2det

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(New page: 200px<br /><applet load="2det" size="450" color="white" frame="true" align="right" spinBox="true" caption="2det, resolution 3.40&Aring;" /> '''Cocrystal structure ...)
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[[Image:2det.gif|left|200px]]<br /><applet load="2det" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="2det, resolution 3.40&Aring;" />
 
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'''Cocrystal structure of an RNA sulfuration enzyme MnmA and tRNA-Glu in the pre-reaction state'''<br />
 
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==Overview==
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==Cocrystal structure of an RNA sulfuration enzyme MnmA and tRNA-Glu in the pre-reaction state==
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Uridine at the first anticodon position (U34) of glutamate, lysine and, glutamine transfer RNAs is universally modified by thiouridylase into, 2-thiouridine (s2U34), which is crucial for precise translation by, restricting codon-anticodon wobble during protein synthesis on the, ribosome. However, it remains unclear how the enzyme incorporates reactive, sulphur into the correct position of the uridine base. Here we present the, crystal structures of the MnmA thiouridylase-tRNA complex in three, discrete forms, which provide snapshots of the sequential chemical, reactions during RNA sulphuration. On enzyme activation, an alpha-helix, overhanging the active site is restructured into an idiosyncratic, beta-hairpin-containing loop, which packs the flipped-out U34 deeply into, the catalytic pocket and triggers the activation of the catalytic cysteine, residues. The adenylated RNA intermediate is trapped. Thus, the active, closed-conformation of the complex ensures accurate sulphur incorporation, into the activated uridine carbon by forming a catalytic chamber to, prevent solvent from accessing the catalytic site. The structures of the, complex with glutamate tRNA further reveal how MnmA specifically, recognizes its three different tRNA substrates. These findings provide the, structural basis for a general mechanism whereby an enzyme incorporates a, reactive atom at a precise position in a biological molecule.
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<StructureSection load='2det' size='340' side='right'caption='[[2det]], [[Resolution|resolution]] 3.40&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[2det]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DET OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DET FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3.4&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2det FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2det OCA], [https://pdbe.org/2det PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2det RCSB], [https://www.ebi.ac.uk/pdbsum/2det PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2det ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/MNMA_ECOLI MNMA_ECOLI] Catalyzes the 2-thiolation of uridine at the wobble position (U34) of tRNA(Lys), tRNA(Glu) and tRNA(Gln), leading to the formation of s(2)U34, the first step of tRNA-mnm(5)s(2)U34 synthesis. Sulfur is provided by IscS, via a sulfur-relay system. Binds ATP and its substrate tRNAs.<ref>PMID:12549933</ref>
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/de/2det_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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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=2det ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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Uridine at the first anticodon position (U34) of glutamate, lysine and glutamine transfer RNAs is universally modified by thiouridylase into 2-thiouridine (s2U34), which is crucial for precise translation by restricting codon-anticodon wobble during protein synthesis on the ribosome. However, it remains unclear how the enzyme incorporates reactive sulphur into the correct position of the uridine base. Here we present the crystal structures of the MnmA thiouridylase-tRNA complex in three discrete forms, which provide snapshots of the sequential chemical reactions during RNA sulphuration. On enzyme activation, an alpha-helix overhanging the active site is restructured into an idiosyncratic beta-hairpin-containing loop, which packs the flipped-out U34 deeply into the catalytic pocket and triggers the activation of the catalytic cysteine residues. The adenylated RNA intermediate is trapped. Thus, the active closed-conformation of the complex ensures accurate sulphur incorporation into the activated uridine carbon by forming a catalytic chamber to prevent solvent from accessing the catalytic site. The structures of the complex with glutamate tRNA further reveal how MnmA specifically recognizes its three different tRNA substrates. These findings provide the structural basis for a general mechanism whereby an enzyme incorporates a reactive atom at a precise position in a biological molecule.
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==About this Structure==
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Snapshots of tRNA sulphuration via an adenylated intermediate.,Numata T, Ikeuchi Y, Fukai S, Suzuki T, Nureki O Nature. 2006 Jul 27;442(7101):419-24. PMID:16871210<ref>PMID:16871210</ref>
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2DET is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] with SO4 as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/tRNA_(5-methylaminomethyl-2-thiouridylate)-methyltransferase tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.61 2.1.1.61] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=2DET OCA].
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==Reference==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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Snapshots of tRNA sulphuration via an adenylated intermediate., Numata T, Ikeuchi Y, Fukai S, Suzuki T, Nureki O, Nature. 2006 Jul 27;442(7101):419-24. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=16871210 16871210]
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</div>
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[[Category: Escherichia coli]]
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<div class="pdbe-citations 2det" style="background-color:#fffaf0;"></div>
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[[Category: Single protein]]
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[[Category: tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase]]
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[[Category: Fukai, S.]]
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[[Category: Ikeuchi, Y.]]
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[[Category: Numata, T.]]
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[[Category: Nureki, O.]]
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[[Category: Suzuki, T.]]
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[[Category: SO4]]
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[[Category: protein-rna complex]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 09:34:25 2007''
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==See Also==
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*[[Transfer RNA (tRNA)|Transfer RNA (tRNA)]]
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== References ==
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<references/>
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__TOC__
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</StructureSection>
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[[Category: Escherichia coli]]
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[[Category: Large Structures]]
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[[Category: Fukai S]]
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[[Category: Ikeuchi Y]]
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[[Category: Numata T]]
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[[Category: Nureki O]]
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[[Category: Suzuki T]]

Current revision

Cocrystal structure of an RNA sulfuration enzyme MnmA and tRNA-Glu in the pre-reaction state

PDB ID 2det

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