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< | ==Crystal Structure Of Archaeosine tRNA-Guanine Transglycosylase Complexed With lambda-form tRNA(Val)== | ||
<StructureSection load='1j2b' size='340' side='right'caption='[[1j2b]], [[Resolution|resolution]] 3.30Å' scene=''> | |||
You may | == Structural highlights == | ||
<table><tr><td colspan='2'>[[1j2b]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_horikoshii Pyrococcus horikoshii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1J2B OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1J2B FirstGlance]. <br> | |||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3.3Å</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=ZN:ZINC+ION'>ZN</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=1j2b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1j2b OCA], [https://pdbe.org/1j2b PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1j2b RCSB], [https://www.ebi.ac.uk/pdbsum/1j2b PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1j2b ProSAT], [https://www.topsan.org/Proteins/RSGI/1j2b TOPSAN]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/ATGT_PYRHO ATGT_PYRHO] Exchanges the guanine residue with 7-cyano-7-deazaguanine (preQ0) at position 15 in the dihydrouridine loop (D-loop) of archaeal tRNAs.[HAMAP-Rule:MF_01634] | |||
== 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/j2/1j2b_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=1j2b ConSurf]. | |||
<div style="clear:both"></div> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Transfer RNA (tRNA) canonically has the clover-leaf secondary structure with the acceptor, D, anticodon, and T arms, which are folded into the L-shaped tertiary structure. To strengthen the L form, posttranscriptional modifications occur on nucleotides buried within the core, but the modification enzymes are paradoxically inaccessible to them in the L form. In this study, we determined the crystal structure of tRNA bound with archaeosine tRNA-guanine transglycosylase, which modifies G15 of the D arm in the core. The bound tRNA assumes an alternative conformation ("lambda form") drastically different from the L form. All of the D-arm secondary base pairs and the canonical tertiary interactions are disrupted. Furthermore, a helical structure is reorganized, while the rest of the D arm is single stranded and protruded. Consequently, the enzyme precisely locates the exposed G15 in the active site, by counting the nucleotide number from G1 to G15 in the lambda form. | |||
Alternative tertiary structure of tRNA for recognition by a posttranscriptional modification enzyme.,Ishitani R, Nureki O, Nameki N, Okada N, Nishimura S, Yokoyama S Cell. 2003 May 2;113(3):383-94. PMID:12732145<ref>PMID:12732145</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 1j2b" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[TRNA-guanine transglycosylase 3D structures|TRNA-guanine transglycosylase 3D structures]] | |||
*[[Transfer RNA (tRNA)|Transfer RNA (tRNA)]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
== | </StructureSection> | ||
[[Category: Large Structures]] | |||
== | |||
[[Category: Pyrococcus horikoshii]] | [[Category: Pyrococcus horikoshii]] | ||
[[Category: Ishitani R]] | |||
[[Category: Ishitani | [[Category: Nameki N]] | ||
[[Category: Nameki | [[Category: Nishimura S]] | ||
[[Category: Nishimura | [[Category: Nureki O]] | ||
[[Category: Nureki | [[Category: Okada N]] | ||
[[Category: Okada | [[Category: Yokoyama S]] | ||
[[Category: Yokoyama | |||
Latest revision as of 10:14, 25 October 2023
Crystal Structure Of Archaeosine tRNA-Guanine Transglycosylase Complexed With lambda-form tRNA(Val)Crystal Structure Of Archaeosine tRNA-Guanine Transglycosylase Complexed With lambda-form tRNA(Val)
Structural highlights
FunctionATGT_PYRHO Exchanges the guanine residue with 7-cyano-7-deazaguanine (preQ0) at position 15 in the dihydrouridine loop (D-loop) of archaeal tRNAs.[HAMAP-Rule:MF_01634] Evolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMedTransfer RNA (tRNA) canonically has the clover-leaf secondary structure with the acceptor, D, anticodon, and T arms, which are folded into the L-shaped tertiary structure. To strengthen the L form, posttranscriptional modifications occur on nucleotides buried within the core, but the modification enzymes are paradoxically inaccessible to them in the L form. In this study, we determined the crystal structure of tRNA bound with archaeosine tRNA-guanine transglycosylase, which modifies G15 of the D arm in the core. The bound tRNA assumes an alternative conformation ("lambda form") drastically different from the L form. All of the D-arm secondary base pairs and the canonical tertiary interactions are disrupted. Furthermore, a helical structure is reorganized, while the rest of the D arm is single stranded and protruded. Consequently, the enzyme precisely locates the exposed G15 in the active site, by counting the nucleotide number from G1 to G15 in the lambda form. Alternative tertiary structure of tRNA for recognition by a posttranscriptional modification enzyme.,Ishitani R, Nureki O, Nameki N, Okada N, Nishimura S, Yokoyama S Cell. 2003 May 2;113(3):383-94. PMID:12732145[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences |
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