3eph - Revision history

OCA at 09:48, 21 February 2024

2024-02-21T09:48:52Z

← Older revision		Revision as of 09:48, 21 February 2024
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	<StructureSection load='3eph' size='340' side='right'caption='[[3eph]], [[Resolution\|resolution]] 2.95Å' scene=''>		<StructureSection load='3eph' size='340' side='right'caption='[[3eph]], [[Resolution\|resolution]] 2.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3eph]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Atcc_18824 Atcc 18824~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3EPH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3EPH FirstGlance]. <br>		<table><tr><td colspan='2'>[[3eph]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3EPH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3EPH FirstGlance]. <br>
	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>~~, ~~<scene name='pdbligand=PPV:PYROPHOSPHATE'>PPV</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 2.95Å</td></tr>
	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max-height: 3em;~~'>~~[[3epj\|3epj]], [[3epk\|3epk]], [[3epl\|3epl]]~~</~~div~~><~~/td></tr>~~		<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PPV:PYROPHOSPHATE'>PPV</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">MOD5~~, ~~YOR274W ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824])~~<~~/td></tr>~~
	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b></td><td class="sblockDat"><span class='plainlinks~~'>~~[https://en.wikipedia.org/wiki/tRNA_dimethylallyltransferase tRNA dimethylallyltransferase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.5.1.75 2.5.1.75]~~ </~~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=3eph FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3eph OCA], [https://pdbe.org/3eph PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3eph RCSB], [https://www.ebi.ac.uk/pdbsum/3eph PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3eph 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=3eph FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3eph OCA], [https://pdbe.org/3eph PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3eph RCSB], [https://www.ebi.ac.uk/pdbsum/3eph PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3eph ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[https://www.uniprot.org/uniprot/MOD5_YEAST MOD5_YEAST]] Catalyzes the transfer of a dimethylallyl group onto the adenine at position 37 in the anticodon loop on a specific subset of tRNAs both in the cytosol and the mitochondrion, leading to the formation of N6-(dimethylallyl)adenosine (i(6)A). This modification optimizes the codon:anticodon fit in the ribosome and promotes translational fidelity. Competes with the farnesyl pyrophosphate synthase ERG20 for the common substrate dimethylallyl diphosphate (DMAPP).<ref>PMID:3031456</ref> <ref>PMID:10618371</ref> <ref>PMID:21873461</ref>		[https://www.uniprot.org/uniprot/MOD5_YEAST MOD5_YEAST] Catalyzes the transfer of a dimethylallyl group onto the adenine at position 37 in the anticodon loop on a specific subset of tRNAs both in the cytosol and the mitochondrion, leading to the formation of N6-(dimethylallyl)adenosine (i(6)A). This modification optimizes the codon:anticodon fit in the ribosome and promotes translational fidelity. Competes with the farnesyl pyrophosphate synthase ERG20 for the common substrate dimethylallyl diphosphate (DMAPP).<ref>PMID:3031456</ref> <ref>PMID:10618371</ref> <ref>PMID:21873461</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3eph ConSurf].		</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3eph ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	~~<div style="background-color:#fffaf0;">~~
	~~== Publication Abstract from PubMed ==~~
	Hypermodifications near the anticodon of tRNA are fundamental for the efficiency and fidelity of protein synthesis. Dimethylallyltransferase (DMATase) catalyzes transfer of a dimethylallyl moiety from dimethylallyl pyrophosphate to N6 of A37 in certain tRNAs. Here we present the crystal structures of Saccharomyces cerevisiae DMATase-tRNA(Cys) complex in four distinct forms, which provide snapshots of the RNA modification reaction catalyzed by DMATase. The structures reveal that the enzyme recognizes the tRNA substrate through indirect sequence readout. The targeted nucleotide A37 flips out from the anticodon loop of tRNA and flips into a channel in DMATase, where it meets its reaction partner di methylallyl pyrophosphate, which enters the channel from the opposite end. Structural changes accompanying the transfer reaction taking place in the crystal result in disengagement of DMATase-tRNA interaction near the reaction center. In addition, structural comparison of DMATase in the complex with unliganded bacterial DMATase provides a molecular basis of ordered substrate binding by DMATase.

	Crystallographic snapshots of eukaryotic dimethylallyltransferase acting on tRNA: insight into tRNA recognition and reaction mechanism.,Zhou C, Huang RH Proc Natl Acad Sci U S A. 2008 Oct 21;105(42):16142-7. Epub 2008 Oct 13. PMID:18852462<ref>PMID:18852462</ref>

	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~
	~~</div>~~
	~~<div class="pdbe-citations 3eph" style="background-color:#fffaf0;"></div>~~

	==See Also==		==See Also==
Line 38:		Line 27:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	~~[[Category: Atcc 18824]]~~
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: ~~TRNA dimethylallyltransferase~~]]		[[Category: Saccharomyces cerevisiae]]
	[[Category: Huang~~, R H~~]]		[[Category: Huang RH]]
	[[Category: Zhou, C]]		[[Category: Zhou C]]
	~~[[Category: Alternative initiation]]~~
	~~[[Category: Atp-binding]]~~
	~~[[Category: Cytoplasm]]~~
	~~[[Category: Mitochondrion]]~~
	~~[[Category: Nucleotide-binding]]~~
	~~[[Category: Nucleus]]~~
	~~[[Category: Transferase]]~~
	~~[[Category: Transferase-rna complex]]~~
	~~[[Category: Trna processing~~]]

OCA at 09:12, 23 February 2022

2022-02-23T09:12:31Z

← Older revision		Revision as of 09:12, 23 February 2022
Line 1:		Line 1:

	==Crystallographic snapshots of eukaryotic dimethylallyltransferase acting on tRNA: Insight into tRNA recognition and reaction mechanism==		==Crystallographic snapshots of eukaryotic dimethylallyltransferase acting on tRNA: Insight into tRNA recognition and reaction mechanism==
	<StructureSection load='3eph' size='340' side='right' caption='[[3eph]], [[Resolution\|resolution]] 2.95Å' scene=''>		<StructureSection load='3eph' size='340' side='right'caption='[[3eph]], [[Resolution\|resolution]] 2.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3eph]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3EPH OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3EPH FirstGlance]. <br>		<table><tr><td colspan='2'>[[3eph]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3EPH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3EPH FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PPV:PYROPHOSPHATE'>PPV</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=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PPV:PYROPHOSPHATE'>PPV</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3epj\|3epj]], [[3epk\|3epk]], [[3epl\|3epl]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3epj\|3epj]], [[3epk\|3epk]], [[3epl\|3epl]]</div></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MOD5, YOR274W ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MOD5, YOR274W ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/tRNA_dimethylallyltransferase tRNA dimethylallyltransferase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.5.1.75 2.5.1.75] </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_dimethylallyltransferase tRNA dimethylallyltransferase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.5.1.75 2.5.1.75] </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=3eph FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3eph OCA], [~~http~~://pdbe.org/3eph PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3eph RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3eph PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3eph 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=3eph FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3eph OCA], [https://pdbe.org/3eph PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3eph RCSB], [https://www.ebi.ac.uk/pdbsum/3eph PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3eph ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[~~http~~://www.uniprot.org/uniprot/MOD5_YEAST MOD5_YEAST]] Catalyzes the transfer of a dimethylallyl group onto the adenine at position 37 in the anticodon loop on a specific subset of tRNAs both in the cytosol and the mitochondrion, leading to the formation of N6-(dimethylallyl)adenosine (i(6)A). This modification optimizes the codon:anticodon fit in the ribosome and promotes translational fidelity. Competes with the farnesyl pyrophosphate synthase ERG20 for the common substrate dimethylallyl diphosphate (DMAPP).<ref>PMID:3031456</ref> <ref>PMID:10618371</ref> <ref>PMID:21873461</ref>		[[https://www.uniprot.org/uniprot/MOD5_YEAST MOD5_YEAST]] Catalyzes the transfer of a dimethylallyl group onto the adenine at position 37 in the anticodon loop on a specific subset of tRNAs both in the cytosol and the mitochondrion, leading to the formation of N6-(dimethylallyl)adenosine (i(6)A). This modification optimizes the codon:anticodon fit in the ribosome and promotes translational fidelity. Competes with the farnesyl pyrophosphate synthase ERG20 for the common substrate dimethylallyl diphosphate (DMAPP).<ref>PMID:3031456</ref> <ref>PMID:10618371</ref> <ref>PMID:21873461</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</StructureSection>		</StructureSection>
	[[Category: Atcc 18824]]		[[Category: Atcc 18824]]
			[[Category: Large Structures]]
	[[Category: TRNA dimethylallyltransferase]]		[[Category: TRNA dimethylallyltransferase]]
	[[Category: Huang, R H]]		[[Category: Huang, R H]]

OCA at 21:50, 2 December 2018

2018-12-02T21:50:51Z

← Older revision		Revision as of 21:50, 2 December 2018
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	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ep/3eph_consurf.spt"</scriptWhenChecked>		<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ep/3eph_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
Line 33:		Line 33:

	==See Also==		==See Also==
	*[[~~TRNA~~\|~~TRNA~~]]		*[[Transfer RNA (tRNA)\|Transfer RNA (tRNA)]]
	== References ==		== References ==
	<references/>		<references/>
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	[[Category: Alternative initiation]]		[[Category: Alternative initiation]]
	[[Category: Atp-binding]]		[[Category: Atp-binding]]
			[[Category: Cytoplasm]]
	[[Category: Mitochondrion]]		[[Category: Mitochondrion]]
	[[Category: Nucleotide-binding]]		[[Category: Nucleotide-binding]]

OCA at 00:33, 5 August 2016

2016-08-05T00:33:36Z

← Older revision		Revision as of 00:33, 5 August 2016
Line 1:		Line 1:

	==Crystallographic snapshots of eukaryotic dimethylallyltransferase acting on tRNA: Insight into tRNA recognition and reaction mechanism==		==Crystallographic snapshots of eukaryotic dimethylallyltransferase acting on tRNA: Insight into tRNA recognition and reaction mechanism==
	<StructureSection load='3eph' size='340' side='right' caption='[[3eph]], [[Resolution\|resolution]] 2.95Å' scene=''>		<StructureSection load='3eph' size='340' side='right' caption='[[3eph]], [[Resolution\|resolution]] 2.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3eph]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Saccharomyces_cerevisiae Saccharomyces cerevisiae~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3EPH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3EPH FirstGlance]. <br>		<table><tr><td colspan='2'>[[3eph]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3EPH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3EPH FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PPV:PYROPHOSPHATE'>PPV</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=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PPV:PYROPHOSPHATE'>PPV</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3epj\|3epj]], [[3epk\|3epk]], [[3epl\|3epl]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3epj\|3epj]], [[3epk\|3epk]], [[3epl\|3epl]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MOD5, YOR274W ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ~~Saccharomyces cerevisiae~~])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MOD5, YOR274W ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/tRNA_dimethylallyltransferase tRNA dimethylallyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.5.1.75 2.5.1.75] </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_dimethylallyltransferase tRNA dimethylallyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.5.1.75 2.5.1.75] </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=3eph FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3eph OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3eph RCSB], [http://www.ebi.ac.uk/pdbsum/3eph 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=3eph FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3eph OCA], [http://pdbe.org/3eph PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3eph RCSB], [http://www.ebi.ac.uk/pdbsum/3eph PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3eph ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 19:		Line 20:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].		</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3eph ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	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 3eph" style="background-color:#fffaf0;"></div>

			==See Also==
			*[[TRNA\|TRNA]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Saccharomyces cerevisiae~~]]		[[Category: Atcc 18824]]
	[[Category: TRNA dimethylallyltransferase]]		[[Category: TRNA dimethylallyltransferase]]
	[[Category: Huang, R H]]		[[Category: Huang, R H]]

OCA at 14:23, 25 December 2014

2014-12-25T14:23:58Z

← Older revision		Revision as of 14:23, 25 December 2014
Line 9:		Line 9:
	<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=3eph FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3eph OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3eph RCSB], [http://www.ebi.ac.uk/pdbsum/3eph 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=3eph FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3eph OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3eph RCSB], [http://www.ebi.ac.uk/pdbsum/3eph PDBsum]</span></td></tr>
	</table>		</table>
			== Function ==
			[[http://www.uniprot.org/uniprot/MOD5_YEAST MOD5_YEAST]] Catalyzes the transfer of a dimethylallyl group onto the adenine at position 37 in the anticodon loop on a specific subset of tRNAs both in the cytosol and the mitochondrion, leading to the formation of N6-(dimethylallyl)adenosine (i(6)A). This modification optimizes the codon:anticodon fit in the ribosome and promotes translational fidelity. Competes with the farnesyl pyrophosphate synthase ERG20 for the common substrate dimethylallyl diphosphate (DMAPP).<ref>PMID:3031456</ref> <ref>PMID:10618371</ref> <ref>PMID:21873461</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 08:34, 26 November 2014

2014-11-26T08:34:37Z

← Older revision		Revision as of 08:34, 26 November 2014
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	[[Image:~~3eph~~.~~png~~\|~~left~~\|~~200px~~]]		==Crystallographic snapshots of eukaryotic dimethylallyltransferase acting on tRNA: Insight into tRNA recognition and reaction mechanism==
			<StructureSection load='3eph' size='340' side='right' caption='[[3eph]], [[Resolution\|resolution]] 2.95Å' scene=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[3eph]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3EPH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3EPH FirstGlance]. <br>
			</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PPV:PYROPHOSPHATE'>PPV</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
			<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3epj\|3epj]], [[3epk\|3epk]], [[3epl\|3epl]]</td></tr>
			<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MOD5, YOR274W ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 Saccharomyces cerevisiae])</td></tr>
			<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/tRNA_dimethylallyltransferase tRNA dimethylallyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.5.1.75 2.5.1.75] </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=3eph FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3eph OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3eph RCSB], [http://www.ebi.ac.uk/pdbsum/3eph PDBsum]</span></td></tr>
			</table>
			== Evolutionary Conservation ==
			[[Image:Consurf_key_small.gif\|200px\|right]]
			Check<jmol>
			<jmolCheckbox>
			<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ep/3eph_consurf.spt"</scriptWhenChecked>
			<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
			<text>to colour the structure by Evolutionary Conservation</text>
			</jmolCheckbox>
			</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
			<div style="clear:both"></div>
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			Hypermodifications near the anticodon of tRNA are fundamental for the efficiency and fidelity of protein synthesis. Dimethylallyltransferase (DMATase) catalyzes transfer of a dimethylallyl moiety from dimethylallyl pyrophosphate to N6 of A37 in certain tRNAs. Here we present the crystal structures of Saccharomyces cerevisiae DMATase-tRNA(Cys) complex in four distinct forms, which provide snapshots of the RNA modification reaction catalyzed by DMATase. The structures reveal that the enzyme recognizes the tRNA substrate through indirect sequence readout. The targeted nucleotide A37 flips out from the anticodon loop of tRNA and flips into a channel in DMATase, where it meets its reaction partner di methylallyl pyrophosphate, which enters the channel from the opposite end. Structural changes accompanying the transfer reaction taking place in the crystal result in disengagement of DMATase-tRNA interaction near the reaction center. In addition, structural comparison of DMATase in the complex with unliganded bacterial DMATase provides a molecular basis of ordered substrate binding by DMATase.

	~~{{STRUCTURE_3eph\| PDB=3eph \| SCENE= }}~~		Crystallographic snapshots of eukaryotic dimethylallyltransferase acting on tRNA: insight into tRNA recognition and reaction mechanism.,Zhou C, Huang RH Proc Natl Acad Sci U S A. 2008 Oct 21;105(42):16142-7. Epub 2008 Oct 13. PMID:18852462<ref>PMID:18852462</ref>

	~~===Crystallographic snapshots~~ of ~~eukaryotic dimethylallyltransferase acting on tRNA: Insight into tRNA recognition and reaction mechanism===~~		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
	~~{{ABSTRACT_PUBMED_18852462}}~~		== References ==
			<references/>
	~~==About this Structure==~~		__TOC__
	~~[[3eph]] is a 4 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=3EPH OCA].~~		</StructureSection>

	==~~Reference~~==
	<~~ref group="xtra">PMID:018852462<~~/~~ref~~><~~references group="xtra"~~/>
	[[Category: Saccharomyces cerevisiae]]		[[Category: Saccharomyces cerevisiae]]
	[[Category: TRNA dimethylallyltransferase]]		[[Category: TRNA dimethylallyltransferase]]
	[[Category: Huang, R H.]]		[[Category: Huang, R H]]
	[[Category: Zhou, C.]]		[[Category: Zhou, C]]
	[[Category: Alternative initiation]]		[[Category: Alternative initiation]]
	[[Category: Atp-binding]]		[[Category: Atp-binding]]

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

2013-02-06T13:18:00Z

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

← Older revision	Revision as of 13:18, 6 February 2013
(No difference)

OCA at 13:17, 6 February 2013

2013-02-06T13:17:57Z

← Older revision		Revision as of 13:17, 6 February 2013
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	~~{{Seed}}~~
	[[Image:3eph.png\|left\|200px]]		[[Image:3eph.png\|left\|200px]]

	~~<!--~~
	~~The line below this paragraph, containing "STRUCTURE_3eph", creates the "Structure Box" on the page.~~
	~~You may change the PDB parameter (which sets the PDB file loaded into the applet)~~
	~~or the SCENE parameter (which sets the initial scene displayed when the page is loaded),~~
	~~or leave the SCENE parameter empty for the default display.~~
	~~-->~~
	{{STRUCTURE_3eph\| PDB=3eph \| SCENE= }}		{{STRUCTURE_3eph\| PDB=3eph \| SCENE= }}

	===Crystallographic snapshots of eukaryotic dimethylallyltransferase acting on tRNA: Insight into tRNA recognition and reaction mechanism===		===Crystallographic snapshots of eukaryotic dimethylallyltransferase acting on tRNA: Insight into tRNA recognition and reaction mechanism===


	~~<!--~~
	~~The line below this paragraph, {{ABSTRACT_PUBMED_18852462}}, adds the Publication Abstract to the page~~
	~~(as it appears on PubMed at http://www.pubmed.gov), where 18852462 is the PubMed ID number.~~
	~~-->~~
	{{ABSTRACT_PUBMED_18852462}}		{{ABSTRACT_PUBMED_18852462}}

	==About this Structure==		==About this Structure==
	~~3EPH~~ is a 4 ~~chains~~ structure with ~~sequences~~ from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3EPH OCA].		[[3eph]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3EPH OCA].

	==Reference==		==Reference==
	<ref group="xtra">PMID:~~18852462~~</ref><references group="xtra"/>		<ref group="xtra">PMID:018852462</ref><references group="xtra"/>
	[[Category: Saccharomyces cerevisiae]]		[[Category: Saccharomyces cerevisiae]]
	[[Category: TRNA dimethylallyltransferase]]		[[Category: TRNA dimethylallyltransferase]]
Line 30:		Line 18:
	[[Category: Alternative initiation]]		[[Category: Alternative initiation]]
	[[Category: Atp-binding]]		[[Category: Atp-binding]]
	~~[[Category: Cytoplasm]]~~
	[[Category: Mitochondrion]]		[[Category: Mitochondrion]]
	[[Category: Nucleotide-binding]]		[[Category: Nucleotide-binding]]
	[[Category: Nucleus]]		[[Category: Nucleus]]
	[[Category: Transferase]]		[[Category: Transferase]]
	[[Category: Transferase/rna complex]]		[[Category: Transferase-rna complex]]
	[[Category: Trna processing]]		[[Category: Trna processing]]

	~~''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Sep 22 11:46:24 2010''~~

OCA at 08:37, 22 September 2010

2010-09-22T08:37:25Z

← Older revision		Revision as of 08:37, 22 September 2010
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	==About this Structure==		==About this Structure==
	3EPH is a ~~[[Protein complex]]~~ structure of sequences from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3EPH OCA].		3EPH is a 4 chains structure with sequences from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3EPH OCA].

	==Reference==		==Reference==
	Crystallographic snapshots of eukaryotic dimethylallyltransferase acting on tRNA: insight into tRNA recognition and reaction mechanism., Zhou C, Huang RH, Proc Natl Acad Sci U S A. 2008 Oct 21;105(42):16142-7. Epub 2008 Oct 13. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/18852462 18852462]~~		<ref group="xtra">PMID:18852462</ref><references group="xtra"/>
	~~[[Category: Protein complex]]~~
	[[Category: Saccharomyces cerevisiae]]		[[Category: Saccharomyces cerevisiae]]
	[[Category: TRNA ~~isopentenyltransferase~~]]		[[Category: TRNA dimethylallyltransferase]]
	[[Category: ~~Pdbx_ordinal=~~, ~~<PDBx~~:~~audit_author~~.]]		[[Category: Huang, R H.]]
			[[Category: Zhou, C.]]
	[[Category: Alternative initiation]]		[[Category: Alternative initiation]]
	[[Category: Atp-binding]]		[[Category: Atp-binding]]
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	[[Category: Trna processing]]		[[Category: Trna processing]]

	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed ~~Feb 25 20~~:09:~~46 2009~~''		''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Sep 22 11:46:24 2010''

OCA at 18:10, 25 February 2009

2009-02-25T18:10:14Z

← Older revision		Revision as of 18:10, 25 February 2009
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	==About this Structure==		==About this Structure==
	3EPH is a ~~4 chains~~ structure of sequences from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3EPH OCA].		3EPH is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3EPH OCA].

	==Reference==		==Reference==
	~~<ref group="xtra">~~PMID:~~18852462<~~/~~ref><references group="xtra"~~/>		Crystallographic snapshots of eukaryotic dimethylallyltransferase acting on tRNA: insight into tRNA recognition and reaction mechanism., Zhou C, Huang RH, Proc Natl Acad Sci U S A. 2008 Oct 21;105(42):16142-7. Epub 2008 Oct 13. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18852462 18852462]
			[[Category: Protein complex]]
	[[Category: Saccharomyces cerevisiae]]		[[Category: Saccharomyces cerevisiae]]
	[[Category: TRNA isopentenyltransferase]]		[[Category: TRNA isopentenyltransferase]]
	[[Category: ~~Huang~~, ~~R H.]]~~		[[Category: Pdbx_ordinal=, <PDBx:audit_author.]]
	~~[[Category~~: ~~Zhou, C~~.]]
	[[Category: Alternative initiation]]		[[Category: Alternative initiation]]
	[[Category: Atp-binding]]		[[Category: Atp-binding]]
Line 38:		Line 38:
	[[Category: Trna processing]]		[[Category: Trna processing]]

	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Tue~~ Feb ~~17 18~~:37:02 2009''		''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 25 20:09:46 2009''