4jwf - Revision history

OCA at 11:28, 30 November 2022

OCA — Wed, 30 Nov 2022 11:28:18 GMT

←Older revision		Revision as of 11:28, 30 November 2022
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	==Crystal structure of spTrm10(74)-SAH complex==		==Crystal structure of spTrm10(74)-SAH complex==
-	<StructureSection load='4jwf' size='340' side='right' caption='[[4jwf]], [[Resolution\|resolution]] 2.40Å' scene=''>	+	<StructureSection load='4jwf' size='340' side='right'caption='[[4jwf]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4jwf]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Fission_yeast Fission yeast~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4JWF OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4JWF FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4jwf]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Schizosaccharomyces_pombe_972h- Schizosaccharomyces pombe 972h-]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4JWF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4JWF FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, ~~<scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene></td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene></td></tr>
-	~~<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</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=4jwf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4jwf OCA], [https://pdbe.org/4jwf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4jwf RCSB], [https://www.ebi.ac.uk/pdbsum/4jwf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4jwf ProSAT]</span></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4jwg\|4jwg]]~~, ~~[[4jwh\|4jwh]], [[4jwj\|4jwj]]~~<~~/td></tr>~~	+
-	~~<tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b></td><td class="sblockDat">SPAC6B12.09, trm10 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=284812 Fission yeast])</td></tr>~~	+
-	~~<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/tRNA_(guanine(9)~~-~~N(1))~~-~~methyltransferase tRNA (guanine(9)~~-~~N(1))-methyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.221 2.1.1.221]~~ </~~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=4jwf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4jwf OCA], [~~http~~://pdbe.org/4jwf PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4jwf RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4jwf PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4jwf ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/TRM10_SCHPO TRM10_SCHPO]] Catalyzes the formation of N(1)-methylguanine at position 9 (m1G9) in cytoplasmic tRNAs (By similarity).	+	[https://www.uniprot.org/uniprot/TRM10_SCHPO TRM10_SCHPO] Catalyzes the formation of N(1)-methylguanine at position 9 (m1G9) in cytoplasmic tRNAs (By similarity).
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 24:		Line 20:

	==See Also==		==See Also==
-	*[[TRNA methyltransferase\|TRNA methyltransferase]]	+	*[[TRNA methyltransferase 3D structures\|TRNA methyltransferase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Fission yeast~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Shao, Z~~]]	+	[[Category: Schizosaccharomyces pombe 972h-]]
-	[[Category: ~~Yan, W~~]]	+	[[Category: Shao Z]]
-	[[Category: ~~Transferase]]~~	+	[[Category: Yan W]]
-	~~[[Category: Trna mtase domain~~]]	+

OCA at 04:07, 5 August 2016

OCA — Fri, 05 Aug 2016 04:07:22 GMT

←Older revision		Revision as of 04:07, 5 August 2016
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		+
	==Crystal structure of spTrm10(74)-SAH complex==		==Crystal structure of spTrm10(74)-SAH complex==
	<StructureSection load='4jwf' size='340' side='right' caption='[[4jwf]], [[Resolution\|resolution]] 2.40Å' scene=''>		<StructureSection load='4jwf' size='340' side='right' caption='[[4jwf]], [[Resolution\|resolution]] 2.40Å' scene=''>
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	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SPAC6B12.09, trm10 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=284812 Fission yeast])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SPAC6B12.09, trm10 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=284812 Fission yeast])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/tRNA_(guanine(9)-N(1))-methyltransferase tRNA (guanine(9)-N(1))-methyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.221 2.1.1.221] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/tRNA_(guanine(9)-N(1))-methyltransferase tRNA (guanine(9)-N(1))-methyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.221 2.1.1.221] </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=4jwf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4jwf OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4jwf RCSB], [http://www.ebi.ac.uk/pdbsum/4jwf 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=4jwf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4jwf OCA], [http://pdbe.org/4jwf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4jwf RCSB], [http://www.ebi.ac.uk/pdbsum/4jwf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4jwf ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 20:		Line 21:
	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 4jwf" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==

OCA at 15:42, 25 December 2014

OCA — Thu, 25 Dec 2014 15:42:45 GMT

←Older revision		Revision as of 15:42, 25 December 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_4jwf\| PDB=4jwf \| SCENE= }}~~	+	==Crystal structure of spTrm10(74)-SAH complex==
-	===Crystal structure of spTrm10(74)-SAH complex===	+	<StructureSection load='4jwf' size='340' side='right' caption='[[4jwf]], [[Resolution\|resolution]] 2.40Å' scene=''>
-	~~{{ABSTRACT_PUBMED_24081582}}~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[4jwf]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Fission_yeast Fission yeast]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4JWF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4JWF FirstGlance]. <br>
-	==Function==	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene></td></tr>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4jwg\|4jwg]], [[4jwh\|4jwh]], [[4jwj\|4jwj]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SPAC6B12.09, trm10 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=284812 Fission yeast])</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/tRNA_(guanine(9)-N(1))-methyltransferase tRNA (guanine(9)-N(1))-methyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.221 2.1.1.221] </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=4jwf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4jwf OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4jwf RCSB], [http://www.ebi.ac.uk/pdbsum/4jwf PDBsum]</span></td></tr>
		+	</table>
		+	== Function ==
	[[http://www.uniprot.org/uniprot/TRM10_SCHPO TRM10_SCHPO]] Catalyzes the formation of N(1)-methylguanine at position 9 (m1G9) in cytoplasmic tRNAs (By similarity).		[[http://www.uniprot.org/uniprot/TRM10_SCHPO TRM10_SCHPO]] Catalyzes the formation of N(1)-methylguanine at position 9 (m1G9) in cytoplasmic tRNAs (By similarity).
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Transfer RNA (tRNA) methylation is necessary for the proper biological function of tRNA. The N1 methylation of guanine at Position 9 (m1G9) of tRNA, which is widely identified in eukaryotes and archaea, was found to be catalyzed by the Trm10 family of methyltransferases (MTases). Here, we report the first crystal structures of the tRNA MTase spTrm10 from Schizosaccharomyces pombe in the presence and absence of its methyl donor product S-adenosyl-homocysteine (SAH) and its ortholog scTrm10 from Saccharomyces cerevisiae in complex with SAH. Our crystal structures indicated that the MTase domain (the catalytic domain) of the Trm10 family displays a typical SpoU-TrmD (SPOUT) fold. Furthermore, small angle X-ray scattering analysis reveals that Trm10 behaves as a monomer in solution, whereas other members of the SPOUT superfamily all function as homodimers. We also performed tRNA MTase assays and isothermal titration calorimetry experiments to investigate the catalytic mechanism of Trm10 in vitro. In combination with mutational analysis and electrophoretic mobility shift assays, our results provide insights into the substrate tRNA recognition mechanism of Trm10 family MTases.
		+
		+	Crystal structure of tRNA m1G9 methyltransferase Trm10: insight into the catalytic mechanism and recognition of tRNA substrate.,Shao Z, Yan W, Peng J, Zuo X, Zou Y, Li F, Gong D, Ma R, Wu J, Shi Y, Zhang Z, Teng M, Li X, Gong Q Nucleic Acids Res. 2013 Sep 29. PMID:24081582<ref>PMID:24081582</ref>

-	~~==About this Structure==~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[4jwf]] is~~ a ~~2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Fission_yeast Fission yeast]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=4JWF OCA].~~	+	</div>

-	==~~Reference~~==	+	==See Also==
-	~~<ref group~~=~~"xtra">PMID:024081582</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	*[[TRNA methyltransferase\|TRNA methyltransferase]]
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Fission yeast]]		[[Category: Fission yeast]]
-	[[Category: Shao, Z.]]	+	[[Category: Shao, Z]]
-	[[Category: Yan, W.]]	+	[[Category: Yan, W]]
	[[Category: Transferase]]		[[Category: Transferase]]
	[[Category: Trna mtase domain]]		[[Category: Trna mtase domain]]

OCA at 03:56, 13 February 2014

OCA — Thu, 13 Feb 2014 03:56:22 GMT

←Older revision		Revision as of 03:56, 13 February 2014
Line 7:		Line 7:

	==About this Structure==		==About this Structure==
-	[[4jwf]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Schizosaccharomyces_pombe_972h- Schizosaccharomyces pombe 972h-~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4JWF OCA].	+	[[4jwf]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Fission_yeast Fission yeast]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4JWF OCA].

	==Reference==		==Reference==
	<ref group="xtra">PMID:024081582</ref><references group="xtra"/><references/>		<ref group="xtra">PMID:024081582</ref><references group="xtra"/><references/>
-	[[Category: ~~Schizosaccharomyces pombe 972h-~~]]	+	[[Category: Fission yeast]]
	[[Category: Shao, Z.]]		[[Category: Shao, Z.]]
	[[Category: Yan, W.]]		[[Category: Yan, W.]]
	[[Category: Transferase]]		[[Category: Transferase]]
	[[Category: Trna mtase domain]]		[[Category: Trna mtase domain]]

OCA at 08:01, 16 October 2013

OCA — Wed, 16 Oct 2013 08:01:07 GMT

←Older revision		Revision as of 08:01, 16 October 2013
Line 1:		Line 1:
-	~~'''Unreleased~~ structure~~'''~~	+	{{STRUCTURE_4jwf\| PDB=4jwf \| SCENE= }}
		+	===Crystal structure of spTrm10(74)-SAH complex===
		+	{{ABSTRACT_PUBMED_24081582}}

-	~~The entry 4jwf is ON HOLD until Paper Publication~~	+	==Function==
		+	[[http://www.uniprot.org/uniprot/TRM10_SCHPO TRM10_SCHPO]] Catalyzes the formation of N(1)-methylguanine at position 9 (m1G9) in cytoplasmic tRNAs (By similarity).

-	~~Authors~~: ~~Yan, W~~.~~, Shao, Z~~.H.	+	==About this Structure==
		+	[[4jwf]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Schizosaccharomyces_pombe_972h- Schizosaccharomyces pombe 972h-]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4JWF OCA].

-	~~Description~~: ~~Crystal structure of se~~-~~sp74-SAH complex~~	+	==Reference==
		+	<ref group="xtra">PMID:024081582</ref><references group="xtra"/><references/>
		+	[[Category: Schizosaccharomyces pombe 972h-]]
		+	[[Category: Shao, Z.]]
		+	[[Category: Yan, W.]]
		+	[[Category: Transferase]]
		+	[[Category: Trna mtase domain]]

OCA at 10:56, 24 April 2013

OCA — Wed, 24 Apr 2013 10:56:16 GMT

←Older revision		Revision as of 10:56, 24 April 2013
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4jwf is ON HOLD	+	The entry 4jwf is ON HOLD until Paper Publication

	Authors: Yan, W., Shao, Z.H.		Authors: Yan, W., Shao, Z.H.

	Description: Crystal structure of se-sp74-SAH complex		Description: Crystal structure of se-sp74-SAH complex

OCA: Protected "4jwf" [edit=sysop:move=sysop]

OCA — Thu, 04 Apr 2013 01:06:46 GMT

Protected "4jwf" [edit=sysop:move=sysop]

←Older revision

Revision as of 01:06, 4 April 2013

OCA: New page: '''Unreleased structure''' The entry 4jwf is ON HOLD Authors: Yan, W., Shao, Z.H. Description: Crystal structure of se-sp74-SAH complex

OCA — Thu, 04 Apr 2013 01:06:45 GMT

New page: '''Unreleased structure''' The entry 4jwf is ON HOLD Authors: Yan, W., Shao, Z.H. Description: Crystal structure of se-sp74-SAH complex

New page

'''Unreleased structure'''

The entry 4jwf is ON HOLD

Authors: Yan, W., Shao, Z.H.

Description: Crystal structure of se-sp74-SAH complex