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New page: left|200px<br /><applet load="1low" size="450" color="white" frame="true" align="right" spinBox="true" caption="1low, resolution 1.9Å" /> '''X-ray structure of th...
 
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[[Image:1low.gif|left|200px]]<br /><applet load="1low" size="450" color="white" frame="true" align="right" spinBox="true"
caption="1low, resolution 1.9&Aring;" />
'''X-ray structure of the H40A mutant of Ribonuclease T1 complexed with 3'-guanosine monophosphate'''<br />


==Overview==
==X-ray structure of the H40A mutant of Ribonuclease T1 complexed with 3'-guanosine monophosphate==
Ribonucleases (RNases) catalyze the cleavage of the phosphodiester bond in, RNA up to 10(15)-fold, as compared with the uncatalyzed reaction. High, resolution crystal structures of these enzymes in complex with, 3'-mononucleotide substrates demonstrate the accommodation of the, nucleophilic 2'-OH group in a binding pocket comprising the catalytic base, (glutamate or histidine) and a charged hydrogen bond donor (lysine or, histidine). Ab initio quantum chemical calculations performed on such, Michaelis complexes of the mammalian RNase A (EC ) and the microbial RNase, T(1) (EC ) show negative charge build up on the 2'-oxygen upon substrate, binding. The increased nucleophilicity results from stronger hydrogen, bonding to the catalytic base, which is mediated by a hydrogen bond from, the charged donor. This hitherto unrecognized catalytic dyad in, ribonucleases constitutes a general mechanism for nucleophile activation, in both enzymic and RNA-catalyzed phosphoryl transfer reactions.
<StructureSection load='1low' size='340' side='right'caption='[[1low]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1low]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Aspergillus_oryzae Aspergillus oryzae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LOW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1LOW 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]] 1.9&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=3GP:GUANOSINE-3-MONOPHOSPHATE'>3GP</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</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=1low FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1low OCA], [https://pdbe.org/1low PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1low RCSB], [https://www.ebi.ac.uk/pdbsum/1low PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1low ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/RNT1_ASPOR RNT1_ASPOR]
== 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/lo/1low_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=1low ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Ribonucleases (RNases) catalyze the cleavage of the phosphodiester bond in RNA up to 10(15)-fold, as compared with the uncatalyzed reaction. High resolution crystal structures of these enzymes in complex with 3'-mononucleotide substrates demonstrate the accommodation of the nucleophilic 2'-OH group in a binding pocket comprising the catalytic base (glutamate or histidine) and a charged hydrogen bond donor (lysine or histidine). Ab initio quantum chemical calculations performed on such Michaelis complexes of the mammalian RNase A (EC ) and the microbial RNase T(1) (EC ) show negative charge build up on the 2'-oxygen upon substrate binding. The increased nucleophilicity results from stronger hydrogen bonding to the catalytic base, which is mediated by a hydrogen bond from the charged donor. This hitherto unrecognized catalytic dyad in ribonucleases constitutes a general mechanism for nucleophile activation in both enzymic and RNA-catalyzed phosphoryl transfer reactions.


==About this Structure==
A nucleophile activation dyad in ribonucleases. A combined X-ray crystallographic/ab initio quantum chemical study.,Mignon P, Steyaert J, Loris R, Geerlings P, Loverix S J Biol Chem. 2002 Sep 27;277(39):36770-4. Epub 2002 Jul 16. PMID:12122018<ref>PMID:12122018</ref>
1LOW is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Aspergillus_oryzae Aspergillus oryzae] with CA and 3GP as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Ribonuclease_T(1) Ribonuclease T(1)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.27.3 3.1.27.3] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1LOW OCA].


==Reference==
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
A nucleophile activation dyad in ribonucleases. A combined X-ray crystallographic/ab initio quantum chemical study., Mignon P, Steyaert J, Loris R, Geerlings P, Loverix S, J Biol Chem. 2002 Sep 27;277(39):36770-4. Epub 2002 Jul 16. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=12122018 12122018]
</div>
<div class="pdbe-citations 1low" style="background-color:#fffaf0;"></div>
 
==See Also==
*[[Ribonuclease 3D structures|Ribonuclease 3D structures]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Aspergillus oryzae]]
[[Category: Aspergillus oryzae]]
[[Category: Ribonuclease T(1)]]
[[Category: Large Structures]]
[[Category: Single protein]]
[[Category: Geerlings P]]
[[Category: Geerlings, P.]]
[[Category: Loris R]]
[[Category: Loris, R.]]
[[Category: Loverix S]]
[[Category: Loverix, S.]]
[[Category: Mignon P]]
[[Category: Mignon, P.]]
[[Category: Steyaert J]]
[[Category: Steyaert, J.]]
[[Category: 3GP]]
[[Category: CA]]
[[Category: ab initio calculations]]
[[Category: catalytic dyad]]
[[Category: nucleophile activation]]
[[Category: rnase]]
 
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Retrieved from "https://proteopedia.org/1low"