7zee - Revision history

OCA at 13:31, 1 February 2024

2024-02-01T13:31:19Z

←Older revision		Revision as of 13:31, 1 February 2024
Line 3:		Line 3:
	<StructureSection load='7zee' size='340' side='right'caption='[[7zee]], [[Resolution\|resolution]] 1.36Å' scene=''>		<StructureSection load='7zee' size='340' side='right'caption='[[7zee]], [[Resolution\|resolution]] 1.36Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[7zee]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7ZEE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7ZEE FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7zee]] is a 1 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=7ZEE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7ZEE FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 1.36Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=7zee FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7zee OCA], [https://pdbe.org/7zee PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7zee RCSB], [https://www.ebi.ac.uk/pdbsum/7zee PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7zee 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=7zee FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7zee OCA], [https://pdbe.org/7zee PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7zee RCSB], [https://www.ebi.ac.uk/pdbsum/7zee PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7zee ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/5NT3B_HUMAN 5NT3B_HUMAN]] Specifically hydrolyzes 7-methylguanosine monophosphate (m(7)GMP) to 7-methylguanosine and inorganic phosphate (PubMed:23223233, PubMed:24603684). The specific activity for m(7)GMP may protect cells against undesired salvage of m(7)GMP and its incorporation into nucleic acids (PubMed:23223233). Also has weak activity for CMP (PubMed:23223233, PubMed:24603684). UMP and purine nucleotides are poor substrates (PubMed:23223233).<ref>PMID:23223233</ref> <ref>PMID:24603684</ref>	+	[https://www.uniprot.org/uniprot/5NT3B_HUMAN 5NT3B_HUMAN] Specifically hydrolyzes 7-methylguanosine monophosphate (m(7)GMP) to 7-methylguanosine and inorganic phosphate (PubMed:23223233, PubMed:24603684). The specific activity for m(7)GMP may protect cells against undesired salvage of m(7)GMP and its incorporation into nucleic acids (PubMed:23223233). Also has weak activity for CMP (PubMed:23223233, PubMed:24603684). UMP and purine nucleotides are poor substrates (PubMed:23223233).<ref>PMID:23223233</ref> <ref>PMID:24603684</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 22:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Baranowski~~, M R~~]]	+	[[Category: Baranowski MR]]
-	[[Category: Basquin, J]]	+	[[Category: Basquin J]]
-	[[Category: Jemielity, J]]	+	[[Category: Jemielity J]]
-	[[Category: Kowalska, J]]	+	[[Category: Kowalska J]]
-	[[Category: Kozarski, M]]	+	[[Category: Kozarski M]]
-	[[Category: Kubacka, D]]	+	[[Category: Kubacka D]]
-	[[Category: Wojcik, R]]	+	[[Category: Wojcik R]]
-	~~[[Category: Cytosolic 5' nucleotidase]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Mrna cap degradation]]~~	+
-	~~[[Category: N7 methylguanosine monophosphate dephosphorylation]]~~	+
-	~~[[Category: Nucleotide level regulation~~]]	+

OCA at 05:38, 8 June 2022

2022-06-08T05:38:04Z

←Older revision		Revision as of 05:38, 8 June 2022
Line 9:		Line 9:
	== Function ==		== Function ==
	[[https://www.uniprot.org/uniprot/5NT3B_HUMAN 5NT3B_HUMAN]] Specifically hydrolyzes 7-methylguanosine monophosphate (m(7)GMP) to 7-methylguanosine and inorganic phosphate (PubMed:23223233, PubMed:24603684). The specific activity for m(7)GMP may protect cells against undesired salvage of m(7)GMP and its incorporation into nucleic acids (PubMed:23223233). Also has weak activity for CMP (PubMed:23223233, PubMed:24603684). UMP and purine nucleotides are poor substrates (PubMed:23223233).<ref>PMID:23223233</ref> <ref>PMID:24603684</ref>		[[https://www.uniprot.org/uniprot/5NT3B_HUMAN 5NT3B_HUMAN]] Specifically hydrolyzes 7-methylguanosine monophosphate (m(7)GMP) to 7-methylguanosine and inorganic phosphate (PubMed:23223233, PubMed:24603684). The specific activity for m(7)GMP may protect cells against undesired salvage of m(7)GMP and its incorporation into nucleic acids (PubMed:23223233). Also has weak activity for CMP (PubMed:23223233, PubMed:24603684). UMP and purine nucleotides are poor substrates (PubMed:23223233).<ref>PMID:23223233</ref> <ref>PMID:24603684</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Cytosolic nucleotidases (cNs) catalyze dephosphorylation of nucleoside 5'-monophosphates and thereby contribute to the regulation of nucleotide levels in cells. cNs have also been shown to dephosphorylate several therapeutically relevant nucleotide analogues. cN-IIIB has shown in vitro a distinctive activity towards 7-mehtylguanosine monophosphate (m(7)GMP), which is one key metabolites of mRNA cap. Consequently, it has been proposed that cN-IIIB participates in mRNA cap turnover and prevents undesired accumulation and salvage of m(7)GMP. Here, we sought to develop molecular tools enabling more advanced studies on the cellular role of cN-IIIB. To that end, we performed substrate and inhibitor property profiling using a library of 41 substrate analogs. The most potent hit compounds (identified among m(7)GMP analogs) were used as a starting point for structure-activity relationship studies. As a result, we identified several 7-benzylguanosine 5'-monophosphate (Bn(7)GMP) derivatives as potent, unhydrolyzable cN-IIIB inhibitors. The mechanism of inhibition was elucidated using X-ray crystallography and molecular docking. Finally, we showed that compounds that potently inhibit recombinant cN-IIIB have the ability to inhibit m(7)GMP decay in cell lysates.
		+
		+	Substrate-Based Design of Cytosolic Nucleotidase IIIB Inhibitors and Structural Insights into Inhibition Mechanism.,Kubacka D, Kozarski M, Baranowski MR, Wojcik R, Panecka-Hofman J, Strzelecka D, Basquin J, Jemielity J, Kowalska J Pharmaceuticals (Basel). 2022 Apr 29;15(5). pii: ph15050554. doi:, 10.3390/ph15050554. PMID:35631380<ref>PMID:35631380</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7zee" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 08:19, 25 May 2022

2022-05-25T08:19:51Z

←Older revision		Revision as of 08:19, 25 May 2022
Line 1:		Line 1:

	==Human cytosolic 5' nucleotidase IIIB==		==Human cytosolic 5' nucleotidase IIIB==
-	<StructureSection load='7zee' size='340' side='right'caption='[[7zee]]' scene=''>	+	<StructureSection load='7zee' size='340' side='right'caption='[[7zee]], [[Resolution\|resolution]] 1.36Å' 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=7ZEE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7ZEE FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7zee]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7ZEE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7ZEE 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=7zee FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7zee OCA], [https://pdbe.org/7zee PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7zee RCSB], [https://www.ebi.ac.uk/pdbsum/7zee PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7zee 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=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=7zee FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7zee OCA], [https://pdbe.org/7zee PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7zee RCSB], [https://www.ebi.ac.uk/pdbsum/7zee PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7zee ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[https://www.uniprot.org/uniprot/5NT3B_HUMAN 5NT3B_HUMAN]] Specifically hydrolyzes 7-methylguanosine monophosphate (m(7)GMP) to 7-methylguanosine and inorganic phosphate (PubMed:23223233, PubMed:24603684). The specific activity for m(7)GMP may protect cells against undesired salvage of m(7)GMP and its incorporation into nucleic acids (PubMed:23223233). Also has weak activity for CMP (PubMed:23223233, PubMed:24603684). UMP and purine nucleotides are poor substrates (PubMed:23223233).<ref>PMID:23223233</ref> <ref>PMID:24603684</ref>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Baranowski MR]]	+	[[Category: Baranowski, M R]]
-	[[Category: Basquin J]]	+	[[Category: Basquin, J]]
-	[[Category: Jemielity J]]	+	[[Category: Jemielity, J]]
-	[[Category: Kowalska J]]	+	[[Category: Kowalska, J]]
-	[[Category: Kozarski M]]	+	[[Category: Kozarski, M]]
-	[[Category: Kubacka D]]	+	[[Category: Kubacka, D]]
-	[[Category: Wojcik R]]	+	[[Category: Wojcik, R]]
		+	[[Category: Cytosolic 5' nucleotidase]]
		+	[[Category: Hydrolase]]
		+	[[Category: Mrna cap degradation]]
		+	[[Category: N7 methylguanosine monophosphate dephosphorylation]]
		+	[[Category: Nucleotide level regulation]]

OCA at 09:50, 13 April 2022

2022-04-13T09:50:21Z

←Older revision		Revision as of 09:50, 13 April 2022
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 7zee ~~is ON HOLD~~	+	==Human cytosolic 5' nucleotidase IIIB==
-		+	<StructureSection load='7zee' size='340' side='right'caption='[[7zee]]' scene=''>
-	~~Authors~~: ~~Kubacka, D~~.~~, Kozarski, M~~., ~~Baranowski, M~~.R., ~~Wojcik, R~~., ~~Jemielity, J~~., ~~Kowalska, J~~., ~~Basquin, J~~.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7ZEE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7ZEE FirstGlance]. <br>
-	~~Description: Human cytosolic 5' nucleotidase IIIB~~	+	</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=7zee FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7zee OCA], [https://pdbe.org/7zee PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7zee RCSB], [https://www.ebi.ac.uk/pdbsum/7zee PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7zee ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
-	[[Category: ~~Jemielity, J~~]]	+	__TOC__
-	[[Category: ~~Kubacka, D~~]]	+	</StructureSection>
-	[[Category: ~~Wojcik, R~~]]	+	[[Category: Large Structures]]
-	[[Category: Kowalska, J]]	+	[[Category: Baranowski MR]]
-	[[Category: Kozarski, M]]	+	[[Category: Basquin J]]
-	[[Category: ~~Basquin, J~~]]	+	[[Category: Jemielity J]]
-	[[Category: ~~Baranowski, M.~~R]]	+	[[Category: Kowalska J]]
		+	[[Category: Kozarski M]]
		+	[[Category: Kubacka D]]
		+	[[Category: Wojcik R]]

OCA: Protected "7zee" [edit=sysop:move=sysop]

2022-04-06T09:25:50Z

Protected "7zee" [edit=sysop:move=sysop]

←Older revision

Revision as of 09:25, 6 April 2022

OCA: New page: '''Unreleased structure''' The entry 7zee is ON HOLD Authors: Kubacka, D., Kozarski, M., Baranowski, M.R., Wojcik, R., Jemielity, J., Kowalska, J., Basquin, J. Description: Human cytos...

2022-04-06T09:25:49Z

New page: '''Unreleased structure''' The entry 7zee is ON HOLD Authors: Kubacka, D., Kozarski, M., Baranowski, M.R., Wojcik, R., Jemielity, J., Kowalska, J., Basquin, J. Description: Human cytos...

New page

'''Unreleased structure'''

The entry 7zee is ON HOLD

Authors: Kubacka, D., Kozarski, M., Baranowski, M.R., Wojcik, R., Jemielity, J., Kowalska, J., Basquin, J.

Description: Human cytosolic 5' nucleotidase IIIB
[[Category: Unreleased Structures]]
[[Category: Jemielity, J]]
[[Category: Kubacka, D]]
[[Category: Wojcik, R]]
[[Category: Kowalska, J]]
[[Category: Kozarski, M]]
[[Category: Basquin, J]]
[[Category: Baranowski, M.R]]