1j1f: Difference between revisions

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-{{Seed}}
-[[Image:1j1f.png|left|200px]]
-<!--
+==Crystal structure of the RNase MC1 mutant N71T in complex with 5'-GMP==
-The line below this paragraph, containing "STRUCTURE_1j1f", creates the "Structure Box" on the page.
+<StructureSection load='1j1f' size='340' side='right'caption='[[1j1f]], [[Resolution|resolution]] 1.60&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'>[[1j1f]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Momordica_charantia Momordica charantia]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1J1F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1J1F 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]] 1.6&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5GP:GUANOSINE-5-MONOPHOSPHATE'>5GP</scene></td></tr>
-{{STRUCTURE_1j1f|  PDB=1j1f  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1j1f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1j1f OCA], [https://pdbe.org/1j1f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1j1f RCSB], [https://www.ebi.ac.uk/pdbsum/1j1f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1j1f ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/RNMC1_MOMCH RNMC1_MOMCH] Ribonuclease cleaving preferentially the 5'-side of uridine.<ref>PMID:10964705</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/j1/1j1f_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=1j1f ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Ribonuclease MC1 (RNase MC1), isolated from bitter gourd seeds, is a uridine specific RNase belonging to the RNase T2 family. Mutations of Asn71 in RNase MC1 to the amino acids Thr (N71T) and Ser (N71S) in guanosine preferential RNases altered the substrate specificity from uridine specific to guanosine specific, as shown by the transphosphorylation of diribonucleoside monophosphates [Numata, T., et al. (2001) Biochemistry 40, 524-530]. To elucidate the structural basis for the alteration of substrate specificity, crystal structures of the RNase MC1 mutants N71T and N71S, free or complexed with 5'-GMP, were determined at resolutions higher than 2 A. In the N71T-5'-GMP and N71S-5'-GMP complexes, the guanine moiety was, as in the case of the uracil moiety bound to wild-type RNase MC1, firmly stabilized in the B2 site by an extensive network of hydrogen bonds and hydrophobic interactions. Structure comparisons showed that mutations of Asn71 to Thr or Ser cause an enlargement of the B2 site, which then make it feasible to insert a guanine base into the B2 site of mutants N71T and N71S. This binding further allows for hydrogen bonding interaction of the side chain hydroxyl groups of Thr71 or Ser71 with the N7 atom of the guanine base. The mode of guanine binding of mutants N71T and N71S was found to be essentially identical to that of a guanosine preferential RNase NW from Nicotiana glutinosa. In particular, hydrogen bonds between the N7 atom of the guanine base and the hydroxyl groups of the amino acids at position 71 (RNase MC1 numbering) were completely conserved in three guanosine preferential enzymes, thereby indicating that the hydrogen bond may play an essential role in guanine binding in guanosine preferential RNases in the RNase T2 family. Consequently, it can be concluded that amino acids at position 71 (RNase MC1 numbering) serve as one of the determinants for substrate specificity (or preference) in the RNase T2 fimily by changing the size and shape of the B2 site.
-===Crystal structure of the RNase MC1 mutant N71T in complex with 5'-GMP===
+Crystal structures of the ribonuclease MC1 mutants N71T and N71S in complex with 5'-GMP: structural basis for alterations in substrate specificity.,Numata T, Suzuki A, Kakuta Y, Kimura K, Yao M, Tanaka I, Yoshida Y, Ueda T, Kimura M Biochemistry. 2003 May 13;42(18):5270-8. PMID:12731868<ref>PMID:12731868</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1j1f" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_12731868}}, adds the Publication Abstract to the page
+*[[Ribonuclease 3D structures|Ribonuclease 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 12731868 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_12731868}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-J1F is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Momordica_charantia Momordica charantia]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1J1F OCA].
-==Reference==
-Crystal structures of the ribonuclease MC1 mutants N71T and N71S in complex with 5'-GMP: structural basis for alterations in substrate specificity., Numata T, Suzuki A, Kakuta Y, Kimura K, Yao M, Tanaka I, Yoshida Y, Ueda T, Kimura M, Biochemistry. 2003 May 13;42(18):5270-8. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12731868 12731868]
 [[Category: Momordica charantia]]
-[[Category: Single protein]]
+[[Category: Kakuta Y]]
-[[Category: Kakuta, Y.]]
+[[Category: Kimura K]]
-[[Category: Kimura, K.]]
+[[Category: Kimura M]]
-[[Category: Kimura, M.]]
+[[Category: Numata T]]
-[[Category: Numata, T.]]
+[[Category: Suzuki A]]
-[[Category: Suzuki, A.]]
+[[Category: Tanaka I]]
-[[Category: Tanaka, I.]]
+[[Category: Ueda T]]
-[[Category: Ueda, T.]]
+[[Category: Yao M]]
-[[Category: Yao, M.]]
+[[Category: Yoshida Y]]
-[[Category: Yoshida, Y.]]
-[[Category: Hydrolase]]
-[[Category: Nucleic acid]]
-[[Category: Rna]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul  1 14:21:10 2008''