1jxb: Difference between revisions

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-[[Image:1jxb.gif|left|200px]]<br /><applet load="1jxb" size="350" color="white" frame="true" align="right" spinBox="true"
-caption="1jxb, resolution 1.6&Aring;" />
-'''I53A, a point mutant of the cysteine-free variant of E. coli Rnase HI'''<br />
-==Overview==
+==I53A, a point mutant of the cysteine-free variant of E. coli Rnase HI==
-A point mutation (I53A) in the core of Escherichia coli RNase H* is known to destabilize both the native conformation (DeltaG(UN)) and the kinetic intermediate (DeltaG(UI)) by 2 kcal/mole. Here, we have used native-state hydrogen deuterium exchange to ask how this destabilization is propagated throughout the molecule. Stability parameters were obtained for individual residues in I53A and compared with those from the wild-type protein. A destabilization of 2 kcal/mole was observed in residues in the core but was not detected in the periphery of the molecule. These results are consistent with the localized destabilization of the core observed in the early intermediate of the kinetic folding pathway, supporting the resemblance of this kinetic intermediate to the partially unfolded form detected in the native state at equilibrium. A thermodynamic cycle also shows no interaction between Ile 53 and a residue in the periphery. There is, however, an increase in the number of denaturant-independent exchange events in the periphery of I53A, showing that effects of the point mutation are communicated to regions outside the core, although perhaps not through changes in stability. In sum, this work shows that localized regions within a protein can be destabilized independently. Furthermore, it implies a correspondence between the kinetic intermediate and the equilibrium PUF, as the magnitude and localization of the destabilization are the same in both.
+<StructureSection load='1jxb' size='340' side='right'caption='[[1jxb]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1jxb]] 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=1JXB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1JXB 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]] 1.6&#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=1jxb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jxb OCA], [https://pdbe.org/1jxb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1jxb RCSB], [https://www.ebi.ac.uk/pdbsum/1jxb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1jxb ProSAT]</span></td></tr>
+</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/jx/1jxb_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=1jxb ConSurf].
+<div style="clear:both"></div>
-==About this Structure==
+==See Also==
-JXB is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Active as [http://en.wikipedia.org/wiki/Ribonuclease_H Ribonuclease H], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.26.4 3.1.26.4] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JXB OCA].
+*[[Ribonuclease 3D structures|Ribonuclease 3D structures]]
+__TOC__
-==Reference==
+</StructureSection>
-Propagation of a single destabilizing mutation throughout the Escherichia coli ribonuclease HI native state., Spudich G, Lorenz S, Marqusee S, Protein Sci. 2002 Mar;11(3):522-8. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=11847275 11847275]
 [[Category: Escherichia coli]]
-[[Category: Ribonuclease H]]
+[[Category: Large Structures]]
-[[Category: Single protein]]
+[[Category: Lorenz S]]
-[[Category: Lorenz, S.]]
+[[Category: Marqusee S]]
-[[Category: Marqusee, S.]]
+[[Category: Spudich G]]
-[[Category: Spudich, G.]]
-[[Category: 4-helix bundle]]
-[[Category: mixed alpha/beta]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 13:27:44 2008''