1det: Difference between revisions

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{{Seed}}
[[Image:1det.png|left|200px]]


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==RIBONUCLEASE T1 CARBOXYMETHYLATED AT GLU 58 IN COMPLEX WITH 2'GMP==
The line below this paragraph, containing "STRUCTURE_1det", creates the "Structure Box" on the page.
<StructureSection load='1det' size='340' side='right'caption='[[1det]], [[Resolution|resolution]] 1.80&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'>[[1det]] 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=1DET OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DET 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]] 1.8&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=2GP:GUANOSINE-2-MONOPHOSPHATE'>2GP</scene>, <scene name='pdbligand=CGA:CARBOXYMETHYLATED+GLUTAMIC+ACID'>CGA</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
{{STRUCTURE_1det|  PDB=1det  |  SCENE=  }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1det FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1det OCA], [https://pdbe.org/1det PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1det RCSB], [https://www.ebi.ac.uk/pdbsum/1det PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1det 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/de/1det_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=1det ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The carboxymethylation of RNase T1 at the gamma-carboxyl group of Glu58 leads to a complete loss of the enzymatic activity while it retains substrate-binding ability. Accompanying the carboxymethylation, RNase T1 undergoes a remarkable thermal stabilization of 9 degrees C in the melting temperature (Tm). In order to clarify the inactivation and stabilization mechanisms of RNase T1 by carboxymethylation, the crystal structure of carboxymethylated RNase T1 (CM-RNase T1) complexed with 2'-GMP was determined at 1.8 A resolution. The structure, including 79 water molecules and two Na+, was refined to an R factor of 0.194 with 10 354 reflections &gt; 1 sigma (F). The carboxyl group of CM-Glu58, which locates in the active site, occupies almost the same position as the phosphate group of 2'-GMP in the crystal structure of intact RNase T1.2'-GMP complex. Therefore, the phosphate group of 2'-GMP cannot locate in the active site but protrudes toward the solvent. This forces 2'-GMP to adopt an anti form, which contrasts with the syn form in the crystal of the intact RNase T1.2'-GMP complex. The inaccessibility of the phosphate group to the active site can account for the lack of the enzymatic activity in CM-RNase T1. One of the carboxyl oxygen atoms of CM-Glu58 forms two hydrogen bonds with the side-chains of Tyr38 and His40. These hydrogen bonds are considered to mainly contribute to the higher thermal stability of CM-RNase T1. Another carboxyl oxygen atoms of CM-Glu58 is situated nearby His40 and Arg77. This may provide additional electrostatic stabilization.


===RIBONUCLEASE T1 CARBOXYMETHYLATED AT GLU 58 IN COMPLEX WITH 2'GMP===
Crystal structure of ribonuclease T1 carboxymethylated at Glu58 in complex with 2'-GMP.,Ishikawa K, Suzuki E, Tanokura M, Takahashi K Biochemistry. 1996 Jun 25;35(25):8329-34. PMID:8679590<ref>PMID:8679590</ref>


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


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==See Also==
The line below this paragraph, {{ABSTRACT_PUBMED_8679590}}, adds the Publication Abstract to the page
*[[Ribonuclease 3D structures|Ribonuclease 3D structures]]
(as it appears on PubMed at http://www.pubmed.gov), where 8679590 is the PubMed ID number.
== References ==
-->
<references/>
{{ABSTRACT_PUBMED_8679590}}
__TOC__
 
</StructureSection>
==About this Structure==
1DET is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Aspergillus_oryzae Aspergillus oryzae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DET OCA].
 
==Reference==
<ref group="xtra">PMID:8679590</ref><references group="xtra"/>
[[Category: Aspergillus oryzae]]
[[Category: Aspergillus oryzae]]
[[Category: Ishikawa, K.]]
[[Category: Large Structures]]
[[Category: Suzuki, E.]]
[[Category: Ishikawa K]]
[[Category: Takahashi, K.]]
[[Category: Suzuki E]]
[[Category: Tanokura, M.]]
[[Category: Takahashi K]]
[[Category: Endonuclease]]
[[Category: Tanokura M]]
[[Category: Endoribonuclease]]
[[Category: Hydrolase]]
[[Category: Nuclease]]
[[Category: Signal]]
 
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Retrieved from "https://proteopedia.org/1det"