2qkb: Difference between revisions

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-[[Image:2qkb.gif|left|200px]]
- {{Structure
+==Human RNase H catalytic domain mutant D210N in complex with 20-mer RNA/DNA hybrid==
-|PDB= 2qkb |SIZE=350|CAPTION= <scene name='initialview01'>2qkb</scene>, resolution 2.40&Aring;
+<StructureSection load='2qkb' size='340' side='right'caption='[[2qkb]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
-|SITE=
+== Structural highlights ==
-|LIGAND= <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene> and <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>
+<table><tr><td colspan='2'>[[2qkb]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QKB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2QKB FirstGlance]. <br>
-|ACTIVITY= [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]
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.4&#8491;</td></tr>
-|GENE= RNASEH1, RNH1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></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=2qkb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qkb OCA], [https://pdbe.org/2qkb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2qkb RCSB], [https://www.ebi.ac.uk/pdbsum/2qkb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2qkb ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/RNH1_HUMAN RNH1_HUMAN] Endonuclease that specifically degrades the RNA of RNA-DNA hybrids.
+== 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/qk/2qkb_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=2qkb ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+We report here crystal structures of human RNase H1 complexed with an RNA/DNA substrate. Unlike B. halodurans RNase H1, human RNase H1 has a basic protrusion, which forms a DNA-binding channel and together with the conserved phosphate-binding pocket confers specificity for the B form and 2'-deoxy DNA. The RNA strand is recognized by four consecutive 2'-OH groups and cleaved by a two-metal ion mechanism. Although RNase H1 is overall positively charged, the substrate interface is neutral to acidic in character, which likely contributes to the catalytic specificity. Positions of the scissile phosphate and two catalytic metal ions are interdependent and highly coupled. Modeling of HIV reverse transcriptase (RT) with RNA/DNA in its RNase H active site suggests that the substrate cannot simultaneously occupy the polymerase active site and must undergo a conformational change to toggle between the two catalytic centers. The region that accommodates this conformational change offers a target to develop HIV-specific inhibitors.
-'''Human RNase H catalytic domain mutant D210N in complex with 20-mer RNA/DNA hybrid'''
+Structure of human RNase H1 complexed with an RNA/DNA hybrid: insight into HIV reverse transcription.,Nowotny M, Gaidamakov SA, Ghirlando R, Cerritelli SM, Crouch RJ, Yang W Mol Cell. 2007 Oct 26;28(2):264-76. PMID:17964265<ref>PMID:17964265</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2qkb" style="background-color:#fffaf0;"></div>
-==Overview==
+==See Also==
-We report here crystal structures of human RNase H1 complexed with an RNA/DNA substrate. Unlike B. halodurans RNase H1, human RNase H1 has a basic protrusion, which forms a DNA-binding channel and together with the conserved phosphate-binding pocket confers specificity for the B form and 2'-deoxy DNA. The RNA strand is recognized by four consecutive 2'-OH groups and cleaved by a two-metal ion mechanism. Although RNase H1 is overall positively charged, the substrate interface is neutral to acidic in character, which likely contributes to the catalytic specificity. Positions of the scissile phosphate and two catalytic metal ions are interdependent and highly coupled. Modeling of HIV reverse transcriptase (RT) with RNA/DNA in its RNase H active site suggests that the substrate cannot simultaneously occupy the polymerase active site and must undergo a conformational change to toggle between the two catalytic centers. The region that accommodates this conformational change offers a target to develop HIV-specific inhibitors.
+*[[Ribonuclease 3D structures|Ribonuclease 3D structures]]
+== References ==
-==About this Structure==
+<references/>
-QKB is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QKB OCA].
+__TOC__
+</StructureSection>
-==Reference==
-Structure of human RNase H1 complexed with an RNA/DNA hybrid: insight into HIV reverse transcription., Nowotny M, Gaidamakov SA, Ghirlando R, Cerritelli SM, Crouch RJ, Yang W, Mol Cell. 2007 Oct 26;28(2):264-76. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17964265 17964265]
 [[Category: Homo sapiens]]
-[[Category: Ribonuclease H]]
+[[Category: Large Structures]]
-[[Category: Single protein]]
+[[Category: Cerritelli SM]]
-[[Category: Cerritelli, S M.]]
+[[Category: Crouch RJ]]
-[[Category: Crouch, R J.]]
+[[Category: Gaidamakov SA]]
-[[Category: Gaidamakov, S A.]]
+[[Category: Ghirlando R]]
-[[Category: Ghirlando, R.]]
+[[Category: Nowotny M]]
-[[Category: Nowotny, M.]]
+[[Category: Yang W]]
-[[Category: Yang, W.]]
-[[Category: EDO]]
-[[Category: SO4]]
-[[Category: hydrolase/dna/rna complex]]
-[[Category: rnase h; rna/dna hybrid]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 18:26:44 2008''