6ybh - Revision history

OCA at 11:52, 1 February 2024

OCA — Thu, 01 Feb 2024 11:52:23 GMT

←Older revision		Revision as of 11:52, 1 February 2024
Line 3:		Line 3:
	<StructureSection load='6ybh' size='340' side='right'caption='[[6ybh]], [[Resolution\|resolution]] 2.40Å' scene=''>		<StructureSection load='6ybh' size='340' side='right'caption='[[6ybh]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6ybh]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Drome Drome~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6YBH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6YBH FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6ybh]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Drosophila_melanogaster Drosophila melanogaster]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6YBH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6YBH FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=8LK:Pyrrolo~~-~~dC'>8LK</scene>~~, ~~<scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 2.4Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~dnk, CG5452 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=~~5&id=7227 DROME])</td~~></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=8LK:Pyrrolo-dC'>8LK</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<~~tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks~~'>~~[https://en.wikipedia.org/wiki/Deoxynucleoside_kinase Deoxynucleoside kinase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.145 2.7.1.145]~~ </~~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=6ybh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ybh OCA], [https://pdbe.org/6ybh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6ybh RCSB], [https://www.ebi.ac.uk/pdbsum/6ybh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6ybh 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=6ybh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ybh OCA], [https://pdbe.org/6ybh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6ybh RCSB], [https://www.ebi.ac.uk/pdbsum/6ybh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6ybh ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/DNK_DROME DNK_DROME]] Deoxyribonucleoside kinase that has a broad specificity phosphorylating thymidine, deoxyadenosine, deoxycytidine and deoxyguanosine. Specificity is higher for pyrimidine nucleosides. Several anti-viral and anti-cancer nucleoside analogs are also efficiently phosphorylated.<ref>PMID:10446143</ref> <ref>PMID:10692477</ref> <ref>PMID:16008571</ref>	+	[https://www.uniprot.org/uniprot/DNK_DROME DNK_DROME] Deoxyribonucleoside kinase that has a broad specificity phosphorylating thymidine, deoxyadenosine, deoxycytidine and deoxyguanosine. Specificity is higher for pyrimidine nucleosides. Several anti-viral and anti-cancer nucleoside analogs are also efficiently phosphorylated.<ref>PMID:10446143</ref> <ref>PMID:10692477</ref> <ref>PMID:16008571</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Imaging of gene-expression patterns in live animals is difficult to achieve with fluorescent proteins because tissues are opaque to visible light. Imaging of transgene expression with magnetic resonance imaging (MRI), which penetrates to deep tissues, has been limited by single reporter visualization capabilities. Moreover, the low-throughput capacity of MRI limits large-scale mutagenesis strategies to improve existing reporters. Here we develop an MRI system, called GeneREFORM, comprising orthogonal reporters for two-color imaging of transgene expression in deep tissues. Starting from two promiscuous deoxyribonucleoside kinases, we computationally designed highly active, orthogonal enzymes ('reporter genes') that specifically phosphorylate two MRI-detectable synthetic deoxyribonucleosides ('reporter probes'). Systemically administered reporter probes exclusively accumulate in cells expressing the designed reporter genes, and their distribution is displayed as pseudo-colored MRI maps based on dynamic proton exchange for noninvasive visualization of transgene expression. We envision that future extensions of GeneREFORM will pave the way to multiplexed deep-tissue mapping of gene expression in live animals.
		+
		+	Computationally designed dual-color MRI reporters for noninvasive imaging of transgene expression.,Allouche-Arnon H, Khersonsky O, Tirukoti ND, Peleg Y, Dym O, Albeck S, Brandis A, Mehlman T, Avram L, Harris T, Yadav NN, Fleishman SJ, Bar-Shir A Nat Biotechnol. 2022 Jul;40(7):1143-1149. doi: 10.1038/s41587-021-01162-5. Epub , 2022 Jan 31. PMID:35102291<ref>PMID:35102291</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6ybh" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Deoxynucleoside kinase]]~~	+	[[Category: Drosophila melanogaster]]
-	~~[[Category: Drome~~]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Allouche-Arnon, H]]	+	[[Category: Allouche-Arnon H]]
-	[[Category: Bar-Shir, A]]	+	[[Category: Bar-Shir A]]
-	[[Category: Dym, O]]	+	[[Category: Dym O]]
-	~~[[Category: Transferase~~]]	+

OCA at 14:08, 17 November 2021

OCA — Wed, 17 Nov 2021 14:08:19 GMT

←Older revision		Revision as of 14:08, 17 November 2021
Line 1:		Line 1:

	==Deoxyribonucleoside Kinase==		==Deoxyribonucleoside Kinase==
-	<StructureSection load='6ybh' size='340' side='right'caption='[[6ybh]]' scene=''>	+	<StructureSection load='6ybh' size='340' side='right'caption='[[6ybh]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6YBH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6YBH FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6ybh]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Drome Drome]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6YBH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6YBH FirstGlance]. <br>
-	</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=6ybh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ybh OCA], [https://pdbe.org/6ybh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6ybh RCSB], [https://www.ebi.ac.uk/pdbsum/6ybh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6ybh ProSAT]</span></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=8LK:Pyrrolo-dC'>8LK</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dnk, CG5452 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=7227 DROME])</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Deoxynucleoside_kinase Deoxynucleoside kinase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.145 2.7.1.145] </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=6ybh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ybh OCA], [https://pdbe.org/6ybh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6ybh RCSB], [https://www.ebi.ac.uk/pdbsum/6ybh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6ybh ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[https://www.uniprot.org/uniprot/DNK_DROME DNK_DROME]] Deoxyribonucleoside kinase that has a broad specificity phosphorylating thymidine, deoxyadenosine, deoxycytidine and deoxyguanosine. Specificity is higher for pyrimidine nucleosides. Several anti-viral and anti-cancer nucleoside analogs are also efficiently phosphorylated.<ref>PMID:10446143</ref> <ref>PMID:10692477</ref> <ref>PMID:16008571</ref>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Deoxynucleoside kinase]]
		+	[[Category: Drome]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Allouche-Arnon H]]	+	[[Category: Allouche-Arnon, H]]
-	[[Category: Bar-~~Sgir~~ A]]	+	[[Category: Bar-Shir, A]]
-	[[Category: Dym O]]	+	[[Category: Dym, O]]
		+	[[Category: Transferase]]

OCA at 10:29, 31 March 2021

OCA — Wed, 31 Mar 2021 10:29:48 GMT

←Older revision		Revision as of 10:29, 31 March 2021
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6ybh ~~is ON HOLD until Paper Publication~~	+	==Deoxyribonucleoside Kinase==
-		+	<StructureSection load='6ybh' size='340' side='right'caption='[[6ybh]]' scene=''>
-	~~Authors~~: ~~Allouche~~-~~Arnon, H~~., ~~Bar~~-~~Sgir~~, A., ~~Dym~~, O.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6YBH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6YBH FirstGlance]. <br>
-	~~Description: Deoxyribonucleoside Kinase~~	+	</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=6ybh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ybh OCA], [https://pdbe.org/6ybh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6ybh RCSB], [https://www.ebi.ac.uk/pdbsum/6ybh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6ybh ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
-	[[Category: Allouche-Arnon, H]]	+	__TOC__
-	[[Category: Bar-Sgir, A]]	+	</StructureSection>
-	[[Category: Dym, O]]	+	[[Category: Large Structures]]
		+	[[Category: Allouche-Arnon H]]
		+	[[Category: Bar-Sgir A]]
		+	[[Category: Dym O]]

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

OCA — Fri, 27 Mar 2020 08:35:35 GMT

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

←Older revision

Revision as of 08:35, 27 March 2020

OCA: New page: '''Unreleased structure''' The entry 6ybh is ON HOLD until Paper Publication Authors: Allouche-Arnon, H., Bar-Sgir, A., Dym, O. Description: Deoxyribonucleoside Kinase [[Category: Unre...

OCA — Fri, 27 Mar 2020 08:35:33 GMT

New page: '''Unreleased structure''' The entry 6ybh is ON HOLD until Paper Publication Authors: Allouche-Arnon, H., Bar-Sgir, A., Dym, O. Description: Deoxyribonucleoside Kinase [[Category: Unre...

New page

'''Unreleased structure'''

The entry 6ybh is ON HOLD until Paper Publication

Authors: Allouche-Arnon, H., Bar-Sgir, A., Dym, O.

Description: Deoxyribonucleoside Kinase
[[Category: Unreleased Structures]]
[[Category: Allouche-Arnon, H]]
[[Category: Bar-Sgir, A]]
[[Category: Dym, O]]