2qca: Difference between revisions

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-[[Image:2qca.jpg|left|200px]]<br /><applet load="2qca" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="2qca, resolution 1.33&Aring;" />
-'''A New Crystal Form of Bovine Pancreatic RNase A in Complex with 2'-Deoxyguanosine-5'-monophosphate'''<br />
-==Overview==
+==A New Crystal Form of Bovine Pancreatic RNase A in Complex with 2'-Deoxyguanosine-5'-monophosphate==
-The structure of bovine pancreatic RNase A has been determined in complex, with 2'-deoxyguanosine-5'-monophosphate (dGMP) at 1.33 A resolution at, room temperature in a previously unreported unit cell belonging to space, group P3(1). There are two molecules of nucleotide per enzyme molecule, one of which lies in the active-site cleft in the productive binding mode, whilst the guanine base of the other dGMP occupies the pyrimidine-specific, binding site in a nonproductive mode such that it forms hydrogen bonds to, the phosphate group of the first dGMP. This is the first RNase A structure, containing a guanine base in the B2 binding site. Each dGMP molecule is, involved in intermolecular interactions with adjacent RNase A molecules in, the lattice and the two nucleotides appear to direct the formation of the, crystal lattice. Because GMP may be produced during degradation of RNA, this association could represent an inhibitor complex and thereby affect, the observed enzyme kinetics.
+<StructureSection load='2qca' size='340' side='right'caption='[[2qca]], [[Resolution|resolution]] 1.33&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[2qca]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QCA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2QCA 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]] 1.33&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DGP:2-DEOXYGUANOSINE-5-MONOPHOSPHATE'>DGP</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=2qca FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qca OCA], [https://pdbe.org/2qca PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2qca RCSB], [https://www.ebi.ac.uk/pdbsum/2qca PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2qca ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/RNAS1_BOVIN RNAS1_BOVIN] Endonuclease that catalyzes the cleavage of RNA on the 3' side of pyrimidine nucleotides. Acts on single stranded and double stranded RNA.<ref>PMID:7479688</ref>
+== 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/qc/2qca_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=2qca ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The structure of bovine pancreatic RNase A has been determined in complex with 2'-deoxyguanosine-5'-monophosphate (dGMP) at 1.33 A resolution at room temperature in a previously unreported unit cell belonging to space group P3(1). There are two molecules of nucleotide per enzyme molecule, one of which lies in the active-site cleft in the productive binding mode, whilst the guanine base of the other dGMP occupies the pyrimidine-specific binding site in a nonproductive mode such that it forms hydrogen bonds to the phosphate group of the first dGMP. This is the first RNase A structure containing a guanine base in the B2 binding site. Each dGMP molecule is involved in intermolecular interactions with adjacent RNase A molecules in the lattice and the two nucleotides appear to direct the formation of the crystal lattice. Because GMP may be produced during degradation of RNA, this association could represent an inhibitor complex and thereby affect the observed enzyme kinetics.
-==About this Structure==
+A new crystal form of bovine pancreatic RNase A in complex with 2'-deoxyguanosine-5'-monophosphate.,Larson SB, Day JS, Cudney R, McPherson A Acta Crystallogr Sect F Struct Biol Cryst Commun. 2007 Sep 1;63(Pt, 9):728-33. Epub 2007 Aug 31. PMID:17768339<ref>PMID:17768339</ref>
-QCA is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Bos_taurus Bos taurus] with DGP as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/Pancreatic_ribonuclease Pancreatic ribonuclease], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.27.5 3.1.27.5] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=2QCA OCA].
-==Reference==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-A new crystal form of bovine pancreatic RNase A in complex with 2'-deoxyguanosine-5'-monophosphate., Larson SB, Day JS, Cudney R, McPherson A, Acta Crystallogr Sect F Struct Biol Cryst Commun. 2007 Sep 1;63(Pt, 9):728-33. Epub 2007 Aug 31. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=17768339 17768339]
+</div>
+<div class="pdbe-citations 2qca" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Ribonuclease 3D structures|Ribonuclease 3D structures]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
 [[Category: Bos taurus]]
-[[Category: Pancreatic ribonuclease]]
+[[Category: Large Structures]]
-[[Category: Single protein]]
+[[Category: Cudney R]]
-[[Category: CHTSB, Center.for.High-Throughput.Structural.Biology.]]
+[[Category: Day JS]]
-[[Category: Cudney, R.]]
+[[Category: Larson SB]]
-[[Category: Day, J.S.]]
+[[Category: McPherson A]]
-[[Category: Larson, S.B.]]
-[[Category: McPherson, A.]]
-[[Category: DGP]]
-[[Category: center for high-throughput structural biology]]
-[[Category: chtsb]]
-[[Category: hydrolase]]
-[[Category: protein structure initiative]]
-[[Category: protein-nucleotide complex]]
-[[Category: psi-2]]
-[[Category: ribonuclease]]
-[[Category: structural genomics]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 13:51:03 2007''