2zm5: Difference between revisions
No edit summary |
No edit summary |
||
| (8 intermediate revisions by the same user not shown) | |||
| Line 1: | Line 1: | ||
< | ==Crystal structure of tRNA modification enzyme MiaA in the complex with tRNA(Phe)== | ||
<StructureSection load='2zm5' size='340' side='right'caption='[[2zm5]], [[Resolution|resolution]] 2.55Å' scene=''> | |||
You may | == Structural highlights == | ||
<table><tr><td colspan='2'>[[2zm5]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZM5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2ZM5 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]] 2.55Å</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=MSE:SELENOMETHIONINE'>MSE</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=2zm5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zm5 OCA], [https://pdbe.org/2zm5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2zm5 RCSB], [https://www.ebi.ac.uk/pdbsum/2zm5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2zm5 ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/MIAA_ECOLI MIAA_ECOLI] Catalyzes the transfer of a dimethylallyl group onto the adenine at position 37 in tRNAs that read codons beginning with uridine, leading to the formation of N6-(dimethylallyl)adenosine (i(6)A).<ref>PMID:9012675</ref> <ref>PMID:9148919</ref> | |||
== 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/zm/2zm5_consurf.spt"</scriptWhenChecked> | |||
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=2zm5 ConSurf]. | |||
<div style="clear:both"></div> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Bacterial and eukaryotic tRNAs that decode codons starting with uridine have a hydrophobically hypermodified adenosine at position 37 (A(37)) adjacent to the 3'-end of the anticodon, which is essential for efficient and highly accurate protein translation by the ribosome. However, it remains unclear as to how the corresponding tRNAs are selected to be modified by alkylation at the correct position of the adenosine base. We have determined a series of crystal structures of bacterial tRNA isopentenyltransferase (MiaA) in apo- and tRNA-bound forms, which completely render snapshots of substrate selections during the modification of RNA. A compact evolutionary inserted domain (herein swinging domain) in MiaA that exhibits as a highly mobile entity moves around the catalytic domain as likely to reach and trap the tRNA substrate. Thereby, MiaA clamps the anticodon stem loop of the tRNA substrate between the catalytic and swinging domains, where the two conserved elongated residues from the swinging domain pinch the two flanking A(36) and A(38) together to squeeze out A(37) into the reaction tunnel. The site-specific isopentenylation of RNA is thus ensured by a characteristic pinch-and-flip mechanism and by a reaction tunnel to confine the substrate selection. Furthermore, combining information from soaking experiments with structural comparisons, we propose a mechanism for the ordered substrate binding of MiaA. | |||
Snapshots of Dynamics in Synthesizing N(6)-Isopentenyladenosine at the tRNA Anticodon.,Chimnaronk S, Forouhar F, Sakai J, Yao M, Tron CM, Atta M, Fontecave M, Hunt JF, Tanaka I Biochemistry. 2009 May 20. PMID:19435325<ref>PMID:19435325</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 2zm5" style="background-color:#fffaf0;"></div> | |||
== | ==See Also== | ||
*[[Transfer RNA (tRNA)|Transfer RNA (tRNA)]] | |||
[[Category: Escherichia coli]] | == References == | ||
[[Category: | <references/> | ||
[[Category: Chimnaronk | __TOC__ | ||
[[Category: Sakai | </StructureSection> | ||
[[Category: Tanaka | [[Category: Escherichia coli K-12]] | ||
[[Category: Yao | [[Category: Large Structures]] | ||
[[Category: Chimnaronk S]] | |||
[[Category: Sakai J]] | |||
[[Category: Tanaka I]] | |||
[[Category: Yao M]] | |||
Latest revision as of 11:09, 23 October 2024
Crystal structure of tRNA modification enzyme MiaA in the complex with tRNA(Phe)Crystal structure of tRNA modification enzyme MiaA in the complex with tRNA(Phe)
Structural highlights
FunctionMIAA_ECOLI Catalyzes the transfer of a dimethylallyl group onto the adenine at position 37 in tRNAs that read codons beginning with uridine, leading to the formation of N6-(dimethylallyl)adenosine (i(6)A).[1] [2] 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 PubMedBacterial and eukaryotic tRNAs that decode codons starting with uridine have a hydrophobically hypermodified adenosine at position 37 (A(37)) adjacent to the 3'-end of the anticodon, which is essential for efficient and highly accurate protein translation by the ribosome. However, it remains unclear as to how the corresponding tRNAs are selected to be modified by alkylation at the correct position of the adenosine base. We have determined a series of crystal structures of bacterial tRNA isopentenyltransferase (MiaA) in apo- and tRNA-bound forms, which completely render snapshots of substrate selections during the modification of RNA. A compact evolutionary inserted domain (herein swinging domain) in MiaA that exhibits as a highly mobile entity moves around the catalytic domain as likely to reach and trap the tRNA substrate. Thereby, MiaA clamps the anticodon stem loop of the tRNA substrate between the catalytic and swinging domains, where the two conserved elongated residues from the swinging domain pinch the two flanking A(36) and A(38) together to squeeze out A(37) into the reaction tunnel. The site-specific isopentenylation of RNA is thus ensured by a characteristic pinch-and-flip mechanism and by a reaction tunnel to confine the substrate selection. Furthermore, combining information from soaking experiments with structural comparisons, we propose a mechanism for the ordered substrate binding of MiaA. Snapshots of Dynamics in Synthesizing N(6)-Isopentenyladenosine at the tRNA Anticodon.,Chimnaronk S, Forouhar F, Sakai J, Yao M, Tron CM, Atta M, Fontecave M, Hunt JF, Tanaka I Biochemistry. 2009 May 20. PMID:19435325[3] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
|
| ||||||||||||||||||