1vs3: Difference between revisions

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[[Image:1vs3.png|left|200px]]


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==Crystal Structure of the tRNA Pseudouridine Synthase TruA From Thermus thermophilus HB8==
The line below this paragraph, containing "STRUCTURE_1vs3", creates the "Structure Box" on the page.
<StructureSection load='1vs3' size='340' side='right'caption='[[1vs3]], [[Resolution|resolution]] 2.25&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'>[[1vs3]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus_HB8 Thermus thermophilus HB8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VS3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1VS3 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]] 2.25&#8491;</td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1vs3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1vs3 OCA], [https://pdbe.org/1vs3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1vs3 RCSB], [https://www.ebi.ac.uk/pdbsum/1vs3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1vs3 ProSAT], [https://www.topsan.org/Proteins/RSGI/1vs3 TOPSAN]</span></td></tr>
{{STRUCTURE_1vs3|  PDB=1vs3  |  SCENE=  }}
</table>
== Function ==
[https://www.uniprot.org/uniprot/TRUA_THET8 TRUA_THET8] Formation of pseudouridine at positions 38, 39 and 40 in the anticodon stem and loop of transfer RNAs (By similarity).[HAMAP-Rule:MF_00171]
== 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/vs/1vs3_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=1vs3 ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The pseudouridine synthase (Psi synthase) TruA catalyzes the conversion of uridine to pseudouridine at positions 38, 39 and/or 40 in the anticodon stem-loop (ASL) of tRNA. We have determined the crystal structure of TruA from Thermus thermophilus HB8 at 2.25 A resolution. TruA and the other (Psi synthases have a completely conserved active site aspartate, which suggests that the members of this enzyme family share a common catalytic mechanism. The T. thermophilus TruA structure reveals the remarkably flexible structural features in the tRNA-binding cleft, which may be responsible for the primary tRNA interaction. In addition, the charged residues occupying the intermediate positions in the cleft may lead the tRNA to the active site for catalysis. Based on the TruB-tRNA complex structure, the T. thermophilus TruA structure reveals that the tRNA probably makes the melting base pairs move into the cleft, and suggests that a conformational change of the substrate tRNA is necessary to facilitate access to the active site aspartate residue, deep within the cleft.


===Crystal Structure of the tRNA Pseudouridine Synthase TruA From Thermus thermophilus HB8===
Crystal structure of tRNA pseudouridine synthase TruA from Thermus thermophilus HB8.,Dong X, Bessho Y, Shibata R, Nishimoto M, Shirouzu M, Kuramitsu S, Yokoyama S RNA Biol. 2006 Jul;3(3):115-22. Epub 2006 Jul 17. PMID:17114947<ref>PMID:17114947</ref>


From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1vs3" style="background-color:#fffaf0;"></div>


<!--
==See Also==
The line below this paragraph, {{ABSTRACT_PUBMED_17114947}}, adds the Publication Abstract to the page
*[[Guide-independent Pseudouridine synthase|Guide-independent Pseudouridine synthase]]
(as it appears on PubMed at http://www.pubmed.gov), where 17114947 is the PubMed ID number.
*[[Pseudouridine synthase 3D structures|Pseudouridine synthase 3D structures]]
-->
== References ==
{{ABSTRACT_PUBMED_17114947}}
<references/>
 
__TOC__
==About this Structure==
</StructureSection>
1VS3 is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VS3 OCA].
[[Category: Large Structures]]
 
[[Category: Thermus thermophilus HB8]]
==Reference==
[[Category: Bessho Y]]
Crystal structure of tRNA pseudouridine synthase TruA from Thermus thermophilus HB8., Dong X, Bessho Y, Shibata R, Nishimoto M, Shirouzu M, Kuramitsu S, Yokoyama S, RNA Biol. 2006 Jul;3(3):115-22. Epub 2006 Jul 17. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17114947 17114947]
[[Category: Dong X]]
[[Category: Thermus thermophilus]]
[[Category: Shirouzu M]]
[[Category: TRNA-pseudouridine synthase I]]
[[Category: Yokoyama S]]
[[Category: Bessho, Y.]]
[[Category: Dong, X.]]
[[Category: RSGI, RIKEN Structural Genomics/Proteomics Initiative.]]
[[Category: Shirouzu, M.]]
[[Category: Yokoyama, S.]]
[[Category: National project on protein structural and functional analyse]]
[[Category: Nppsfa]]
[[Category: Pseudouridine synthase]]
[[Category: Riken structural genomics/proteomics initiative]]
[[Category: Rsgi]]
[[Category: Structural genomic]]
[[Category: Trna modification]]
[[Category: Trua]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Nov 16 15:34:37 2008''

Latest revision as of 03:05, 28 December 2023

Crystal Structure of the tRNA Pseudouridine Synthase TruA From Thermus thermophilus HB8Crystal Structure of the tRNA Pseudouridine Synthase TruA From Thermus thermophilus HB8

Structural highlights

1vs3 is a 2 chain structure with sequence from Thermus thermophilus HB8. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.25Å
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT, TOPSAN

Function

TRUA_THET8 Formation of pseudouridine at positions 38, 39 and 40 in the anticodon stem and loop of transfer RNAs (By similarity).[HAMAP-Rule:MF_00171]

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 PubMed

The pseudouridine synthase (Psi synthase) TruA catalyzes the conversion of uridine to pseudouridine at positions 38, 39 and/or 40 in the anticodon stem-loop (ASL) of tRNA. We have determined the crystal structure of TruA from Thermus thermophilus HB8 at 2.25 A resolution. TruA and the other (Psi synthases have a completely conserved active site aspartate, which suggests that the members of this enzyme family share a common catalytic mechanism. The T. thermophilus TruA structure reveals the remarkably flexible structural features in the tRNA-binding cleft, which may be responsible for the primary tRNA interaction. In addition, the charged residues occupying the intermediate positions in the cleft may lead the tRNA to the active site for catalysis. Based on the TruB-tRNA complex structure, the T. thermophilus TruA structure reveals that the tRNA probably makes the melting base pairs move into the cleft, and suggests that a conformational change of the substrate tRNA is necessary to facilitate access to the active site aspartate residue, deep within the cleft.

Crystal structure of tRNA pseudouridine synthase TruA from Thermus thermophilus HB8.,Dong X, Bessho Y, Shibata R, Nishimoto M, Shirouzu M, Kuramitsu S, Yokoyama S RNA Biol. 2006 Jul;3(3):115-22. Epub 2006 Jul 17. PMID:17114947[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

See Also

References

  1. Dong X, Bessho Y, Shibata R, Nishimoto M, Shirouzu M, Kuramitsu S, Yokoyama S. Crystal structure of tRNA pseudouridine synthase TruA from Thermus thermophilus HB8. RNA Biol. 2006 Jul;3(3):115-22. Epub 2006 Jul 17. PMID:17114947

1vs3, resolution 2.25Å

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