1i39: Difference between revisions
New page: left|200px<br /><applet load="1i39" size="450" color="white" frame="true" align="right" spinBox="true" caption="1i39, resolution 1.95Å" /> '''RNASE HII FROM ARCHA... |
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== | ==RNASE HII FROM ARCHAEOGLOBUS FULGIDUS== | ||
DNA replication and cellular survival requires efficient removal of RNA | <StructureSection load='1i39' size='340' side='right'caption='[[1i39]], [[Resolution|resolution]] 1.95Å' scene=''> | ||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[1i39]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Archaeoglobus_fulgidus Archaeoglobus fulgidus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1I39 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1I39 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]] 1.95Å</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=1i39 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1i39 OCA], [https://pdbe.org/1i39 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1i39 RCSB], [https://www.ebi.ac.uk/pdbsum/1i39 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1i39 ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/RNH2_ARCFU RNH2_ARCFU] Endonuclease that specifically degrades the RNA of RNA-DNA hybrids (By similarity).[HAMAP-Rule:MF_00052_A] | |||
== 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/i3/1i39_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=1i39 ConSurf]. | |||
<div style="clear:both"></div> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
DNA replication and cellular survival requires efficient removal of RNA primers during lagging strand DNA synthesis. In eukaryotes, RNA primer removal is initiated by type 2 RNase H, which specifically cleaves the RNA portion of an RNA-DNA/DNA hybrid duplex. This conserved type 2 RNase H family of replicative enzymes shares little sequence similarity with the well-characterized prokaryotic type 1 RNase H enzymes, yet both possess similar enzymatic properties. Crystal structures and structure-based mutational analysis of RNase HII from Archaeoglobus fulgidus, both with and without a bound metal ion, identify the active site for type 2 RNase H enzymes that provides the general nuclease activity necessary for catalysis. The two-domain architecture of type 2 RNase H creates a positively charged binding groove and links the unique C-terminal helix-loop-helix cap domain to the active site catalytic domain. This architectural arrangement apparently couples directional A-form duplex binding, by a hydrogen-bonding Arg-Lys phosphate ruler motif, to substrate-discrimination, by a tyrosine finger motif, thereby providing substrate-specific catalytic activity. Combined kinetic and mutational analyses of structurally implicated substrate binding residues validate this binding mode. These structural and mutational results together suggest a molecular mechanism for type 2 RNase H enzymes for the specific recognition and cleavage of RNA in the RNA-DNA junction within hybrid duplexes, which reconciles the broad substrate binding affinity with the catalytic specificity observed in biochemical assays. In combination with a recent independent structural analysis, these results furthermore identify testable molecular hypotheses for the activity and function of the type 2 RNase H family of enzymes, including structural complementarity, substrate-mediated conformational changes and coordination with subsequent FEN-1 activity. | |||
Structural biochemistry of a type 2 RNase H: RNA primer recognition and removal during DNA replication.,Chapados BR, Chai Q, Hosfield DJ, Qiu J, Shen B, Tainer JA J Mol Biol. 2001 Mar 23;307(2):541-56. PMID:11254381<ref>PMID:11254381</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 1i39" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[Ribonuclease 3D structures|Ribonuclease 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Archaeoglobus fulgidus]] | [[Category: Archaeoglobus fulgidus]] | ||
[[Category: | [[Category: Large Structures]] | ||
[[Category: Chai Q]] | |||
[[Category: Chai | [[Category: Chapados BR]] | ||
[[Category: Chapados | [[Category: Hosfield DJ]] | ||
[[Category: Hosfield | [[Category: Qiu J]] | ||
[[Category: Qiu | [[Category: Shen B]] | ||
[[Category: Shen | [[Category: Tainer JA]] | ||
[[Category: Tainer | |||
