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1det

From Proteopedia

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(New page: 200px<br /><applet load="1det" size="450" color="white" frame="true" align="right" spinBox="true" caption="1det, resolution 1.8&Aring;" /> '''RIBONUCLEASE T1 CARBO...)
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[[Image:1det.gif|left|200px]]<br /><applet load="1det" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1det, resolution 1.8&Aring;" />
 
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'''RIBONUCLEASE T1 CARBOXYMETHYLATED AT GLU 58 IN COMPLEX WITH 2'GMP'''<br />
 
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==Overview==
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==RIBONUCLEASE T1 CARBOXYMETHYLATED AT GLU 58 IN COMPLEX WITH 2'GMP==
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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.
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<StructureSection load='1det' size='340' side='right'caption='[[1det]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
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== Structural highlights ==
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<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>
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</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>
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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=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>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/RNT1_ASPOR RNT1_ASPOR]
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/de/1det_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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].
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<div style="clear:both"></div>
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==About this Structure==
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==See Also==
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1DET 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 NA and 2GP 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=1DET OCA].
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*[[Ribonuclease 3D structures|Ribonuclease 3D structures]]
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__TOC__
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==Reference==
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</StructureSection>
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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:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=8679590 8679590]
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[[Category: Aspergillus oryzae]]
[[Category: Aspergillus oryzae]]
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[[Category: Ribonuclease T(1)]]
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[[Category: Large Structures]]
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[[Category: Single protein]]
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[[Category: Ishikawa K]]
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[[Category: Ishikawa, K.]]
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[[Category: Suzuki E]]
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[[Category: Suzuki, E.]]
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[[Category: Takahashi K]]
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[[Category: Takahashi, K.]]
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[[Category: Tanokura M]]
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[[Category: Tanokura, M.]]
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[[Category: 2GP]]
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[[Category: NA]]
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[[Category: endonuclease]]
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[[Category: endoribonuclease]]
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[[Category: hydrolase]]
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[[Category: nuclease]]
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[[Category: signal]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 13:13:41 2007''
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Current revision

RIBONUCLEASE T1 CARBOXYMETHYLATED AT GLU 58 IN COMPLEX WITH 2'GMP

PDB ID 1det

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