1q2s

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{{Seed}}
 
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[[Image:1q2s.png|left|200px]]
 
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==Chemical trapping and crystal structure of a catalytic tRNA guanine transglycosylase covalent intermediate==
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The line below this paragraph, containing "STRUCTURE_1q2s", creates the "Structure Box" on the page.
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<StructureSection load='1q2s' size='340' side='right'caption='[[1q2s]], [[Resolution|resolution]] 3.20&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[1q2s]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Zymomonas_mobilis Zymomonas mobilis] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Q2S OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1Q2S 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]] 3.2&#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=9DG:9-DEAZAGUANINE'>9DG</scene>, <scene name='pdbligand=N:ANY+5-MONOPHOSPHATE+NUCLEOTIDE'>N</scene>, <scene name='pdbligand=PQ1:PHOSPHORIC+ACID+MONO-[5-(2-AMINO-5-AMINOMETHYL-4-OXO-3,5-DIHYDRO-4H-PYRIDO[2,3-D]PYRIMIDIN-8-YL)-3,4-DIHYDROXY-TETRAHYDRO-FURAN-2-YLMETHYL]+ESTER'>PQ1</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
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{{STRUCTURE_1q2s| PDB=1q2s | SCENE= }}
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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=1q2s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1q2s OCA], [https://pdbe.org/1q2s PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1q2s RCSB], [https://www.ebi.ac.uk/pdbsum/1q2s PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1q2s ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/TGT_ZYMMO TGT_ZYMMO] Exchanges the guanine residue with 7-aminomethyl-7-deazaguanine in tRNAs with GU(N) anticodons (tRNA-Asp, -Asn, -His and -Tyr). After this exchange, a cyclopentendiol moiety is attached to the 7-aminomethyl group of 7-deazaguanine, resulting in the hypermodified nucleoside queuosine (Q) (7-(((4,5-cis-dihydroxy-2-cyclopenten-1-yl)amino)methyl)-7-deazaguanosine).[HAMAP-Rule:MF_00168]
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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/q2/1q2s_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=1q2s 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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Prokaryotic tRNA guanine transglycosylase (TGT) catalyzes replacement of guanine (G) by 7-aminomethyl-7-deazaguanine (PreQ1) at the wobble position of four specific tRNAs. Addition of 9-deazaguanine (9dzG) to a reaction mixture of Zymomonas mobilis TGT and an RNA substrate allowed us to trap, purify and crystallize a chemically competent covalent intermediate of the TGT-catalyzed reaction. The crystal structure of the TGT-RNA-9dzG ternary complex at a resolution of 2.9 A reveals, unexpectedly, that RNA is tethered to TGT through the side chain of Asp280. Thus, Asp280, instead of the previously proposed Asp102, acts as the nucleophile for the reaction. The RNA substrate adopts an unusual conformation, with four out of seven nucleotides in the loop region flipped out. Interactions between TGT and RNA revealed by the structure provide the molecular basis of the RNA substrate requirements by TGT. Furthermore, reaction of PreQ1 with the crystallized covalent intermediate provides insight into the necessary structural changes required for the TGT-catalyzed reaction to occur.
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===Chemical trapping and crystal structure of a catalytic tRNA guanine transglycosylase covalent intermediate===
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Chemical trapping and crystal structure of a catalytic tRNA guanine transglycosylase covalent intermediate.,Xie W, Liu X, Huang RH Nat Struct Biol. 2003 Oct;10(10):781-8. Epub 2003 Aug 31. PMID:12949492<ref>PMID:12949492</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 1q2s" style="background-color:#fffaf0;"></div>
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==See Also==
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The line below this paragraph, {{ABSTRACT_PUBMED_12949492}}, adds the Publication Abstract to the page
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*[[TRNA-guanine transglycosylase 3D structures|TRNA-guanine transglycosylase 3D structures]]
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(as it appears on PubMed at http://www.pubmed.gov), where 12949492 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_12949492}}
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__TOC__
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</StructureSection>
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==About this Structure==
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[[Category: Large Structures]]
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1Q2S is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Zymomonas_mobilis Zymomonas mobilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Q2S OCA].
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[[Category: Synthetic construct]]
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==Reference==
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Chemical trapping and crystal structure of a catalytic tRNA guanine transglycosylase covalent intermediate., Xie W, Liu X, Huang RH, Nat Struct Biol. 2003 Oct;10(10):781-8. Epub 2003 Aug 31. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12949492 12949492]
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[[Category: Queuine tRNA-ribosyltransferase]]
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[[Category: Single protein]]
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[[Category: Zymomonas mobilis]]
[[Category: Zymomonas mobilis]]
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[[Category: Huang, R H.]]
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[[Category: Huang RH]]
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[[Category: Liu, X.]]
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[[Category: Liu X]]
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[[Category: Xie, W.]]
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[[Category: Xie W]]
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[[Category: Covalent intermediat]]
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[[Category: Protein-rna complex]]
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[[Category: Tim barrel]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jul 28 12:31:21 2008''
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Current revision

Chemical trapping and crystal structure of a catalytic tRNA guanine transglycosylase covalent intermediate

PDB ID 1q2s

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