View source for 1zl3


==Coupling of active site motions and RNA binding==
<StructureSection load='1zl3' size='340' side='right'caption='[[1zl3]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1zl3]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ZL3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1ZL3 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]] 2.8&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=UD5:5-FLUOROURIDINE'>UD5</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=1zl3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1zl3 OCA], [https://pdbe.org/1zl3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1zl3 RCSB], [https://www.ebi.ac.uk/pdbsum/1zl3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1zl3 ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/TRUB_ECOLI TRUB_ECOLI] Responsible for synthesis of pseudouridine from uracil-55 in the psi GC loop of transfer RNAs.<ref>PMID:7489483</ref> <ref>PMID:11142385</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/zl/1zl3_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=1zl3 ConSurf].
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== Publication Abstract from PubMed ==
The pseudouridine synthase TruB is responsible for the universally conserved post-transcriptional modification of residue 55 of elongator tRNAs. In addition to the active site, the "thumb", a peripheral domain unique to the TruB family of enzymes, makes extensive interactions with the substrate. To coordinate RNA binding and release with catalysis, the thumb may be able to sense progress of the reaction in the active site. To establish whether there is a structural correlate of communication between the active site and the RNA-sequestering thumb, we have solved the structure of a catalytically inactive point mutant of TruB in complex with a substrate RNA, and compared it to the previously determined structure of an active TruB bound to a reaction product. Superposition of the two structures shows that they are extremely similar, except in the active site and, intriguingly, in the relative position of the thumb. Because the two structures were solved using isomorphous crystals, and because the thumb is very well ordered in both structures, the displacement of the thumb we observe likely reflects preferential propagation of active site perturbations to this RNA-binding domain. One of the interactions between the active site and the thumb involves an active site residue whose hydrogen-bonding status changes during the reaction. This may allow the peripheral RNA-binding domain to monitor progress of the pseudouridylation reaction.

Precursor complex structure of pseudouridine synthase TruB suggests coupling of active site perturbations to an RNA-sequestering peripheral protein domain.,Hoang C, Hamilton CS, Mueller EG, Ferre-D'Amare AR Protein Sci. 2005 Aug;14(8):2201-6. Epub 2005 Jun 29. PMID:15987897<ref>PMID:15987897</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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<div class="pdbe-citations 1zl3" style="background-color:#fffaf0;"></div>

==See Also==
*[[Guide-independent Pseudouridine synthase|Guide-independent Pseudouridine synthase]]
*[[Pseudouridine synthase 3D structures|Pseudouridine synthase 3D structures]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Escherichia coli]]
[[Category: Large Structures]]
[[Category: Ferre-D'Amare AR]]
[[Category: Hamilton CS]]
[[Category: Hoang C]]
[[Category: Mueller EG]]