6puq - Revision history

OCA at 10:09, 22 May 2024

2024-05-22T10:09:00Z

←Older revision		Revision as of 10:09, 22 May 2024
Line 3:		Line 3:
	<StructureSection load='6puq' size='340' side='right'caption='[[6puq]], [[Resolution\|resolution]] 1.56Å' scene=''>		<StructureSection load='6puq' size='340' side='right'caption='[[6puq]], [[Resolution\|resolution]] 1.56Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6puq]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Fission_yeast Fission yeast~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6PUQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6PUQ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6puq]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Schizosaccharomyces_japonicus_yFS275 Schizosaccharomyces japonicus yFS275]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6PUQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6PUQ FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</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]] 1.56Å</td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SJAG_04265 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=402676 Fission yeast])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</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=6puq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6puq OCA], [https://pdbe.org/6puq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6puq RCSB], [https://www.ebi.ac.uk/pdbsum/6puq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6puq 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=6puq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6puq OCA], [https://pdbe.org/6puq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6puq RCSB], [https://www.ebi.ac.uk/pdbsum/6puq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6puq ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/B6K6D6_SCHJY B6K6D6_SCHJY]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
	The S-adenosyl-L-methionine-dependent tRNA 4-demethylwyosine synthase TYW1 catalyzes biosynthesis of 4-demethylwyosine (imG-14), the precursor for wyosine, the hypermodified guanine-derived nucleotide present at position 37 of phenylalanine tRNAs of archaea and eukarya. Eukaryotic TYW1 enzymes contain N-terminal flavodoxin-like and C-terminal radical-SAM domains. We determined co-crystal structures of the flavodoxin-like domain of the putative Tyw1 from Schizosaccharomyces japonicus in complex with flavin mononucleotide (FMN), exploiting an unexpected anomalous scatterer present in the recombinant protein. Our results show how eukaryotic TYW1 enzymes bind the coenzyme FMN and will help further elucidation of the structural enzymology of 4-demethylwyosine synthesis.		The S-adenosyl-L-methionine-dependent tRNA 4-demethylwyosine synthase TYW1 catalyzes biosynthesis of 4-demethylwyosine (imG-14), the precursor for wyosine, the hypermodified guanine-derived nucleotide present at position 37 of phenylalanine tRNAs of archaea and eukarya. Eukaryotic TYW1 enzymes contain N-terminal flavodoxin-like and C-terminal radical-SAM domains. We determined co-crystal structures of the flavodoxin-like domain of the putative Tyw1 from Schizosaccharomyces japonicus in complex with flavin mononucleotide (FMN), exploiting an unexpected anomalous scatterer present in the recombinant protein. Our results show how eukaryotic TYW1 enzymes bind the coenzyme FMN and will help further elucidation of the structural enzymology of 4-demethylwyosine synthesis.

-	Biochemical and structural characterization of the flavodoxin-like domain of the Schizosaccharomyces japonicus putative tRNA (Phe) 4-demethylwyosine synthase Tyw1 in complex with FMN.,Sjekloca L, Ferre-D'Amare AR MicroPubl Biol. 2022 Jun 8;2022. doi: 10.17912/micropub.biology.000570., eCollection 2022. PMID:35693892<ref>PMID:35693892</ref>	+	Biochemical and structural characterization of the flavodoxin-like domain of the Schizosaccharomyces japonicus putative tRNA (Phe) 4-demethylwyosine synthase Tyw1 in complex with FMN.,Sjekloca L, Ferre-D'Amare AR MicroPubl Biol. 2022 Jun 8;2022:10.17912/micropub.biology.000570. doi: , 10.17912/micropub.biology.000570. eCollection 2022. PMID:35693892<ref>PMID:35693892</ref>

	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>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Fission yeast]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Amare, A R.Ferre-D~~]]	+	[[Category: Schizosaccharomyces japonicus yFS275]]
-	[[Category: ~~Sjekloca, L~~]]	+	[[Category: Ferre-D'Amare AR]]
-	[[Category: ~~Flavoprotein]]~~	+	[[Category: Sjekloca L]]
-	~~[[Category: Hypermodification]]~~	+
-	~~[[Category: Trna]]~~	+
-	~~[[Category: Wyosine~~]]	+

OCA at 09:50, 22 June 2022

2022-06-22T09:50:38Z

←Older revision		Revision as of 09:50, 22 June 2022
Line 1:		Line 1:

-	==1.56 A crystal structure of flavodoxin-like domain of Schizosaccharomyces japonicus putative tRNAPhe 4-demethylwyosine synthase ~~TYW1~~ in complex with FMN==	+	==1.56 A crystal structure of flavodoxin-like domain of Schizosaccharomyces japonicus putative tRNAPhe 4-demethylwyosine synthase Tyw1 in complex with FMN==
-	<StructureSection load='6puq' size='340' side='right'caption='[[6puq]]' scene=''>	+	<StructureSection load='6puq' size='340' side='right'caption='[[6puq]], [[Resolution\|resolution]] 1.56Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6PUQ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6PUQ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6puq]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Fission_yeast Fission yeast]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6PUQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6PUQ FirstGlance]. <br>
-	</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=6puq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6puq OCA], [~~http~~://pdbe.org/6puq PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6puq RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6puq PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6puq ProSAT]</span></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SJAG_04265 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=402676 Fission yeast])</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=6puq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6puq OCA], [https://pdbe.org/6puq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6puq RCSB], [https://www.ebi.ac.uk/pdbsum/6puq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6puq ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The S-adenosyl-L-methionine-dependent tRNA 4-demethylwyosine synthase TYW1 catalyzes biosynthesis of 4-demethylwyosine (imG-14), the precursor for wyosine, the hypermodified guanine-derived nucleotide present at position 37 of phenylalanine tRNAs of archaea and eukarya. Eukaryotic TYW1 enzymes contain N-terminal flavodoxin-like and C-terminal radical-SAM domains. We determined co-crystal structures of the flavodoxin-like domain of the putative Tyw1 from Schizosaccharomyces japonicus in complex with flavin mononucleotide (FMN), exploiting an unexpected anomalous scatterer present in the recombinant protein. Our results show how eukaryotic TYW1 enzymes bind the coenzyme FMN and will help further elucidation of the structural enzymology of 4-demethylwyosine synthesis.
		+
		+	Biochemical and structural characterization of the flavodoxin-like domain of the Schizosaccharomyces japonicus putative tRNA (Phe) 4-demethylwyosine synthase Tyw1 in complex with FMN.,Sjekloca L, Ferre-D'Amare AR MicroPubl Biol. 2022 Jun 8;2022. doi: 10.17912/micropub.biology.000570., eCollection 2022. PMID:35693892<ref>PMID:35693892</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6puq" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Fission yeast]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Ferre D~~'Amare AR~~]]	+	[[Category: Amare, A R.Ferre-D]]
-	[[Category: Sjekloca L]]	+	[[Category: Sjekloca, L]]
		+	[[Category: Flavoprotein]]
		+	[[Category: Hypermodification]]
		+	[[Category: Trna]]
		+	[[Category: Wyosine]]

OCA at 10:46, 22 July 2020

2020-07-22T10:46:55Z

←Older revision		Revision as of 10:46, 22 July 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry 6puq is ON HOLD until Paper Publication~~	+	==1.56 A crystal structure of flavodoxin-like domain of Schizosaccharomyces japonicus putative tRNAPhe 4-demethylwyosine synthase TYW1 in complex with FMN==
-		+	<StructureSection load='6puq' size='340' side='right'caption='[[6puq]]' scene=''>
-	~~Authors: Sjekloca, L., Ferre D'Amare, A.R.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6PUQ OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6PUQ FirstGlance]. <br>
-	~~Description:~~ 1.56 A crystal structure of flavodoxin-like domain of Schizosaccharomyces japonicus putative tRNAPhe 4-demethylwyosine synthase TYW1 in complex with FMN	+	</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=6puq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6puq OCA], [http://pdbe.org/6puq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6puq RCSB], [http://www.ebi.ac.uk/pdbsum/6puq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6puq ProSAT]</span></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	</table>
-	[[~~Category~~: ~~Sjekloca~~, L]]	+	__TOC__
-	[[Category: Ferre D'Amare~~, A.R~~]]	+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Ferre D'Amare AR]]
		+	[[Category: Sjekloca L]]

OCA at 07:14, 2 October 2019

2019-10-02T07:14:02Z

←Older revision		Revision as of 07:14, 2 October 2019
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Sjekloca, L., Ferre D'Amare, A.R.		Authors: Sjekloca, L., Ferre D'Amare, A.R.

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

2019-07-24T04:37:07Z

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

←Older revision

Revision as of 04:37, 24 July 2019

OCA: New page: '''Unreleased structure''' The entry 6puq is ON HOLD Authors: Sjekloca, L., Ferre D'Amare, A.R. Description: 1.56 A crystal structure of flavodoxin-like domain of Schizosaccharomyces j...

2019-07-24T04:37:06Z

New page: '''Unreleased structure''' The entry 6puq is ON HOLD Authors: Sjekloca, L., Ferre D'Amare, A.R. Description: 1.56 A crystal structure of flavodoxin-like domain of Schizosaccharomyces j...

New page

'''Unreleased structure'''

The entry 6puq is ON HOLD

Authors: Sjekloca, L., Ferre D'Amare, A.R.

Description: 1.56 A crystal structure of flavodoxin-like domain of Schizosaccharomyces japonicus putative tRNAPhe 4-demethylwyosine synthase TYW1 in complex with FMN
[[Category: Unreleased Structures]]
[[Category: Sjekloca, L]]
[[Category: Ferre D'Amare, A.R]]