6qkv - Revision history

OCA at 12:02, 24 January 2024

OCA — Wed, 24 Jan 2024 12:02:57 GMT

←Older revision		Revision as of 12:02, 24 January 2024
Line 3:		Line 3:
	<StructureSection load='6qkv' size='340' side='right'caption='[[6qkv]], [[Resolution\|resolution]] 2.01Å' scene=''>		<StructureSection load='6qkv' size='340' side='right'caption='[[6qkv]], [[Resolution\|resolution]] 2.01Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6qkv]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"bacillus_aeruginosus"_(schroeter_1872)_trevisan_1885 "bacillus aeruginosus" (schroeter 1872) trevisan 1885~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6QKV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6QKV FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6qkv]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_aeruginosa Pseudomonas aeruginosa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6QKV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6QKV FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>~~, ~~<scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 2.01Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>trmL, C0044_37955, C8257_31370, DZ962_17365, PAMH19_2880 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~287~~ "~~Bacillus aeruginosus~~" ~~(Schroeter 1872) Trevisan 1885])</td~~><~~/tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks~~'>[https://en.wikipedia.org/wiki/tRNA_(cytidine(34)-2'-O)-methyltransferase tRNA (cytidine(34)-2'-O)-methyltransferase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.207 2.1.1.207] </~~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=6qkv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6qkv OCA], [https://pdbe.org/6qkv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6qkv RCSB], [https://www.ebi.ac.uk/pdbsum/6qkv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6qkv 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=6qkv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6qkv OCA], [https://pdbe.org/6qkv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6qkv RCSB], [https://www.ebi.ac.uk/pdbsum/6qkv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6qkv ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/~~A0A071LCY6_PSEAI A0A071LCY6_PSEAI]~~] Methylates the ribose at the nucleotide 34 wobble position in the two leucyl isoacceptors tRNA(Leu)(CmAA) and tRNA(Leu)(cmnm5UmAA). Catalyzes the methyl transfer from S-adenosyl-L-methionine to the 2'-OH of the wobble nucleotide.[HAMAP-Rule:MF_01885]	+	[https://www.uniprot.org/uniprot/Q9HU57_PSEAE Q9HU57_PSEAE] Methylates the ribose at the nucleotide 34 wobble position in the two leucyl isoacceptors tRNA(Leu)(CmAA) and tRNA(Leu)(cmnm5UmAA). Catalyzes the methyl transfer from S-adenosyl-L-methionine to the 2'-OH of the wobble nucleotide.[HAMAP-Rule:MF_01885]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Iwai, H~~]]	+	[[Category: Pseudomonas aeruginosa]]
-	[[Category: ~~Mikula, K M~~]]	+	[[Category: Iwai H]]
-	[[Category: ~~Tascon, I~~]]	+	[[Category: Mikula KM]]
-	[[Category: ~~Methyltransferase]]~~	+	[[Category: Tascon I]]
-	~~[[Category: Transferase~~]]	+

OCA at 10:40, 28 July 2021

OCA — Wed, 28 Jul 2021 10:40:02 GMT

←Older revision		Revision as of 10:40, 28 July 2021
Line 3:		Line 3:
	<StructureSection load='6qkv' size='340' side='right'caption='[[6qkv]], [[Resolution\|resolution]] 2.01Å' scene=''>		<StructureSection load='6qkv' size='340' side='right'caption='[[6qkv]], [[Resolution\|resolution]] 2.01Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6qkv]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6QKV OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca.weizmann.ac~~.~~il/oca-docs~~/fgij/fg.htm?mol=6QKV FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6qkv]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_aeruginosus"_(schroeter_1872)_trevisan_1885 "bacillus aeruginosus" (schroeter 1872) trevisan 1885]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6QKV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6QKV FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/tRNA_(cytidine(34)-2'-O)-methyltransferase tRNA (cytidine(34)-2'-O)-methyltransferase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.207 2.1.1.207] </span></td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">trmL, C0044_37955, C8257_31370, DZ962_17365, PAMH19_2880 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=287 "Bacillus aeruginosus" (Schroeter 1872) Trevisan 1885])</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=6qkv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6qkv OCA], [~~http~~://pdbe.org/6qkv PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6qkv RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6qkv PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6qkv ProSAT]</span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/tRNA_(cytidine(34)-2'-O)-methyltransferase tRNA (cytidine(34)-2'-O)-methyltransferase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.207 2.1.1.207] </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=6qkv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6qkv OCA], [https://pdbe.org/6qkv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6qkv RCSB], [https://www.ebi.ac.uk/pdbsum/6qkv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6qkv ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/A0A071LCY6_PSEAI A0A071LCY6_PSEAI]] Methylates the ribose at the nucleotide 34 wobble position in the two leucyl isoacceptors tRNA(Leu)(CmAA) and tRNA(Leu)(cmnm5UmAA). Catalyzes the methyl transfer from S-adenosyl-L-methionine to the 2'-OH of the wobble nucleotide.[HAMAP-Rule:MF_01885]	+	[[https://www.uniprot.org/uniprot/A0A071LCY6_PSEAI A0A071LCY6_PSEAI]] Methylates the ribose at the nucleotide 34 wobble position in the two leucyl isoacceptors tRNA(Leu)(CmAA) and tRNA(Leu)(cmnm5UmAA). Catalyzes the methyl transfer from S-adenosyl-L-methionine to the 2'-OH of the wobble nucleotide.[HAMAP-Rule:MF_01885]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Knots have attracted scientists in mathematics, physics, biology, and engineering. Long flexible thin strings easily knot and tangle as experienced in our daily life. Similarly, long polymer chains inevitably tend to get trapped into knots. Little is known about their formation or function in proteins despite >1,000 knotted proteins identified in nature. However, these protein knots are not mathematical knots with their backbone polypeptide chains because of their open termini, and the presence of a "knot" depends on the algorithm used to create path closure. Furthermore, it is generally not possible to control the topology of the unfolded states of proteins, therefore making it challenging to characterize functional and physicochemical properties of knotting in any polymer. Covalently linking the amino and carboxyl termini of the deeply trefoil-knotted YibK from Pseudomonas aeruginosa allowed us to create the truly backbone knotted protein by enzymatic peptide ligation. Moreover, we produced and investigated backbone cyclized YibK without any knotted structure. Thus, we could directly probe the effect of the backbone knot and the decrease in conformational entropy on protein folding. The backbone cyclization did not perturb the native structure and its cofactor binding affinity, but it substantially increased the thermal stability and reduced the aggregation propensity. The enhanced stability of a backbone knotted YibK could be mainly originated from an increased ruggedness of its free energy landscape and the destabilization of the denatured state by backbone cyclization with little contribution from a knot structure. Despite the heterogeneity in the side-chain compositions, the chemically unfolded cyclized YibK exhibited several macroscopic physico-chemical attributes that agree with theoretical predictions derived from polymer physics.
		+
		+	Tying up the Loose Ends: A Mathematically Knotted Protein.,Hsu SD, Lee YC, Mikula KM, Backlund SM, Tascon I, Goldman A, Iwai H Front Chem. 2021 May 24;9:663241. doi: 10.3389/fchem.2021.663241. eCollection, 2021. PMID:34109153<ref>PMID:34109153</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6qkv" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[TRNA methyltransferase 3D structures\|TRNA methyltransferase 3D structures]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 06:28, 19 February 2020

OCA — Wed, 19 Feb 2020 06:28:47 GMT

←Older revision		Revision as of 06:28, 19 February 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6qkv is ~~ON HOLD until Paper Publication~~	+	==Structure of YibK from P. aeruginosa==
-		+	<StructureSection load='6qkv' size='340' side='right'caption='[[6qkv]], [[Resolution\|resolution]] 2.01Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6qkv]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6QKV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6QKV FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/tRNA_(cytidine(34)-2'-O)-methyltransferase tRNA (cytidine(34)-2'-O)-methyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.207 2.1.1.207] </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=6qkv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6qkv OCA], [http://pdbe.org/6qkv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6qkv RCSB], [http://www.ebi.ac.uk/pdbsum/6qkv PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6qkv ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/A0A071LCY6_PSEAI A0A071LCY6_PSEAI]] Methylates the ribose at the nucleotide 34 wobble position in the two leucyl isoacceptors tRNA(Leu)(CmAA) and tRNA(Leu)(cmnm5UmAA). Catalyzes the methyl transfer from S-adenosyl-L-methionine to the 2'-OH of the wobble nucleotide.[HAMAP-Rule:MF_01885]
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Iwai, H]]
		+	[[Category: Mikula, K M]]
		+	[[Category: Tascon, I]]
		+	[[Category: Methyltransferase]]
		+	[[Category: Transferase]]

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

OCA — Wed, 13 Feb 2019 08:01:32 GMT

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

←Older revision

Revision as of 08:01, 13 February 2019

OCA: New page: '''Unreleased structure''' The entry 6qkv is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

OCA — Wed, 13 Feb 2019 08:01:30 GMT

New page: '''Unreleased structure''' The entry 6qkv is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6qkv is ON HOLD until Paper Publication

Authors:

Description:
[[Category: Unreleased Structures]]