1lav: Difference between revisions

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-[[Image:1lav.gif|left|200px]]
-<!--
+==STABILIZATION OF ESCHERICHIA COLI RIBONUCLEASE HI BY CAVITY-FILLING MUTATIONS WITHIN A HYDROPHOBIC CORE==
-The line below this paragraph, containing "STRUCTURE_1lav", creates the "Structure Box" on the page.
+<StructureSection load='1lav' size='340' side='right'caption='[[1lav]], [[Resolution|resolution]] 1.80&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'>[[1lav]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LAV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1LAV 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]] 1.8&#8491;</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=1lav FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lav OCA], [https://pdbe.org/1lav PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1lav RCSB], [https://www.ebi.ac.uk/pdbsum/1lav PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1lav ProSAT]</span></td></tr>
-{{STRUCTURE_1lav|  PDB=1lav  |  SCENE=  }}
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/RNH_ECOLI RNH_ECOLI] Endonuclease that specifically degrades the RNA of RNA-DNA hybrids. RNase H participates in DNA replication; it helps to specify the origin of genomic replication by suppressing initiation at origins other than the oriC locus; along with the 5'-3' exonuclease of pol1, it removes RNA primers from the Okazaki fragments of lagging strand synthesis; and it defines the origin of replication for ColE1-type plasmids by specific cleavage of an RNA preprimer.[HAMAP-Rule:MF_00042]
+== 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/la/1lav_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.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=1lav ConSurf].
+<div style="clear:both"></div>
-'''STABILIZATION OF ESCHERICHIA COLI RIBONUCLEASE HI BY CAVITY-FILLING MUTATIONS WITHIN A HYDROPHOBIC CORE'''
+==See Also==
+*[[Ribonuclease 3D structures|Ribonuclease 3D structures]]
+__TOC__
-==Overview==
+</StructureSection>
-The crystal structure of Escherichia coli ribonuclease HI has a cavity near Val-74 within the protein core. In order to fill the cavity space, we constructed two mutant proteins, V74L and V74I, in which Val-74 was replaced with either Leu or Ile, respectively. The mutant proteins are stabilized, as revealed by a 2.1-3.7 degrees C increase in the Tm values, as compared to the wild-type protein at pH values of 3.0 and 5.5. The mutant protein V74A, in which Val-74 is replaced with Ala, was also constructed to analyze the reverse effect. The stability of V74A decreases by 7.6 degrees C at pH 3.0 and 12.7 degrees C at pH 5.5 in Tm as compared to those values for the wild-type protein. None of the three mutations significantly affect the enzymatic activity. The crystal structures of V74L and V74I, determined at 1.8-A resolution, are almost identical to that of the wild-type protein, except for the mutation site. In the two mutant proteins, calculation by the Voronoi procedure shows that the cavity volumes around the individual mutation sites are remarkably reduced as compared to that in the wild-type protein. These results indicate that the introduction of a methylene group into the cavity, without causing steric clash, contributes to an increase in the hydrophobic interaction within the protein core and thereby enhances protein stability. We also discuss the role of the Leu side chain, which can assume many different local conformations on a helix without sacrificing thermostability.
-==About this Structure==
-LAV is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LAV OCA].
-==Reference==
-Stabilization of Escherichia coli ribonuclease HI by cavity-filling mutations within a hydrophobic core., Ishikawa K, Nakamura H, Morikawa K, Kanaya S, Biochemistry. 1993 Jun 22;32(24):6171-8. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/8390295 8390295]
 [[Category: Escherichia coli]]
-[[Category: Ribonuclease H]]
+[[Category: Large Structures]]
-[[Category: Single protein]]
+[[Category: Ishikawa K]]
-[[Category: Ishikawa, K.]]
+[[Category: Kanaya S]]
-[[Category: Kanaya, S.]]
+[[Category: Morikawa K]]
-[[Category: Morikawa, K.]]
+[[Category: Nakamura H]]
-[[Category: Nakamura, H.]]
-[[Category: Hydrolase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May  2 23:44:02 2008''