3vrh - Revision history

OCA at 19:00, 27 July 2022

OCA — Wed, 27 Jul 2022 19:00:01 GMT

←Older revision		Revision as of 19:00, 27 July 2022
Line 1:		Line 1:

	==Crystal structure of ph0300==		==Crystal structure of ph0300==
-	<StructureSection load='3vrh' size='340' side='right' caption='[[3vrh]], [[Resolution\|resolution]] 2.10Å' scene=''>	+	<StructureSection load='3vrh' size='340' side='right'caption='[[3vrh]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3vrh]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Pyrococcus_horikoshii Pyrococcus horikoshii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VRH OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3VRH FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3vrh]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_horikoshii Pyrococcus horikoshii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VRH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3VRH FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BCN:BICINE'>BCN</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BCN:BICINE'>BCN</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PH0300 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=70601 Pyrococcus horikoshii])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PH0300 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=70601 Pyrococcus horikoshii])</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=3vrh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vrh OCA], [~~http~~://pdbe.org/3vrh PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3vrh RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3vrh PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3vrh 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=3vrh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vrh OCA], [https://pdbe.org/3vrh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3vrh RCSB], [https://www.ebi.ac.uk/pdbsum/3vrh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3vrh ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Pyrococcus horikoshii]]		[[Category: Pyrococcus horikoshii]]
	[[Category: Goto-Ito, S]]		[[Category: Goto-Ito, S]]

OCA at 07:16, 18 October 2016

OCA — Tue, 18 Oct 2016 07:16:46 GMT

←Older revision		Revision as of 07:16, 18 October 2016
Line 3:		Line 3:
	<StructureSection load='3vrh' size='340' side='right' caption='[[3vrh]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='3vrh' size='340' side='right' caption='[[3vrh]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3vrh]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Pyrho Pyrho~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VRH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3VRH FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3vrh]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrococcus_horikoshii Pyrococcus horikoshii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VRH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3VRH FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BCN:BICINE'>BCN</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BCN:BICINE'>BCN</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PH0300 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=70601 ~~PYRHO~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PH0300 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=70601 Pyrococcus horikoshii])</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=3vrh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vrh OCA], [http://pdbe.org/3vrh PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3vrh RCSB], [http://www.ebi.ac.uk/pdbsum/3vrh PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3vrh 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=3vrh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vrh OCA], [http://pdbe.org/3vrh PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3vrh RCSB], [http://www.ebi.ac.uk/pdbsum/3vrh PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3vrh ProSAT]</span></td></tr>
	</table>		</table>
Line 21:		Line 21:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Pyrho~~]]	+	[[Category: Pyrococcus horikoshii]]
	[[Category: Goto-Ito, S]]		[[Category: Goto-Ito, S]]
	[[Category: Ito, T]]		[[Category: Ito, T]]

OCA at 15:56, 5 August 2016

OCA — Fri, 05 Aug 2016 15:56:45 GMT

←Older revision		Revision as of 15:56, 5 August 2016
Line 1:		Line 1:
		+
	==Crystal structure of ph0300==		==Crystal structure of ph0300==
	<StructureSection load='3vrh' size='340' side='right' caption='[[3vrh]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='3vrh' size='340' side='right' caption='[[3vrh]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3vrh]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Pyrococcus_horikoshii_ot3 Pyrococcus horikoshii ot3~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VRH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3VRH FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3vrh]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrho Pyrho]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VRH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3VRH FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BCN:BICINE'>BCN</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BCN:BICINE'>BCN</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PH0300 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=70601 ~~Pyrococcus horikoshii OT3~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PH0300 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=70601 PYRHO])</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=3vrh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vrh OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3vrh RCSB], [http://www.ebi.ac.uk/pdbsum/3vrh 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=3vrh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vrh OCA], [http://pdbe.org/3vrh PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3vrh RCSB], [http://www.ebi.ac.uk/pdbsum/3vrh PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3vrh ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 15:		Line 16:
	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 3vrh" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Pyrococcus horikoshii ot3~~]]	+	[[Category: Pyrho]]
	[[Category: Goto-Ito, S]]		[[Category: Goto-Ito, S]]
	[[Category: Ito, T]]		[[Category: Ito, T]]

OCA at 08:24, 18 December 2014

OCA — Thu, 18 Dec 2014 08:24:43 GMT

←Older revision		Revision as of 08:24, 18 December 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_3vrh\| PDB~~=3vrh \| ~~SCENE~~= }}	+	==Crystal structure of ph0300==
-	===~~Crystal~~ structure ~~of ph0300~~===	+	<StructureSection load='3vrh' size='340' side='right' caption='[[3vrh]], [[Resolution\|resolution]] 2.10Å' scene=''>
-	~~{{ABSTRACT_PUBMED_23444054}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3vrh]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrococcus_horikoshii_ot3 Pyrococcus horikoshii ot3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VRH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3VRH FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BCN:BICINE'>BCN</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PH0300 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=70601 Pyrococcus horikoshii OT3])</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=3vrh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vrh OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3vrh RCSB], [http://www.ebi.ac.uk/pdbsum/3vrh PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	In thermophilic bacteria, specific 2-thiolation occurs on the conserved ribothymidine at position 54 (T54) in tRNAs, which is necessary for survival at high temperatures. T54 2-thiolation is achieved by the tRNA thiouridine synthetase TtuA and sulfur-carrier proteins. TtuA has five conserved CXXC/H motifs and the signature PP motif, and belongs to the TtcA family of tRNA 2-thiolation enzymes, for which there is currently no structural information. In this study, we determined the crystal structure of a TtuA homologue from the hyperthermophilic archeaon Pyrococcus horikoshii at 2.1 A resolution. The P. horikoshii TtuA forms a homodimer, and each subunit contains a catalytic domain and unique N- and C-terminal zinc fingers. The catalytic domain has much higher structural similarity to that of another tRNA modification enzyme, TilS (tRNA(Ile) (2) lysidine synthetase), than to the other type of tRNA 2-thiolation enzyme, MnmA. Three conserved cysteine residues are clustered in the putative catalytic site, which is not present in TilS. An in vivo mutational analysis in the bacterium Thermus thermophilus demonstrated that the three conserved cysteine residues and the putative ATP-binding residues in the catalytic domain are important for the TtuA activity. A positively-charged surface that includes the catalytic site and the two zinc fingers is likely to provide the tRNA binding site. Proteins 2013. (c) 2013 Wiley Periodicals, Inc.

-	~~==About this Structure==~~	+	Crystallographic and mutational studies on the tRNA thiouridine synthetase TtuA.,Nakagawa H, Kuratani M, Goto-Ito S, Ito T, Katsura K, Terada T, Shirouzu M, Sekine SI, Shigi N, Yokoyama S Proteins. 2013 Feb 27. doi: 10.1002/prot.24273. PMID:23444054<ref>PMID:23444054</ref>
-	~~[[3vrh]] is a 1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki~~/~~Pyrococcus_horikoshii_ot3 Pyrococcus horikoshii ot3]~~. ~~Full crystallographic information is available from [http~~://~~oca~~.~~weizmann~~.ac.il/~~oca-bin/ocashort?id~~=~~3VRH OCA].~~	+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Pyrococcus horikoshii ot3]]		[[Category: Pyrococcus horikoshii ot3]]
-	[[Category: Goto-Ito, S.]]	+	[[Category: Goto-Ito, S]]
-	[[Category: Ito, T.]]	+	[[Category: Ito, T]]
-	[[Category: Kuratani, M.]]	+	[[Category: Kuratani, M]]
-	[[Category: Nakagawa, H.]]	+	[[Category: Nakagawa, H]]
-	[[Category: Sekine, S I.]]	+	[[Category: Sekine, S I]]
-	[[Category: Yokoyama, S.]]	+	[[Category: Yokoyama, S]]
	[[Category: Atpase]]		[[Category: Atpase]]
	[[Category: Rna binding protein]]		[[Category: Rna binding protein]]
	[[Category: Thiolation]]		[[Category: Thiolation]]
	[[Category: Trna modification enzyme]]		[[Category: Trna modification enzyme]]

OCA at 10:25, 13 March 2013

OCA — Wed, 13 Mar 2013 10:25:09 GMT

←Older revision		Revision as of 10:25, 13 March 2013
Line 1:		Line 1:
-	~~'''Unreleased~~ structure~~'''~~	+	{{STRUCTURE_3vrh\| PDB=3vrh \| SCENE= }}
		+	===Crystal structure of ph0300===
		+	{{ABSTRACT_PUBMED_23444054}}

-	~~The entry~~ 3vrh is ~~ON HOLD until Paper Publication~~	+	==About this Structure==
-		+	[[3vrh]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrococcus_horikoshii_ot3 Pyrococcus horikoshii ot3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VRH OCA].
-	~~Authors~~: ~~Nakagawa, H~~.~~, Kuratani, M~~., Goto-Ito, S., Ito, T., Sekine, S.I., Yokoyama, S.	+	[[Category: Pyrococcus horikoshii ot3]]
-		+	[[Category: Goto-Ito, S.]]
-	~~Description~~: ~~Crystal structure of ph0300~~	+	[[Category: Ito, T.]]
		+	[[Category: Kuratani, M.]]
		+	[[Category: Nakagawa, H.]]
		+	[[Category: Sekine, S I.]]
		+	[[Category: Yokoyama, S.]]
		+	[[Category: Atpase]]
		+	[[Category: Rna binding protein]]
		+	[[Category: Thiolation]]
		+	[[Category: Trna modification enzyme]]

OCA at 05:29, 23 May 2012

OCA — Wed, 23 May 2012 05:29:52 GMT

←Older revision		Revision as of 05:29, 23 May 2012
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 3vrh is ON HOLD	+	The entry 3vrh is ON HOLD until Paper Publication

	Authors: Nakagawa, H., Kuratani, M., Goto-Ito, S., Ito, T., Sekine, S.I., Yokoyama, S.		Authors: Nakagawa, H., Kuratani, M., Goto-Ito, S., Ito, T., Sekine, S.I., Yokoyama, S.

	Description: Crystal structure of ph0300		Description: Crystal structure of ph0300

OCA: Protected "3vrh" [edit=sysop:move=sysop]

OCA — Wed, 18 Apr 2012 07:22:34 GMT

Protected "3vrh" [edit=sysop:move=sysop]

←Older revision

Revision as of 07:22, 18 April 2012

OCA: New page: '''Unreleased structure''' The entry 3vrh is ON HOLD Authors: Nakagawa, H., Kuratani, M., Goto-Ito, S., Ito, T., Sekine, S.I., Yokoyama, S. Description: Crystal structure of ph0300

OCA — Wed, 18 Apr 2012 07:22:33 GMT

New page: '''Unreleased structure''' The entry 3vrh is ON HOLD Authors: Nakagawa, H., Kuratani, M., Goto-Ito, S., Ito, T., Sekine, S.I., Yokoyama, S. Description: Crystal structure of ph0300

New page

'''Unreleased structure'''

The entry 3vrh is ON HOLD

Authors: Nakagawa, H., Kuratani, M., Goto-Ito, S., Ito, T., Sekine, S.I., Yokoyama, S.

Description: Crystal structure of ph0300