1bvi

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(New page: 200px<br /><applet load="1bvi" size="450" color="white" frame="true" align="right" spinBox="true" caption="1bvi, resolution 1.90&Aring;" /> '''RIBONUCLEASE T1 (WIL...)
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[[Image:1bvi.gif|left|200px]]<br /><applet load="1bvi" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1bvi, resolution 1.90&Aring;" />
 
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'''RIBONUCLEASE T1 (WILDTYPE) COMPLEXED WITH 2'GMP'''<br />
 
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==Overview==
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==RIBONUCLEASE T1 (WILDTYPE) COMPLEXED WITH 2'GMP==
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The reoccurrence of water molecules in crystal structures of RNase T1 was, investigated. Five waters were found to be invariant in RNase T1 as well, as in six other related fungal RNases. The structural, dynamical, and, functional characteristics of one of these conserved hydration sites, (WAT1) were analyzed by protein engineering, X-ray crystallography, and, (17)O and 2H nuclear magnetic relaxation dispersion (NMRD). The position, of WAT1 and its surrounding hydrogen bond network are unaffected by, deletions of two neighboring side chains. In the mutant Thr93Gln, the, Gln93N epsilon2 nitrogen replaces WAT1 and participates in a similar, hydrogen bond network involving Cys6, Asn9, Asp76, and Thr91. The ability, of WAT1 to form four hydrogen bonds may explain why evolution has, preserved a water molecule, rather than a side-chain atom, at the center, of this intricate hydrogen bond network. Comparison of the (17)O NMRD, profiles from wild-type and Thr93Gln RNase T1 yield a mean residence time, of 7 ns at 27 degrees C and an orientational order parameter of 0.45. The, effects of mutations around WAT1 on the kinetic parameters of RNase T1 are, small but significant and probably relate to the dynamics of the active, site.
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<StructureSection load='1bvi' size='340' side='right'caption='[[1bvi]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1bvi]] is a 4 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=1BVI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1BVI 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]] 1.9&#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=CA:CALCIUM+ION'>CA</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=1bvi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bvi OCA], [https://pdbe.org/1bvi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1bvi RCSB], [https://www.ebi.ac.uk/pdbsum/1bvi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1bvi 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/bv/1bvi_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=1bvi ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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The reoccurrence of water molecules in crystal structures of RNase T1 was investigated. Five waters were found to be invariant in RNase T1 as well as in six other related fungal RNases. The structural, dynamical, and functional characteristics of one of these conserved hydration sites (WAT1) were analyzed by protein engineering, X-ray crystallography, and (17)O and 2H nuclear magnetic relaxation dispersion (NMRD). The position of WAT1 and its surrounding hydrogen bond network are unaffected by deletions of two neighboring side chains. In the mutant Thr93Gln, the Gln93N epsilon2 nitrogen replaces WAT1 and participates in a similar hydrogen bond network involving Cys6, Asn9, Asp76, and Thr91. The ability of WAT1 to form four hydrogen bonds may explain why evolution has preserved a water molecule, rather than a side-chain atom, at the center of this intricate hydrogen bond network. Comparison of the (17)O NMRD profiles from wild-type and Thr93Gln RNase T1 yield a mean residence time of 7 ns at 27 degrees C and an orientational order parameter of 0.45. The effects of mutations around WAT1 on the kinetic parameters of RNase T1 are small but significant and probably relate to the dynamics of the active site.
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==About this Structure==
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Dissection of the structural and functional role of a conserved hydration site in RNase T1.,Langhorst U, Loris R, Denisov VP, Doumen J, Roose P, Maes D, Halle B, Steyaert J Protein Sci. 1999 Apr;8(4):722-30. PMID:10211818<ref>PMID:10211818</ref>
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1BVI 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 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=1BVI OCA].
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==Reference==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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Dissection of the structural and functional role of a conserved hydration site in RNase T1., Langhorst U, Loris R, Denisov VP, Doumen J, Roose P, Maes D, Halle B, Steyaert J, Protein Sci. 1999 Apr;8(4):722-30. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=10211818 10211818]
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</div>
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[[Category: Aspergillus oryzae]]
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<div class="pdbe-citations 1bvi" style="background-color:#fffaf0;"></div>
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[[Category: Ribonuclease T(1)]]
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[[Category: Single protein]]
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[[Category: Denisov, V.P.]]
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[[Category: Doumen, J.]]
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[[Category: Halle, B.]]
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[[Category: Langhorst, U.]]
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[[Category: Loris, R.]]
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[[Category: Maes, D.]]
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[[Category: Roose, P.]]
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[[Category: Steyaert, J.]]
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[[Category: 2GP]]
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[[Category: CA]]
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[[Category: endonuclease]]
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[[Category: endoribonuclease]]
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[[Category: hydrolase]]
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[[Category: ribonuclease]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 11:57:11 2007''
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==See Also==
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*[[Ribonuclease 3D structures|Ribonuclease 3D structures]]
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== References ==
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<references/>
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__TOC__
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</StructureSection>
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[[Category: Aspergillus oryzae]]
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[[Category: Large Structures]]
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[[Category: Denisov VP]]
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[[Category: Doumen J]]
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[[Category: Halle B]]
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[[Category: Langhorst U]]
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[[Category: Loris R]]
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[[Category: Maes D]]
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[[Category: Roose P]]
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[[Category: Steyaert J]]

Current revision

RIBONUCLEASE T1 (WILDTYPE) COMPLEXED WITH 2'GMP

PDB ID 1bvi

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