3u3g: Difference between revisions

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-[[Image:3u3g.jpg|left|200px]]
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+==Structure of LC11-RNase H1 Isolated from Compost by Metagenomic Approach: Insight into the Structural Bases for Unusual Enzymatic Properties of Sto-RNase H1==
-The line below this paragraph, containing "STRUCTURE_3u3g", creates the "Structure Box" on the page.
+<StructureSection load='3u3g' size='340' side='right'caption='[[3u3g]], [[Resolution|resolution]] 1.40&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'>[[3u3g]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Uncultured_organism Uncultured organism]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3U3G OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3U3G 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]] 1.4&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=UNL:UNKNOWN+LIGAND'>UNL</scene></td></tr>
-{{STRUCTURE_3u3g|  PDB=3u3g  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3u3g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3u3g OCA], [https://pdbe.org/3u3g PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3u3g RCSB], [https://www.ebi.ac.uk/pdbsum/3u3g PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3u3g ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/E0X767_9ZZZZ E0X767_9ZZZZ]
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Metagenome-derived LC11-RNase H1 is a homolog of Sulfolobus tokodaii RNase H1 (Sto-RNase H1). It lacks a C-terminal tail, which is responsible for hyperstabilization of Sto-RNase H1. Sto-RNase H1 is characterized by its ability to cleave not only an RNA/DNA hybrid but also a double-stranded RNA (dsRNA). To examine whether LC11-RNase H1 also exhibits both RNase H and dsRNase activities, LC11-RNase H1 was overproduced in Escherichia coli, purified, and characterized. LC11-RNase H1 exhibited RNase H activity with similar metal ion preference, optimum pH, and cleavage mode of substrate with those of Sto-RNase H1. However, LC11-RNase H1 did not exhibit dsRNase activity at any condition examined. LC11-RNase H1 was less stable than Sto-RNases H1 and its derivative lacking the C-terminal tail (Sto-RNase H1DeltaC6) by 37 and 13 degrees C in T(m) , respectively. To understand the structural bases for these differences, the crystal structure of LC11-RNase H1 was determined at 1.4 A resolution. The LC11-RNase H1 structure is highly similar to the Sto-RNase H1 structure. However, LC11-RNase H1 has two grooves on protein surface, one containing the active site and the other containing DNA-phosphate binding pocket, while Sto-RNase H1 has one groove containing the active site. In addition, LC11-RNase H1 contains more cavities and buried charged residues than Sto-RNase H1. We propose that LC11-RNase H1 does not exhibit dsRNase activity because dsRNA cannot fit to the two grooves on protein surface and that LC11-RNase H1 is less stable than Sto-RNase H1DeltaC6 because of the increase in cavity volume and number of buried charged residues.
-===Structure of LC11-RNase H1 Isolated from Compost by Metagenomic Approach: Insight into the Structural Bases for Unusual Enzymatic Properties of Sto-RNase H1===
+Activity, stability, and structure of metagenome-derived LC11-RNase H1, a homolog of Sulfolobus tokodaii RNase H1.,Nguyen TN, Angkawidjaja C, Kanaya E, Koga Y, Takano K, Kanaya S Protein Sci. 2012 Apr;21(4):553-61. doi: 10.1002/pro.2043. Epub 2012 Mar 2. PMID:22389131<ref>PMID:22389131</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 3u3g" style="background-color:#fffaf0;"></div>
-==About this Structure==
+==See Also==
-[[3u3g]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Uncultured_organism Uncultured organism]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3U3G OCA].
+*[[Ribonuclease 3D structures|Ribonuclease 3D structures]]
-[[Category: Ribonuclease H]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
 [[Category: Uncultured organism]]
-[[Category: Angkawidjaja, C.]]
+[[Category: Angkawidjaja C]]
-[[Category: Kanaya, E.]]
+[[Category: Kanaya E]]
-[[Category: Kanaya, S.]]
+[[Category: Kanaya S]]
-[[Category: Koga, Y.]]
+[[Category: Koga Y]]
-[[Category: Nguyen, T N.]]
+[[Category: Nguyen TN]]
-[[Category: Takano, K.]]
+[[Category: Takano K]]
-[[Category: Cleave the rna strand of rna/dna hybrid]]
-[[Category: Hydrolase]]