|
|
| (12 intermediate revisions not shown.) |
| Line 1: |
Line 1: |
| - | [[Image:1wkf.jpg|left|200px]] | |
| | | | |
| - | {{Structure
| + | ==TRNA-GUANINE TRANSGLYCOSYLASE== |
| - | |PDB= 1wkf |SIZE=350|CAPTION= <scene name='initialview01'>1wkf</scene>, resolution 2.2Å
| + | <StructureSection load='1wkf' size='340' side='right'caption='[[1wkf]], [[Resolution|resolution]] 2.20Å' scene=''> |
| - | |SITE=
| + | == Structural highlights == |
| - | |LIGAND= <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene>
| + | <table><tr><td colspan='2'>[[1wkf]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Zymomonas_mobilis Zymomonas mobilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WKF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1WKF FirstGlance]. <br> |
| - | |ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Queuine_tRNA-ribosyltransferase Queuine tRNA-ribosyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.2.29 2.4.2.29] </span>
| + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.2Å</td></tr> |
| - | |GENE= TGT ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=542 Zymomonas mobilis])
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr> |
| - | |DOMAIN=
| + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1wkf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wkf OCA], [https://pdbe.org/1wkf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1wkf RCSB], [https://www.ebi.ac.uk/pdbsum/1wkf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1wkf ProSAT]</span></td></tr> |
| - | |RELATEDENTRY= | + | </table> |
| - | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1wkf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wkf OCA], [http://www.ebi.ac.uk/pdbsum/1wkf PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1wkf RCSB]</span>
| + | == Function == |
| - | }}
| + | [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] |
| | + | == 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/wk/1wkf_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/main_output.php?pdb_ID=1wkf ConSurf]. |
| | + | <div style="clear:both"></div> |
| | | | |
| - | '''TRNA-GUANINE TRANSGLYCOSYLASE'''
| + | ==See Also== |
| - | | + | *[[TRNA-guanine transglycosylase 3D structures|TRNA-guanine transglycosylase 3D structures]] |
| - | | + | __TOC__ |
| - | ==Overview== | + | </StructureSection> |
| - | Procaryotic tRNA-guanine transglycosylase (TGT) catalyzes the posttranscriptional base exchange of the queuine precursor 7-aminomethyl-7-deazaguanine (preQ1) with the genetically encoded guanine at the wobble position of tRNAs specific for Asn, Asp, His, and Tyr. The X-ray structures of Zymomonas mobilis TGT and of its complex with preQ1 [Romier, C., Reuter, K., Suck, D., & Ficner, R. (1996) EMBO J. 15, 2850-2857] have revealed a specific preQ1 binding pocket and allowed a proposal for tRNA binding and recognition. We have used band-shift experiments in denaturing conditions to study the enzymatic reaction performed by TGT. The presence of shifted protein bands after incubation with tRNA followed by protein denaturation indicates a reaction mechanism involving a covalent intermediate. Inspection of the X-ray structures and comparison of the different procaryotic TGT sequences highlighted the conserved aspartate 102 as the most likely nucleophile. Mutation of this residue into alanine by site-directed mutagenesis leads to an inactive mutant unable to form a covalent intermediate with tRNA, proving that aspartate 102 is the active site nucleophile in TGT. To investigate the recognition of the wobble guanine in the preQ1 binding pocket, we mutated aspartate 156, the major recognition element for preQ1, into alanine and tyrosine. Both mutants are inactive in producing the final product, but the mutant D156A is able to form the covalent intermediate with tRNA in the first step of the reaction mechanism in comparable amounts to wild-type protein. Therefore, the binding of the wobble guanine in the preQ1 binding pocket is required for the cleavage of the glycosidic bond. The three mutants were crystallized and their X-ray structures determined. The mutants display only subtle changes to the wild-type protein, confirming that the observed biochemical results are due to the chemical substitutions rather than structural rearrangements.
| + | [[Category: Large Structures]] |
| - | | + | |
| - | ==About this Structure==
| + | |
| - | 1WKF 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=1WKF OCA].
| + | |
| - | | + | |
| - | ==Reference==
| + | |
| - | Mutagenesis and crystallographic studies of Zymomonas mobilis tRNA-guanine transglycosylase reveal aspartate 102 as the active site nucleophile., Romier C, Reuter K, Suck D, Ficner R, Biochemistry. 1996 Dec 10;35(49):15734-9. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/8961936 8961936]
| + | |
| - | [[Category: Queuine tRNA-ribosyltransferase]]
| + | |
| - | [[Category: Single protein]] | + | |
| | [[Category: Zymomonas mobilis]] | | [[Category: Zymomonas mobilis]] |
| - | [[Category: Ficner, R.]] | + | [[Category: Ficner R]] |
| - | [[Category: Reuter, K.]] | + | [[Category: Reuter K]] |
| - | [[Category: Romier, C.]] | + | [[Category: Romier C]] |
| - | [[Category: Suck, D.]] | + | [[Category: Suck D]] |
| - | [[Category: trna-modifying enzyme]]
| + | |
| - | | + | |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 00:37:24 2008''
| + | |
