2z1h: Difference between revisions

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-[[Image:2z1h.jpg|left|200px]]
- {{Structure
+==Crystal structure of E.coli RNase HI surface charged mutant(Q4R/T92K/Q105K/Q113R/Q115K/N143K/T145K)==
-|PDB= 2z1h |SIZE=350|CAPTION= <scene name='initialview01'>2z1h</scene>, resolution 2.60&Aring;
+<StructureSection load='2z1h' size='340' side='right'caption='[[2z1h]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
-|SITE=
+== Structural highlights ==
-|LIGAND=
+<table><tr><td colspan='2'>[[2z1h]] 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=2Z1H OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Z1H FirstGlance]. <br>
-|ACTIVITY= <span class='plainlinks'>[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] </span>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.6&#8491;</td></tr>
-|GENE=
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2z1h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z1h OCA], [https://pdbe.org/2z1h PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2z1h RCSB], [https://www.ebi.ac.uk/pdbsum/2z1h PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2z1h ProSAT]</span></td></tr>
-|DOMAIN=
+</table>
-|RELATEDENTRY=[[2z1g|2Z1G]], [[2z1i|2Z1I]], [[2z1j|2Z1J]]
+== Function ==
-|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2z1h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z1h OCA], [http://www.ebi.ac.uk/pdbsum/2z1h PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2z1h RCSB]</span>
+[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/z1/2z1h_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=2z1h ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Using the information from the genome projects, recent comparative studies of thermostable proteins have revealed a certain trend of amino acid composition in which polar residues are scarce and charged residues are rich on the protein surface. To clarify experimentally the effect of the amino acid composition of surface residues on the thermostability of Escherichia coli Ribonuclease HI (RNase HI), we constructed six variants in which five to eleven polar residues were replaced by charged residues (5C, 7Ca, 7Cb, 9Ca, 9Cb and 11C). The thermal denaturation experiments indicated that all of the variant proteins are 3.2-10.1 degrees C in Tm less stable than the wild proteins. The crystal structures of resultant protein variants 7Ca, 7Cb, 9Ca and 11C closely resemble that of E. coli RNase HI in their global fold, and several different hydrogen bonding and ion-pair interactions are formed by the mutations. Comparison of the crystal structures of these variant proteins with that of E. coli RNase HI reveals that thermal destabilization is apparently related to electrostatic repulsion of the charged residues with neighbours. This result suggests that charged residues of natural thermostable proteins are strictly posted on the surface with optimal interactions and without repulsive interactions.
-'''Crystal structure of E.coli RNase HI surface charged mutant(Q4R/T92K/Q105K/Q113R/Q115K/N143K/T145K)'''
+Protein thermostabilization requires a fine-tuned placement of surface-charged residues.,You DJ, Fukuchi S, Nishikawa K, Koga Y, Takano K, Kanaya S J Biochem. 2007 Oct;142(4):507-16. Epub 2007 Aug 30. PMID:17761696<ref>PMID:17761696</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2z1h" style="background-color:#fffaf0;"></div>
-==Overview==
+==See Also==
-Using the information from the genome projects, recent comparative studies of thermostable proteins have revealed a certain trend of amino acid composition in which polar residues are scarce and charged residues are rich on the protein surface. To clarify experimentally the effect of the amino acid composition of surface residues on the thermostability of Escherichia coli Ribonuclease HI (RNase HI), we constructed six variants in which five to eleven polar residues were replaced by charged residues (5C, 7Ca, 7Cb, 9Ca, 9Cb and 11C). The thermal denaturation experiments indicated that all of the variant proteins are 3.2-10.1 degrees C in Tm less stable than the wild proteins. The crystal structures of resultant protein variants 7Ca, 7Cb, 9Ca and 11C closely resemble that of E. coli RNase HI in their global fold, and several different hydrogen bonding and ion-pair interactions are formed by the mutations. Comparison of the crystal structures of these variant proteins with that of E. coli RNase HI reveals that thermal destabilization is apparently related to electrostatic repulsion of the charged residues with neighbours. This result suggests that charged residues of natural thermostable proteins are strictly posted on the surface with optimal interactions and without repulsive interactions.
+*[[Ribonuclease 3D structures|Ribonuclease 3D structures]]
+== References ==
-==About this Structure==
+<references/>
-Z1H 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=2Z1H OCA].
+__TOC__
+</StructureSection>
-==Reference==
-Protein thermostabilization requires a fine-tuned placement of surface-charged residues., You DJ, Fukuchi S, Nishikawa K, Koga Y, Takano K, Kanaya S, J Biochem. 2007 Oct;142(4):507-16. Epub 2007 Aug 30. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17761696 17761696]
 [[Category: Escherichia coli]]
-[[Category: Ribonuclease H]]
+[[Category: Large Structures]]
-[[Category: Single protein]]
+[[Category: Fukuchi S]]
-[[Category: Fukuchi, S.]]
+[[Category: Kanaya S]]
-[[Category: Kanaya, S.]]
+[[Category: Koga Y]]
-[[Category: Koga, Y.]]
+[[Category: Nishikawa K]]
-[[Category: Nishikawa, K.]]
+[[Category: Takano K]]
-[[Category: Takano, K.]]
+[[Category: You DJ]]
-[[Category: You, D J.]]
-[[Category: hydrolase]]
-[[Category: rnase hi]]
-[[Category: surface-charge residue]]
-[[Category: thermostability]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 05:17:27 2008''