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3syu

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==Re-refined coordinates for pdb entry 1det - ribonuclease T1 carboxymethylated at GLU 58 in complex with 2'GMP==
==Re-refined coordinates for pdb entry 1det - ribonuclease T1 carboxymethylated at GLU 58 in complex with 2'GMP==
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<StructureSection load='3syu' size='340' side='right' caption='[[3syu]], [[Resolution|resolution]] 1.95&Aring;' scene=''>
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<StructureSection load='3syu' size='340' side='right'caption='[[3syu]], [[Resolution|resolution]] 1.95&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[3syu]] is a 1 chain structure with 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=3SYU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3SYU FirstGlance]. <br>
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<table><tr><td colspan='2'>[[3syu]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Aspergillus_oryzae_RIB40 Aspergillus oryzae RIB40]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3SYU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3SYU FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=2GP:GUANOSINE-2-MONOPHOSPHATE'>2GP</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=UNX:UNKNOWN+ATOM+OR+ION'>UNX</scene></td></tr>
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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]] 1.95&#8491;</td></tr>
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<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CGA:CARBOXYMETHYLATED+GLUTAMIC+ACID'>CGA</scene></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>, <scene name='pdbligand=UNX:UNKNOWN+ATOM+OR+ION'>UNX</scene></td></tr>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1det|1det]]</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=3syu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3syu OCA], [https://pdbe.org/3syu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3syu RCSB], [https://www.ebi.ac.uk/pdbsum/3syu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3syu ProSAT]</span></td></tr>
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<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[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] </span></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3syu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3syu OCA], [http://pdbe.org/3syu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3syu RCSB], [http://www.ebi.ac.uk/pdbsum/3syu PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3syu ProSAT]</span></td></tr>
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</table>
</table>
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<div style="background-color:#fffaf0;">
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== Function ==
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== Publication Abstract from PubMed ==
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[https://www.uniprot.org/uniprot/RNT1_ASPOR RNT1_ASPOR]
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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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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>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 3syu" style="background-color:#fffaf0;"></div>
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==See Also==
==See Also==
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*[[Ribonuclease|Ribonuclease]]
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*[[Ribonuclease 3D structures|Ribonuclease 3D structures]]
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*[[Temp|Temp]]
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== References ==
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<references/>
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Aspergillus oryzae]]
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[[Category: Aspergillus oryzae RIB40]]
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[[Category: Bricogne, G]]
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[[Category: Large Structures]]
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[[Category: Smart, O S]]
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[[Category: Bricogne G]]
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[[Category: Womack, T O]]
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[[Category: Smart OS]]
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[[Category: Endoribonuclease]]
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[[Category: Womack TO]]
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[[Category: Hydrolase]]
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Current revision

Re-refined coordinates for pdb entry 1det - ribonuclease T1 carboxymethylated at GLU 58 in complex with 2'GMP

PDB ID 3syu

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