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New page: left|200px<br /><applet load="1xty" size="450" color="white" frame="true" align="right" spinBox="true" caption="1xty, resolution 1.8Å" /> '''Crystal structure of ...
 
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[[Image:1xty.gif|left|200px]]<br /><applet load="1xty" size="450" color="white" frame="true" align="right" spinBox="true"
caption="1xty, resolution 1.8&Aring;" />
'''Crystal structure of Sulfolobus solfataricus peptidyl-tRNA hydrolase'''<br />


==Overview==
==Crystal structure of Sulfolobus solfataricus peptidyl-tRNA hydrolase==
The 3-D structure of the peptidyl-tRNA hydrolase from the archaea, Sulfolobus solfataricus has been solved at 1.8 A resolution. Homologues of, this enzyme are found in archaea and eucarya. Bacteria display a different, type of peptidyl-tRNA hydrolase that is also encountered in eucarya. In, solution, the S. solfataricus hydrolase behaves as a dimer. In agreement, the crystalline structure of this enzyme indicates the formation of a, dimer. Each protomer is made of a mixed five-stranded beta-sheet, surrounded by two groups of two alpha-helices. The dimer interface is, mainly formed by van der Waals interactions between hydrophobic residues, belonging to the two N-terminal alpha1 helices contributed by two, protomers. Site-directed mutagenesis experiments were designed for probing, the basis of specificity of the archaeal hydrolase. Among the strictly, conserved residues within the archaeal/eucaryal peptidyl-tRNA hydrolase, family, three residues, K18, D86, and T90, appear of utmost importance for, activity. They are located in the N-part of alpha1 and in the beta3-beta4, loop. K18 and D86, which form a salt bridge, might play a role in the, catalysis thanks to their acid and basic functions, whereas the OH group, of T90 could act as a nucleophile. These observations clearly distinguish, the active site of the archaeal/eucaryal hydrolases from that of the, bacterial/eucaryal ones, where a histidine is believed to serve as the, catalytic base.
<StructureSection load='1xty' size='340' side='right'caption='[[1xty]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1xty]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharolobus_solfataricus_P2 Saccharolobus solfataricus P2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XTY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1XTY 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]] 1.8&#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></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=1xty FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xty OCA], [https://pdbe.org/1xty PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1xty RCSB], [https://www.ebi.ac.uk/pdbsum/1xty PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1xty ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/PTH_SACS2 PTH_SACS2] The natural substrate for this enzyme may be peptidyl-tRNAs which drop off the ribosome during protein synthesis.[HAMAP-Rule:MF_00628]<ref>PMID:12799450</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/xt/1xty_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=1xty ConSurf].
<div style="clear:both"></div>


==About this Structure==
==See Also==
1XTY is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Pyrococcus_abyssi Pyrococcus abyssi] with SO4 as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/Aminoacyl-tRNA_hydrolase Aminoacyl-tRNA hydrolase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.1.29 3.1.1.29] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1XTY OCA].
*[[Peptidyl-tRNA hydrolase|Peptidyl-tRNA hydrolase]]
 
== References ==
==Reference==
<references/>
Crystal structure at 1.8 A resolution and identification of active site residues of Sulfolobus solfataricus peptidyl-tRNA hydrolase., Fromant M, Schmitt E, Mechulam Y, Lazennec C, Plateau P, Blanquet S, Biochemistry. 2005 Mar 22;44(11):4294-301. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=15766258 15766258]
__TOC__
[[Category: Aminoacyl-tRNA hydrolase]]
</StructureSection>
[[Category: Pyrococcus abyssi]]
[[Category: Large Structures]]
[[Category: Single protein]]
[[Category: Saccharolobus solfataricus P2]]
[[Category: Blanquet, S.]]
[[Category: Blanquet S]]
[[Category: Fromant, M.]]
[[Category: Fromant M]]
[[Category: Lazennec, C.]]
[[Category: Lazennec C]]
[[Category: Mechulam, Y.]]
[[Category: Mechulam Y]]
[[Category: Plateau, P.]]
[[Category: Plateau P]]
[[Category: Schmitt, E.]]
[[Category: Schmitt E]]
[[Category: SO4]]
[[Category: mixed beta sheet]]
 
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Retrieved from "https://proteopedia.org/1xty"