauridine, 5-fluorouridine, 4-thiouridine, 5-bromouridine, N(4)-acetylcytidine, N(4)-benzoylcytidine, 5-fluorocytidine, 2-thiocytidine, 5-methylcytidine, and N(4)-anisoylcytidine.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Tissues and organs are composed of diverse cell types, which poses a major challenge for cell-type-specific profiling of gene expression. Current metabolic labeling methods rely on exogenous pyrimidine analogs that are only incorporated into RNA in cells expressing an exogenous enzyme. This approach assumes that off-target cells cannot incorporate these analogs. We disprove this assumption and identify and characterize the enzymatic pathways responsible for high background incorporation. We demonstrate that mammalian cells can incorporate uracil analogs and characterize the enzymatic pathways responsible for high background incorporation. To overcome these limitations, we developed a new small molecule-enzyme pair consisting of uridine/cytidine kinase 2 and 2'-azidouridine. We demonstrate that 2'-azidouridine is only incorporated in cells expressing uridine/cytidine kinase 2 and characterize selectivity mechanisms using molecular dynamics and X-ray crystallography. Furthermore, this pair can be used to purify and track RNA from specific cellular populations, making it ideal for high-resolution cell-specific RNA labeling. Overall, these results reveal new aspects of mammalian salvage pathways and serve as a new benchmark for designing, characterizing and evaluating methodologies for cell-specific labeling of biomolecules.
		+
		+	An optimized chemical-genetic method for cell-specific metabolic labeling of RNA.,Nainar S, Cuthbert BJ, Lim NM, England WE, Ke K, Sophal K, Quechol R, Mobley DL, Goulding CW, Spitale RC Nat Methods. 2020 Feb 3. pii: 10.1038/s41592-019-0726-y. doi:, 10.1038/s41592-019-0726-y. PMID:32015544<ref>PMID:32015544</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6n54" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Uridine kinase]]		[[Category: Uridine kinase]]

OCA at 06:49, 27 November 2019

OCA — Wed, 27 Nov 2019 06:49:33 GMT

←Older revision		Revision as of 06:49, 27 November 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6n54 is ~~ON HOLD until Nov 21 2020~~	+	==Crystal structure of human uridine-cytidine kinase 2 complexed with 2'-azidocytidine monophosphate==
-		+	<StructureSection load='6n54' size='340' side='right'caption='[[6n54]], [[Resolution\|resolution]] 2.42Å' scene=''>
-	~~Authors~~: ~~Cuthbert~~, B.J., ~~Nainar~~, S., ~~Spitale~~, R.C., ~~Goulding, C~~.W.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6n54]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6N54 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6N54 FirstGlance]. <br>
-	~~Description~~: ~~Crystal structure of human~~ uridine-cytidine ~~kinase~~ 2 ~~complexed with 2'~~-~~azidocytidine monophosphate~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=KEA:2-azido-2-deoxycytidine+5-(dihydrogen+phosphate)'>KEA</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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/Uridine_kinase Uridine kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.48 2.7.1.48] </span></td></tr>
-	[[Category: Cuthbert, B.J]]	+	<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=6n54 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6n54 OCA], [http://pdbe.org/6n54 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6n54 RCSB], [http://www.ebi.ac.uk/pdbsum/6n54 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6n54 ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/UCK2_HUMAN UCK2_HUMAN]] Phosphorylates uridine and cytidine to uridine monophosphate and cytidine monophosphate. Does not phosphorylate deoxyribonucleosides or purine ribonucleosides. Can use ATP or GTP as a phosphate donor. Can also phosphorylate cytidine and uridine nucleoside analogs such as 6-azauridine, 5-fluorouridine, 4-thiouridine, 5-bromouridine, N(4)-acetylcytidine, N(4)-benzoylcytidine, 5-fluorocytidine, 2-thiocytidine, 5-methylcytidine, and N(4)-anisoylcytidine.
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Uridine kinase]]
		+	[[Category: Cuthbert, B J]]
		+	[[Category: Goulding, C W]]
	[[Category: Nainar, S]]		[[Category: Nainar, S]]
-	[[Category: ~~Goulding~~, C.W]]	+	[[Category: Spitale, R C]]
-	[[Category: ~~Spitale, R.C~~]]	+	[[Category: Azide]]
		+	[[Category: Complex]]
		+	[[Category: Cytosolic protein]]
		+	[[Category: Kinase]]
		+	[[Category: Uck2]]
		+	[[Category: Uridine-cytidine kinase 2]]

OCA at 06:25, 30 January 2019

OCA — Wed, 30 Jan 2019 06:25:16 GMT

←Older revision		Revision as of 06:25, 30 January 2019
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6n54 is ON HOLD	+	The entry 6n54 is ON HOLD until Nov 21 2020

	Authors: Cuthbert, B.J., Nainar, S., Spitale, R.C., Goulding, C.W.		Authors: Cuthbert, B.J., Nainar, S., Spitale, R.C., Goulding, C.W.

OCA: Protected "6n54" [edit=sysop:move=sysop]

OCA — Sun, 02 Dec 2018 19:17:43 GMT

Protected "6n54" [edit=sysop:move=sysop]

←Older revision

Revision as of 19:17, 2 December 2018

OCA: New page: '''Unreleased structure''' The entry 6n54 is ON HOLD Authors: Cuthbert, B.J., Nainar, S., Spitale, R.C., Goulding, C.W. Description: Crystal structure of human uridine-cytidine kinase ...

OCA — Sun, 02 Dec 2018 19:17:41 GMT

New page: '''Unreleased structure''' The entry 6n54 is ON HOLD Authors: Cuthbert, B.J., Nainar, S., Spitale, R.C., Goulding, C.W. Description: Crystal structure of human uridine-cytidine kinase ...

New page

'''Unreleased structure'''

The entry 6n54 is ON HOLD

Authors: Cuthbert, B.J., Nainar, S., Spitale, R.C., Goulding, C.W.

Description: Crystal structure of human uridine-cytidine kinase 2 complexed with 2'-azidocytidine monophosphate
[[Category: Unreleased Structures]]
[[Category: Cuthbert, B.J]]
[[Category: Nainar, S]]
[[Category: Goulding, C.W]]
[[Category: Spitale, R.C]]