5wu2 - Revision history

OCA at 09:18, 20 March 2024

OCA — Wed, 20 Mar 2024 09:18:57 GMT

←Older revision		Revision as of 09:18, 20 March 2024
Line 3:		Line 3:
	<StructureSection load='5wu2' size='340' side='right'caption='[[5wu2]], [[Resolution\|resolution]] 2.95Å' scene=''>		<StructureSection load='5wu2' size='340' side='right'caption='[[5wu2]], [[Resolution\|resolution]] 2.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5wu2]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5WU2 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5WU2 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5wu2]] 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=5WU2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5WU2 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BA:BARIUM+ION'>BA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=UTP:URIDINE+5-TRIPHOSPHATE'>UTP</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]] 2.95Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5wu6\|5wu6]], [[5wu5\|5wu5]], [[5wu4\|5wu4]], [[5wu3\|5wu3]], [[5wu1\|5wu1]]~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BA:BARIUM+ION'>BA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=UTP:URIDINE+5-TRIPHOSPHATE'>UTP</scene></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=5wu2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5wu2 OCA], [~~http~~://pdbe.org/5wu2 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5wu2 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5wu2 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5wu2 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=5wu2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5wu2 OCA], [https://pdbe.org/5wu2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5wu2 RCSB], [https://www.ebi.ac.uk/pdbsum/5wu2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5wu2 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/STPAP_HUMAN STPAP_HUMAN]] Poly(A) polymerase that creates the 3'-poly(A) tail of specific pre-mRNAs. Localizes to nuclear speckles together with PIP5K1A and mediates polyadenylation of a select set of mRNAs, such as HMOX1. In addition to polyadenylation, it is also required for the 3'-end cleavage of pre-mRNAs: binds to the 3'UTR of targeted pre-mRNAs and promotes the recruitment and assembly of the CPSF complex on the 3'UTR of pre-mRNAs. In addition to adenylyltransferase activity, also has uridylyltransferase activity. However, the ATP ratio is higher than UTP in cells, suggesting that it functions primarily as a poly(A) polymerase. Acts as a specific terminal uridylyltransferase for U6 snRNA in vitro: responsible for a controlled elongation reaction that results in the restoration of the four 3'-terminal UMP-residues found in newly transcribed U6 snRNA. Not involved in replication-dependent histone mRNA degradation.<ref>PMID:16790842</ref> <ref>PMID:18288197</ref> <ref>PMID:21102410</ref>	+	[https://www.uniprot.org/uniprot/STPAP_HUMAN STPAP_HUMAN] Poly(A) polymerase that creates the 3'-poly(A) tail of specific pre-mRNAs. Localizes to nuclear speckles together with PIP5K1A and mediates polyadenylation of a select set of mRNAs, such as HMOX1. In addition to polyadenylation, it is also required for the 3'-end cleavage of pre-mRNAs: binds to the 3'UTR of targeted pre-mRNAs and promotes the recruitment and assembly of the CPSF complex on the 3'UTR of pre-mRNAs. In addition to adenylyltransferase activity, also has uridylyltransferase activity. However, the ATP ratio is higher than UTP in cells, suggesting that it functions primarily as a poly(A) polymerase. Acts as a specific terminal uridylyltransferase for U6 snRNA in vitro: responsible for a controlled elongation reaction that results in the restoration of the four 3'-terminal UMP-residues found in newly transcribed U6 snRNA. Not involved in replication-dependent histone mRNA degradation.<ref>PMID:16790842</ref> <ref>PMID:18288197</ref> <ref>PMID:21102410</ref>
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	The terminal uridylyltransferase, TUT1, builds or repairs the 3'-oligo-uridylylated tail of U6 snRNA. The 3'-oligo-uridylylated tail is the Lsm-binding site for U4/U6 di-snRNP formation and U6 snRNA recycling for pre-mRNA splicing. Here, we report crystallographic and biochemical analyses of human TUT1, which revealed the mechanisms for the specific uridylylation of the 3'-end of U6 snRNA by TUT1. The O2 and O4 atoms of the UTP base form hydrogen bonds with the conserved His and Asn in the catalytic pocket, respectively, and TUT1 preferentially incorporates UMP onto the 3'-end of RNAs. TUT1 recognizes the entire U6 snRNA molecule by its catalytic domains, N-terminal RNA-recognition motifs and a previously unidentified C-terminal RNA-binding domain. Each domain recognizes specific regions within U6 snRNA, and the recognition is coupled with the domain movements and U6 snRNA structural changes. Hence, TUT1 functions as the U6 snRNA-specific terminal uridylyltransferase required for pre-mRNA splicing.	+
-		+
-	Crystal structures of U6 snRNA-specific terminal uridylyltransferase.,Yamashita S, Takagi Y, Nagaike T, Tomita K Nat Commun. 2017 Jun 7;8:15788. doi: 10.1038/ncomms15788. PMID:28589955<ref>PMID:28589955</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 5wu2" style="background-color:#fffaf0;"></div~~>	+

	==See Also==		==See Also==
-	*[[Poly(A) ~~Polymerase~~\|Poly(A) ~~Polymerase~~]]	+	*[[Poly(A) polymerase 3D structures\|Poly(A) polymerase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Tomita, K]]	+	[[Category: Tomita K]]
-	[[Category: Yamashita, S]]	+	[[Category: Yamashita S]]
-	~~[[Category: Terminal nucleotidyl transferase]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 07:17, 7 October 2020

OCA — Wed, 07 Oct 2020 07:17:13 GMT

←Older revision		Revision as of 07:17, 7 October 2020
Line 1:		Line 1:

	==Crystal structure of human Tut1 bound with BaUTP, form I==		==Crystal structure of human Tut1 bound with BaUTP, form I==
-	<StructureSection load='5wu2' size='340' side='right' caption='[[5wu2]], [[Resolution\|resolution]] 2.95Å' scene=''>	+	<StructureSection load='5wu2' size='340' side='right'caption='[[5wu2]], [[Resolution\|resolution]] 2.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5wu2]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5WU2 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5WU2 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5wu2]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5WU2 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5WU2 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BA:BARIUM+ION'>BA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=UTP:URIDINE+5-TRIPHOSPHATE'>UTP</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BA:BARIUM+ION'>BA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=UTP:URIDINE+5-TRIPHOSPHATE'>UTP</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5wu6\|5wu6]], [[5wu5\|5wu5]], [[5wu4\|5wu4]], [[5wu3\|5wu3]], [[5wu1\|5wu1]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5wu6\|5wu6]], [[5wu5\|5wu5]], [[5wu4\|5wu4]], [[5wu3\|5wu3]], [[5wu1\|5wu1]]</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=5wu2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5wu2 OCA], [http://pdbe.org/5wu2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5wu2 RCSB], [http://www.ebi.ac.uk/pdbsum/5wu2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5wu2 ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5wu2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5wu2 OCA], [http://pdbe.org/5wu2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5wu2 RCSB], [http://www.ebi.ac.uk/pdbsum/5wu2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5wu2 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 19:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 5wu2" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5wu2" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Poly(A) Polymerase\|Poly(A) Polymerase]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Tomita, K]]		[[Category: Tomita, K]]
	[[Category: Yamashita, S]]		[[Category: Yamashita, S]]
	[[Category: Terminal nucleotidyl transferase]]		[[Category: Terminal nucleotidyl transferase]]
	[[Category: Transferase]]		[[Category: Transferase]]

OCA at 08:40, 3 August 2017

OCA — Thu, 03 Aug 2017 08:40:02 GMT

←Older revision		Revision as of 08:40, 3 August 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5wu2 is ~~ON HOLD~~ ~~until Paper~~ Publication	+	==Crystal structure of human Tut1 bound with BaUTP, form I==
		+	<StructureSection load='5wu2' size='340' side='right' caption='[[5wu2]], [[Resolution\|resolution]] 2.95Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5wu2]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5WU2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5WU2 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BA:BARIUM+ION'>BA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=UTP:URIDINE+5-TRIPHOSPHATE'>UTP</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5wu6\|5wu6]], [[5wu5\|5wu5]], [[5wu4\|5wu4]], [[5wu3\|5wu3]], [[5wu1\|5wu1]]</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=5wu2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5wu2 OCA], [http://pdbe.org/5wu2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5wu2 RCSB], [http://www.ebi.ac.uk/pdbsum/5wu2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5wu2 ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/STPAP_HUMAN STPAP_HUMAN]] Poly(A) polymerase that creates the 3'-poly(A) tail of specific pre-mRNAs. Localizes to nuclear speckles together with PIP5K1A and mediates polyadenylation of a select set of mRNAs, such as HMOX1. In addition to polyadenylation, it is also required for the 3'-end cleavage of pre-mRNAs: binds to the 3'UTR of targeted pre-mRNAs and promotes the recruitment and assembly of the CPSF complex on the 3'UTR of pre-mRNAs. In addition to adenylyltransferase activity, also has uridylyltransferase activity. However, the ATP ratio is higher than UTP in cells, suggesting that it functions primarily as a poly(A) polymerase. Acts as a specific terminal uridylyltransferase for U6 snRNA in vitro: responsible for a controlled elongation reaction that results in the restoration of the four 3'-terminal UMP-residues found in newly transcribed U6 snRNA. Not involved in replication-dependent histone mRNA degradation.<ref>PMID:16790842</ref> <ref>PMID:18288197</ref> <ref>PMID:21102410</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The terminal uridylyltransferase, TUT1, builds or repairs the 3'-oligo-uridylylated tail of U6 snRNA. The 3'-oligo-uridylylated tail is the Lsm-binding site for U4/U6 di-snRNP formation and U6 snRNA recycling for pre-mRNA splicing. Here, we report crystallographic and biochemical analyses of human TUT1, which revealed the mechanisms for the specific uridylylation of the 3'-end of U6 snRNA by TUT1. The O2 and O4 atoms of the UTP base form hydrogen bonds with the conserved His and Asn in the catalytic pocket, respectively, and TUT1 preferentially incorporates UMP onto the 3'-end of RNAs. TUT1 recognizes the entire U6 snRNA molecule by its catalytic domains, N-terminal RNA-recognition motifs and a previously unidentified C-terminal RNA-binding domain. Each domain recognizes specific regions within U6 snRNA, and the recognition is coupled with the domain movements and U6 snRNA structural changes. Hence, TUT1 functions as the U6 snRNA-specific terminal uridylyltransferase required for pre-mRNA splicing.

-	~~Authors~~:	+	Crystal structures of U6 snRNA-specific terminal uridylyltransferase.,Yamashita S, Takagi Y, Nagaike T, Tomita K Nat Commun. 2017 Jun 7;8:15788. doi: 10.1038/ncomms15788. PMID:28589955<ref>PMID:28589955</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5wu2" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Tomita, K]]
		+	[[Category: Yamashita, S]]
		+	[[Category: Terminal nucleotidyl transferase]]
		+	[[Category: Transferase]]

OCA at 15:11, 18 January 2017

OCA — Wed, 18 Jan 2017 15:11:18 GMT

←Older revision		Revision as of 15:11, 18 January 2017
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5wu2 is ON HOLD	+	The entry 5wu2 is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "5wu2" [edit=sysop:move=sysop]

OCA — Thu, 22 Dec 2016 20:43:00 GMT

Protected "5wu2" [edit=sysop:move=sysop]

←Older revision

Revision as of 20:43, 22 December 2016

OCA: New page: '''Unreleased structure''' The entry 5wu2 is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Thu, 22 Dec 2016 20:42:59 GMT

New page: '''Unreleased structure''' The entry 5wu2 is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5wu2 is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]