3qen - Revision history

OCA at 11:43, 14 March 2024

OCA — Thu, 14 Mar 2024 11:43:12 GMT

←Older revision		Revision as of 11:43, 14 March 2024
Line 3:		Line 3:
	<StructureSection load='3qen' size='340' side='right'caption='[[3qen]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='3qen' size='340' side='right'caption='[[3qen]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3qen]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Human Human~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QEN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3QEN FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3qen]] 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=3QEN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3QEN FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=5BT:5~~-~~BROMO-2-DEOXYCYTIDINE'>5BT</scene>~~, ~~<scene name='pdbligand=UDP:URIDINE-5-DIPHOSPHATE'>UDP</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]] 1.997Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>~~[[~~Related_structure~~\|~~Related:~~]]~~</b></td><td class="sblockDat"><div style='overflow: auto~~; ~~max-height: 3em;'>[[3qej\|3qej]], [[3qeo\|3qeo]]</div>~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5BT:5-BROMO-2-DEOXYCYTIDINE'>5BT</scene>, <scene name='pdbligand=UDP:URIDINE-5-DIPHOSPHATE'>UDP</scene></td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>DCK ([https://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~~'>~~[https://en.wikipedia.org/wiki/Deoxycytidine_kinase Deoxycytidine kinase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.74 2.7.1.74]~~ </~~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=3qen FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qen OCA], [https://pdbe.org/3qen PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3qen RCSB], [https://www.ebi.ac.uk/pdbsum/3qen PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3qen 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=3qen FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qen OCA], [https://pdbe.org/3qen PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3qen RCSB], [https://www.ebi.ac.uk/pdbsum/3qen PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3qen ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/DCK_HUMAN DCK_HUMAN]] Required for the phosphorylation of the deoxyribonucleosides deoxycytidine (dC), deoxyguanosine (dG) and deoxyadenosine (dA). Has broad substrate specificity, and does not display selectivity based on the chirality of the substrate. It is also an essential enzyme for the phosphorylation of numerous nucleoside analogs widely employed as antiviral and chemotherapeutic agents.<ref>PMID:18377927</ref> <ref>PMID:20614893</ref>	+	[https://www.uniprot.org/uniprot/DCK_HUMAN DCK_HUMAN] Required for the phosphorylation of the deoxyribonucleosides deoxycytidine (dC), deoxyguanosine (dG) and deoxyadenosine (dA). Has broad substrate specificity, and does not display selectivity based on the chirality of the substrate. It is also an essential enzyme for the phosphorylation of numerous nucleoside analogs widely employed as antiviral and chemotherapeutic agents.<ref>PMID:18377927</ref> <ref>PMID:20614893</ref>
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	Deoxycytidine kinase (dCK) uses either ATP or UTP as phosphoryl donors to catalyze the phosphorylation of nucleoside acceptors. The kinetic properties of human dCK are modulated in vivo by phosphorylation of serine 74. This residue is a part of the insert region and is situated distant to the active site. Replacing the serine with a glutamic acid (S74E variant) can mimic phosphorylation of Ser74. To understand how phosphorylation affects the catalytic properties of dCK, we examined the S74E variant of dCK both structurally and kinetically. We observe that the presence of a glutamic acid at position 74 favors the enzyme adopting the open conformation. Glu74 stabilizes the open conformation by directly interacting with the indole side chain of Trp58, a residue that is in close proximity to the base of the nucleoside substrate. The open dCK conformation is competent for the binding of nucleoside but not for phosphoryl transfer. In contrast, the closed conformation is competent for phosphoryl transfer but not for product release. Thus, dCK must transition between the open and closed states during the catalytic cycle. We propose a reaction scheme for dCK that incorporates the transition between the open and closed states, and this serves to rationalize the observed kinetic differences between wild type dCK and the S74E variant.	+
-		+
-	Post-translational phosphorylation of serine 74 of human deoxycytidine kinase favors the enzyme adopting the open conformation making it competent for nucleoside binding and release.,Hazra S, Szewczak A, Ort S, Konrad M, Lavie A Biochemistry. 2011 Feb 25. PMID:21351740<ref>PMID:21351740</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 3qen" style="background-color:#fffaf0;"></div~~>	+

	==See Also==		==See Also==
Line 28:		Line 17:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Deoxycytidine kinase]]~~	+	[[Category: Homo sapiens]]
-	~~[[Category: Human~~]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Hazra, S]]	+	[[Category: Hazra S]]
-	[[Category: Lavie, A]]	+	[[Category: Lavie A]]
-	~~[[Category: Alpha/beta]]~~	+
-	~~[[Category: Phosphoryl transfer]]~~	+
-	~~[[Category: Phosphorylation]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 06:05, 8 June 2022

OCA — Wed, 08 Jun 2022 06:05:27 GMT

←Older revision		Revision as of 06:05, 8 June 2022
Line 1:		Line 1:

	==S74E dCK in complex with 5-bromodeoxycytidine and UDP==		==S74E dCK in complex with 5-bromodeoxycytidine and UDP==
-	<StructureSection load='3qen' size='340' side='right' caption='[[3qen]], [[Resolution\|resolution]] 2.00Å' scene=''>	+	<StructureSection load='3qen' size='340' side='right'caption='[[3qen]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3qen]] 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=3QEN OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3QEN FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3qen]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QEN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3QEN FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=5BT:5-BROMO-2-DEOXYCYTIDINE'>5BT</scene>, <scene name='pdbligand=UDP:URIDINE-5-DIPHOSPHATE'>UDP</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5BT:5-BROMO-2-DEOXYCYTIDINE'>5BT</scene>, <scene name='pdbligand=UDP:URIDINE-5-DIPHOSPHATE'>UDP</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3qej\|3qej]], [[3qeo\|3qeo]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3qej\|3qej]], [[3qeo\|3qeo]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">DCK ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">DCK ([https://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/Deoxycytidine_kinase Deoxycytidine kinase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.74 2.7.1.74] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Deoxycytidine_kinase Deoxycytidine kinase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.74 2.7.1.74] </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=3qen FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qen OCA], [~~http~~://pdbe.org/3qen PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3qen RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3qen PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3qen 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=3qen FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qen OCA], [https://pdbe.org/3qen PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3qen RCSB], [https://www.ebi.ac.uk/pdbsum/3qen PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3qen ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/DCK_HUMAN DCK_HUMAN]] Required for the phosphorylation of the deoxyribonucleosides deoxycytidine (dC), deoxyguanosine (dG) and deoxyadenosine (dA). Has broad substrate specificity, and does not display selectivity based on the chirality of the substrate. It is also an essential enzyme for the phosphorylation of numerous nucleoside analogs widely employed as antiviral and chemotherapeutic agents.<ref>PMID:18377927</ref> <ref>PMID:20614893</ref>	+	[[https://www.uniprot.org/uniprot/DCK_HUMAN DCK_HUMAN]] Required for the phosphorylation of the deoxyribonucleosides deoxycytidine (dC), deoxyguanosine (dG) and deoxyadenosine (dA). Has broad substrate specificity, and does not display selectivity based on the chirality of the substrate. It is also an essential enzyme for the phosphorylation of numerous nucleoside analogs widely employed as antiviral and chemotherapeutic agents.<ref>PMID:18377927</ref> <ref>PMID:20614893</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 23:		Line 23:

	==See Also==		==See Also==
-	*[[Deoxycytidine kinase\|Deoxycytidine kinase]]	+	*[[Deoxycytidine kinase 3D structures\|Deoxycytidine kinase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 30:		Line 30:
	[[Category: Deoxycytidine kinase]]		[[Category: Deoxycytidine kinase]]
	[[Category: Human]]		[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Hazra, S]]		[[Category: Hazra, S]]
	[[Category: Lavie, A]]		[[Category: Lavie, A]]

OCA at 09:13, 4 August 2016

OCA — Thu, 04 Aug 2016 09:13:42 GMT

←Older revision		Revision as of 09:13, 4 August 2016
Line 1:		Line 1:
		+
	==S74E dCK in complex with 5-bromodeoxycytidine and UDP==		==S74E dCK in complex with 5-bromodeoxycytidine and UDP==
	<StructureSection load='3qen' size='340' side='right' caption='[[3qen]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='3qen' size='340' side='right' caption='[[3qen]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3qen]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Homo_sapiens Homo sapiens~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QEN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3QEN FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3qen]] 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=3QEN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3QEN FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=5BT:5-BROMO-2-DEOXYCYTIDINE'>5BT</scene>, <scene name='pdbligand=UDP:URIDINE-5-DIPHOSPHATE'>UDP</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=5BT:5-BROMO-2-DEOXYCYTIDINE'>5BT</scene>, <scene name='pdbligand=UDP:URIDINE-5-DIPHOSPHATE'>UDP</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3qej\|3qej]], [[3qeo\|3qeo]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3qej\|3qej]], [[3qeo\|3qeo]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">DCK ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 ~~Homo sapiens~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">DCK ([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/Deoxycytidine_kinase Deoxycytidine kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.74 2.7.1.74] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Deoxycytidine_kinase Deoxycytidine kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.74 2.7.1.74] </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=3qen FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qen OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3qen RCSB], [http://www.ebi.ac.uk/pdbsum/3qen 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=3qen FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qen OCA], [http://pdbe.org/3qen PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3qen RCSB], [http://www.ebi.ac.uk/pdbsum/3qen PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3qen 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 3qen" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 27:		Line 29:
	</StructureSection>		</StructureSection>
	[[Category: Deoxycytidine kinase]]		[[Category: Deoxycytidine kinase]]
-	[[Category: ~~Homo sapiens~~]]	+	[[Category: Human]]
	[[Category: Hazra, S]]		[[Category: Hazra, S]]
	[[Category: Lavie, A]]		[[Category: Lavie, A]]

OCA at 07:42, 25 December 2014

OCA — Thu, 25 Dec 2014 07:42:31 GMT

←Older revision		Revision as of 07:42, 25 December 2014
Line 9:		Line 9:
	<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=3qen FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qen OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3qen RCSB], [http://www.ebi.ac.uk/pdbsum/3qen 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=3qen FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qen OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3qen RCSB], [http://www.ebi.ac.uk/pdbsum/3qen PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/DCK_HUMAN DCK_HUMAN]] Required for the phosphorylation of the deoxyribonucleosides deoxycytidine (dC), deoxyguanosine (dG) and deoxyadenosine (dA). Has broad substrate specificity, and does not display selectivity based on the chirality of the substrate. It is also an essential enzyme for the phosphorylation of numerous nucleoside analogs widely employed as antiviral and chemotherapeutic agents.<ref>PMID:18377927</ref> <ref>PMID:20614893</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==

OCA at 10:46, 19 December 2014

OCA — Fri, 19 Dec 2014 10:46:16 GMT

←Older revision		Revision as of 10:46, 19 December 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_3qen\| PDB=3qen \| SCENE= }}~~	+	==S74E dCK in complex with 5-bromodeoxycytidine and UDP==
-	===S74E dCK in complex with 5-bromodeoxycytidine and UDP===	+	<StructureSection load='3qen' size='340' side='right' caption='[[3qen]], [[Resolution\|resolution]] 2.00Å' scene=''>
-	~~{{ABSTRACT_PUBMED_21351740}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3qen]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QEN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3QEN FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=5BT:5-BROMO-2-DEOXYCYTIDINE'>5BT</scene>, <scene name='pdbligand=UDP:URIDINE-5-DIPHOSPHATE'>UDP</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3qej\|3qej]], [[3qeo\|3qeo]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">DCK ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Deoxycytidine_kinase Deoxycytidine kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.74 2.7.1.74] </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=3qen FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qen OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3qen RCSB], [http://www.ebi.ac.uk/pdbsum/3qen PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Deoxycytidine kinase (dCK) uses either ATP or UTP as phosphoryl donors to catalyze the phosphorylation of nucleoside acceptors. The kinetic properties of human dCK are modulated in vivo by phosphorylation of serine 74. This residue is a part of the insert region and is situated distant to the active site. Replacing the serine with a glutamic acid (S74E variant) can mimic phosphorylation of Ser74. To understand how phosphorylation affects the catalytic properties of dCK, we examined the S74E variant of dCK both structurally and kinetically. We observe that the presence of a glutamic acid at position 74 favors the enzyme adopting the open conformation. Glu74 stabilizes the open conformation by directly interacting with the indole side chain of Trp58, a residue that is in close proximity to the base of the nucleoside substrate. The open dCK conformation is competent for the binding of nucleoside but not for phosphoryl transfer. In contrast, the closed conformation is competent for phosphoryl transfer but not for product release. Thus, dCK must transition between the open and closed states during the catalytic cycle. We propose a reaction scheme for dCK that incorporates the transition between the open and closed states, and this serves to rationalize the observed kinetic differences between wild type dCK and the S74E variant.

-	~~==Function==~~	+	Post-translational phosphorylation of serine 74 of human deoxycytidine kinase favors the enzyme adopting the open conformation making it competent for nucleoside binding and release.,Hazra S, Szewczak A, Ort S, Konrad M, Lavie A Biochemistry. 2011 Feb 25. PMID:21351740<ref>PMID:21351740</ref>
-	~~[[http://www.uniprot.org/uniprot/DCK_HUMAN DCK_HUMAN]] Required for the~~ phosphorylation of ~~the deoxyribonucleosides~~ deoxycytidine ~~(dC), deoxyguanosine (dG) and deoxyadenosine (dA). Has broad substrate specificity, and does not display selectivity based on~~ the ~~chirality of~~ the ~~substrate. It is also an essential enzyme~~ for ~~the phosphorylation of numerous~~ nucleoside ~~analogs widely employed as antiviral~~ and ~~chemotherapeutic agents~~.~~<ref>~~PMID:~~18377927</ref>~~ <ref>PMID:~~20614893~~</ref>	+

-	~~==About this Structure==~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[3qen]] is~~ a ~~2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Homo_sapiens Homo sapiens]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=3QEN OCA].~~	+	</div>

	==See Also==		==See Also==
	*[[Deoxycytidine kinase\|Deoxycytidine kinase]]		*[[Deoxycytidine kinase\|Deoxycytidine kinase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	~~<ref group="xtra">PMID:021351740</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Deoxycytidine kinase]]		[[Category: Deoxycytidine kinase]]
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
-	[[Category: Hazra, S.]]	+	[[Category: Hazra, S]]
-	[[Category: Lavie, A.]]	+	[[Category: Lavie, A]]
	[[Category: Alpha/beta]]		[[Category: Alpha/beta]]
	[[Category: Phosphoryl transfer]]		[[Category: Phosphoryl transfer]]
	[[Category: Phosphorylation]]		[[Category: Phosphorylation]]
	[[Category: Transferase]]		[[Category: Transferase]]

OCA at 08:13, 8 May 2013

OCA — Wed, 08 May 2013 08:13:31 GMT

←Older revision		Revision as of 08:13, 8 May 2013
Line 1:		Line 1:
-	[[Image:3qen.png\|left\|200px]]
-
-	<!--
-	The line below this paragraph, containing "STRUCTURE_3qen", creates the "Structure Box" on the page.
-	You may change the PDB parameter (which sets the PDB file loaded into the applet)
-	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-	or leave the SCENE parameter empty for the default display.
-	-->
	{{STRUCTURE_3qen\| PDB=3qen \| SCENE= }}		{{STRUCTURE_3qen\| PDB=3qen \| SCENE= }}
-
	===S74E dCK in complex with 5-bromodeoxycytidine and UDP===		===S74E dCK in complex with 5-bromodeoxycytidine and UDP===
		+	{{ABSTRACT_PUBMED_21351740}}

-		+	==Function==
-	~~<!--~~	+	[[http://www.uniprot.org/uniprot/DCK_HUMAN DCK_HUMAN]] Required for the phosphorylation of the deoxyribonucleosides deoxycytidine (dC), deoxyguanosine (dG) and deoxyadenosine (dA). Has broad substrate specificity, and does not display selectivity based on the chirality of the substrate. It is also an essential enzyme for the phosphorylation of numerous nucleoside analogs widely employed as antiviral and chemotherapeutic agents.<ref>PMID:18377927</ref> <ref>PMID:20614893</ref>
-	~~The line below this paragraph, {{ABSTRACT_PUBMED_21351740}}, adds the Publication Abstract to the page~~	+
-	~~(as it appears on PubMed at~~ http://www.~~pubmed~~.~~gov~~), ~~where 21351740~~ is the ~~PubMed ID number~~.	+
-	-->	+
-	~~{{ABSTRACT_PUBMED_21351740}}~~	+

	==About this Structure==		==About this Structure==
	[[3qen]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QEN OCA].		[[3qen]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QEN OCA].
		+
		+	==See Also==
		+	*[[Deoxycytidine kinase\|Deoxycytidine kinase]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~21351740~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:021351740</ref><references group="xtra"/><references/>
	[[Category: Deoxycytidine kinase]]		[[Category: Deoxycytidine kinase]]
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Hazra, S.]]		[[Category: Hazra, S.]]
	[[Category: Lavie, A.]]		[[Category: Lavie, A.]]
		+	[[Category: Alpha/beta]]
		+	[[Category: Phosphoryl transfer]]
		+	[[Category: Phosphorylation]]
		+	[[Category: Transferase]]

OCA at 09:56, 21 April 2011

OCA — Thu, 21 Apr 2011 09:56:31 GMT

←Older revision		Revision as of 09:56, 21 April 2011
Line 1:		Line 1:
-	[[Image:3qen.~~jpg~~\|left\|200px]]	+	[[Image:3qen.png\|left\|200px]]

	<!--		<!--

OCA at 08:22, 16 March 2011

OCA — Wed, 16 Mar 2011 08:22:20 GMT

←Older revision		Revision as of 08:22, 16 March 2011
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	[[Image:3qen.jpg\|left\|200px]]

-	The ~~entry 3qen~~ is ~~ON HOLD~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_3qen", creates the "Structure Box" on the page.
		+	You may change the PDB parameter (which sets the PDB file loaded into the applet)
		+	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
		+	or leave the SCENE parameter empty for the default display.
		+	-->
		+	{{STRUCTURE_3qen\| PDB=3qen \| SCENE= }}

-	~~Authors: Lavie, A., Hazra, S.~~	+	===S74E dCK in complex with 5-bromodeoxycytidine and UDP===

-	~~Description~~: ~~S74E dCK in complex~~ with 5-~~bromodeoxycytidine and UDP~~	+
		+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_21351740}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 21351740 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_21351740}}
		+
		+	==About this Structure==
		+	[[3qen]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QEN OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:21351740</ref><references group="xtra"/>
		+	[[Category: Deoxycytidine kinase]]
		+	[[Category: Homo sapiens]]
		+	[[Category: Hazra, S.]]
		+	[[Category: Lavie, A.]]

OCA: Protected "3qen" [edit=sysop:move=sysop]

OCA — Wed, 26 Jan 2011 12:47:36 GMT

Protected "3qen" [edit=sysop:move=sysop]

←Older revision

Revision as of 12:47, 26 January 2011

OCA: New page: '''Unreleased structure''' The entry 3qen is ON HOLD Authors: Lavie, A., Hazra, S. Description: S74E dCK in complex with 5-bromodeoxycytidine and UDP

OCA — Wed, 26 Jan 2011 12:47:35 GMT

New page: '''Unreleased structure''' The entry 3qen is ON HOLD Authors: Lavie, A., Hazra, S. Description: S74E dCK in complex with 5-bromodeoxycytidine and UDP

New page

'''Unreleased structure'''

The entry 3qen is ON HOLD

Authors: Lavie, A., Hazra, S.

Description: S74E dCK in complex with 5-bromodeoxycytidine and UDP