6jyj - Revision history

OCA at 10:40, 27 March 2024

OCA — Wed, 27 Mar 2024 10:40:18 GMT

←Older revision		Revision as of 10:40, 27 March 2024
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	<StructureSection load='6jyj' size='340' side='right'caption='[[6jyj]], [[Resolution\|resolution]] 2.69Å' scene=''>		<StructureSection load='6jyj' size='340' side='right'caption='[[6jyj]], [[Resolution\|resolution]] 2.69Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6jyj]] is a 3 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Silurana_(xenopus)_tropicalis Silurana (xenopus)~~ tropicalis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6JYJ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6JYJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6jyj]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Xenopus_tropicalis Xenopus tropicalis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6JYJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6JYJ FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=FLC:CITRATE+ANION'>FLC</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]] 2.693199Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~tent5b, fam46b ([http~~:/~~/www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=8364 Silurana (Xenopus) tropicalis])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FLC:CITRATE+ANION'>FLC</scene></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=6jyj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jyj OCA], [~~http~~://pdbe.org/6jyj PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6jyj RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6jyj PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6jyj 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=6jyj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jyj OCA], [https://pdbe.org/6jyj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6jyj RCSB], [https://www.ebi.ac.uk/pdbsum/6jyj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6jyj ProSAT]</span></td></tr>
	</table>		</table>
-	~~<div style~~=~~"background-color:#fffaf0;">~~	+	== Function ==
-	=~~= Publication Abstract from PubMed~~ ==	+	[https://www.uniprot.org/uniprot/TET5B_XENTR TET5B_XENTR] Catalyzes the transfer of one adenosine molecule from an ATP to an mRNA poly(A) tail bearing a 3'-OH terminal group in an ATP hydrolysis-dependent manner and participates in cytoplasmic polyadenylation (PubMed:34048638). May be involved in maintaining the translation efficiency of at least some genes through preventing degradation of their mRNAs (By similarity).[UniProtKB:Q96A09]<ref>PMID:34048638</ref>
-	~~Family with sequence similarity (FAM46) proteins are newly identified metazoan-specific poly(A) polymerases (PAPs)~~. ~~Although predicted as Gld-2-like eukaryotic non-canonical PAPs, the detailed architecture of FAM46 proteins is still unclear~~. ~~Exact biological functions for most of FAM46 proteins also remain largely unknown. Here, we report~~ the ~~first crystal structure~~ of ~~a FAM46 protein, FAM46B. FAM46B is composed of a prominently larger N-terminal catalytic domain as compared~~ to ~~known eukaryotic PAPs, and~~ a C-terminal ~~helical domain. FAM46B resembles prokaryotic PAP/CCA-adding enzymes~~ in ~~overall folding as well as certain inter-domain connections, which distinguishes FAM46B from other eukaryotic non-canonical PAPs. Biochemical analysis reveals that FAM46B is~~ an ~~active PAP, and prefers adenosine~~-~~rich substrate RNAs. FAM46B is uniquely~~ and ~~highly expressed~~ in ~~human pre-implantation embryos and pluripotent stem cells, but sharply down-regulated following differentiation~~. FAM46B is localized to both cell nucleus and cytosol, and is indispensable for the viability of human embryonic stem cells. Knock-out of FAM46B is lethal. Knock-down of FAM46B induces apoptosis and restricts protein synthesis. The identification of the bacterial-like FAM46B, as a pluripotent stem cell-specific PAP involved in the ~~maintenance of translational~~ efficiency~~, provides important clues for further functional studies~~ of ~~this PAP in the early embryonic development~~ of ~~high eukaryotes.~~	+
-		+
-	~~FAM46B is a prokaryotic-like cytoplasmic poly~~(A) ~~polymerase essential in human embryonic stem cells~~.,Hu JL, Liang H, Zhang H, Yang MZ, Sun W, Zhang P, Luo L, Feng JX, Bai H, Liu F, Zhang T, Yang JY, Gao Q, Long Y, Ma XY, Chen Y, Zhong Q, Yu B, Liao S, Wang Y, Zhao Y, Zeng MS, Cao N, Wang J, Chen W, Yang HT, Gao S Nucleic Acids Res. 2020 Mar 18;48(5):2733-2748. doi: 10.1093/nar/gkaa049. PMID:~~32009146~~<ref>PMID:~~32009146~~</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 6jyj" style="background-color:#fffaf0;"></div~~>	+
	== References ==		== References ==
	<references/>		<references/>
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Gao, S~~]]	+	[[Category: Xenopus tropicalis]]
-	[[Category: ~~Hu, J L~~]]	+	[[Category: Gao S]]
-	[[Category: ~~Zhang, H~~]]	+	[[Category: Hu JL]]
-	[[Category: ~~Gene regulation~~]]	+	[[Category: Zhang H]]

OCA at 10:13, 18 March 2020

OCA — Wed, 18 Mar 2020 10:13:16 GMT

←Older revision		Revision as of 10:13, 18 March 2020
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	<StructureSection load='6jyj' size='340' side='right'caption='[[6jyj]], [[Resolution\|resolution]] 2.69Å' scene=''>		<StructureSection load='6jyj' size='340' side='right'caption='[[6jyj]], [[Resolution\|resolution]] 2.69Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6jyj]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6JYJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6JYJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6jyj]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Silurana_(xenopus)_tropicalis Silurana (xenopus) tropicalis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6JYJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6JYJ FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FLC:CITRATE+ANION'>FLC</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FLC:CITRATE+ANION'>FLC</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">tent5b, fam46b ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=8364 Silurana (Xenopus) tropicalis])</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=6jyj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jyj OCA], [http://pdbe.org/6jyj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6jyj RCSB], [http://www.ebi.ac.uk/pdbsum/6jyj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6jyj 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=6jyj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jyj OCA], [http://pdbe.org/6jyj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6jyj RCSB], [http://www.ebi.ac.uk/pdbsum/6jyj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6jyj ProSAT]</span></td></tr>
	</table>		</table>

OCA at 06:40, 4 March 2020

OCA — Wed, 04 Mar 2020 06:40:25 GMT

←Older revision		Revision as of 06:40, 4 March 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6jyj is ~~ON HOLD until Paper~~ Publication	+	==Crystal structure of FAM46B (TENT5B)==
		+	<StructureSection load='6jyj' size='340' side='right'caption='[[6jyj]], [[Resolution\|resolution]] 2.69Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6jyj]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6JYJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6JYJ FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FLC:CITRATE+ANION'>FLC</scene></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=6jyj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jyj OCA], [http://pdbe.org/6jyj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6jyj RCSB], [http://www.ebi.ac.uk/pdbsum/6jyj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6jyj ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Family with sequence similarity (FAM46) proteins are newly identified metazoan-specific poly(A) polymerases (PAPs). Although predicted as Gld-2-like eukaryotic non-canonical PAPs, the detailed architecture of FAM46 proteins is still unclear. Exact biological functions for most of FAM46 proteins also remain largely unknown. Here, we report the first crystal structure of a FAM46 protein, FAM46B. FAM46B is composed of a prominently larger N-terminal catalytic domain as compared to known eukaryotic PAPs, and a C-terminal helical domain. FAM46B resembles prokaryotic PAP/CCA-adding enzymes in overall folding as well as certain inter-domain connections, which distinguishes FAM46B from other eukaryotic non-canonical PAPs. Biochemical analysis reveals that FAM46B is an active PAP, and prefers adenosine-rich substrate RNAs. FAM46B is uniquely and highly expressed in human pre-implantation embryos and pluripotent stem cells, but sharply down-regulated following differentiation. FAM46B is localized to both cell nucleus and cytosol, and is indispensable for the viability of human embryonic stem cells. Knock-out of FAM46B is lethal. Knock-down of FAM46B induces apoptosis and restricts protein synthesis. The identification of the bacterial-like FAM46B, as a pluripotent stem cell-specific PAP involved in the maintenance of translational efficiency, provides important clues for further functional studies of this PAP in the early embryonic development of high eukaryotes.

-	~~Authors~~:	+	FAM46B is a prokaryotic-like cytoplasmic poly(A) polymerase essential in human embryonic stem cells.,Hu JL, Liang H, Zhang H, Yang MZ, Sun W, Zhang P, Luo L, Feng JX, Bai H, Liu F, Zhang T, Yang JY, Gao Q, Long Y, Ma XY, Chen Y, Zhong Q, Yu B, Liao S, Wang Y, Zhao Y, Zeng MS, Cao N, Wang J, Chen W, Yang HT, Gao S Nucleic Acids Res. 2020 Mar 18;48(5):2733-2748. doi: 10.1093/nar/gkaa049. PMID:32009146<ref>PMID:32009146</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
		+	<div class="pdbe-citations 6jyj" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Gao, S]]
		+	[[Category: Hu, J L]]
		+	[[Category: Zhang, H]]
		+	[[Category: Gene regulation]]

OCA at 03:51, 22 May 2019

OCA — Wed, 22 May 2019 03:51:53 GMT

←Older revision		Revision as of 03:51, 22 May 2019
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6jyj is ON HOLD	+	The entry 6jyj is ON HOLD until Paper Publication

	Authors:		Authors:

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

OCA — Tue, 21 May 2019 05:37:12 GMT

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

←Older revision

Revision as of 05:37, 21 May 2019

OCA: New page: '''Unreleased structure''' The entry 6jyj is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Tue, 21 May 2019 05:37:10 GMT

New page: '''Unreleased structure''' The entry 6jyj is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6jyj is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]