2zxi: Difference between revisions

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{{Seed}}
[[Image:2zxi.jpg|left|200px]]


<!--
==Structure of Aquifex aeolicus GidA in the form II crystal==
The line below this paragraph, containing "STRUCTURE_2zxi", creates the "Structure Box" on the page.
<StructureSection load='2zxi' size='340' side='right'caption='[[2zxi]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
You may change the PDB parameter (which sets the PDB file loaded into the applet)  
== Structural highlights ==
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
<table><tr><td colspan='2'>[[2zxi]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Aquifex_aeolicus Aquifex aeolicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZXI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2ZXI FirstGlance]. <br>
or leave the SCENE parameter empty for the default display.
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.3&#8491;</td></tr>
-->
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene></td></tr>
{{STRUCTURE_2zxi|  PDB=2zxi  |  SCENE=  }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2zxi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zxi OCA], [https://pdbe.org/2zxi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2zxi RCSB], [https://www.ebi.ac.uk/pdbsum/2zxi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2zxi ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/MNMG_AQUAE MNMG_AQUAE] NAD-binding protein involved in the addition of a carboxymethylaminomethyl (cmnm) group at the wobble position (U34) of certain tRNAs, forming tRNA-cmnm(5)s(2)U34 (By similarity).[HAMAP-Rule:MF_00129]
== 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/zx/2zxi_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=2zxi ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The 5-carboxymethylaminomethyl modification of uridine (cmnm(5)U) at the anticodon first position occurs in tRNAs that read split codon boxes ending with purine. This modification is crucial for correct translation, by restricting codon-anticodon wobbling. Two conserved enzymes, GidA and MnmE, participate in the cmnm(5)U modification process. Here we determined the crystal structure of Aquifex aeolicus GidA at 2.3 A resolution. The structure revealed the tight interaction of GidA with FAD. Structure-based mutation analyses allowed us to identify two conserved Cys residues in the vicinity of the FAD-binding site that are essential for the cmnm(5)U modification in vivo. Together with mutational analysis of MnmE, we propose a mechanism for the cmnm(5)U modification process where GidA, but not MnmE, attacks the C6 atom of uridine by a mechanism analogous to that of thymidylate synthase. We also present a tRNA-docking model that provides structural insights into the tRNA recognition mechanism for efficient modification.


===Structure of Aquifex aeolicus GidA in the form II crystal===
Conserved cysteine residues of GidA are essential for biogenesis of 5-carboxymethylaminomethyluridine at tRNA anticodon.,Osawa T, Ito K, Inanaga H, Nureki O, Tomita K, Numata T Structure. 2009 May 13;17(5):713-24. PMID:19446527<ref>PMID:19446527</ref>


 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
==About this Structure==
</div>
2ZXI is a 4 chains structure of sequences from [http://en.wikipedia.org/wiki/Aquifex_aeolicus Aquifex aeolicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZXI OCA].
<div class="pdbe-citations 2zxi" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Aquifex aeolicus]]
[[Category: Aquifex aeolicus]]
[[Category: Numata, T.]]
[[Category: Large Structures]]
[[Category: Osawa, T.]]
[[Category: Numata T]]
[[Category: 5-carboxymethylaminomethyl uridine]]
[[Category: Osawa T]]
[[Category: Fad]]
[[Category: Fad-binding protein]]
[[Category: Modification]]
[[Category: Trna]]
[[Category: Trna modification enzyme]]
[[Category: Wobble uridine]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed May 20 17:55:08 2009''
Retrieved from "https://proteopedia.org/2zxi"