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[[Image:1i39.jpg|left|200px]]


{{Structure
==RNASE HII FROM ARCHAEOGLOBUS FULGIDUS==
|PDB= 1i39 |SIZE=350|CAPTION= <scene name='initialview01'>1i39</scene>, resolution 1.95&Aring;
<StructureSection load='1i39' size='340' side='right'caption='[[1i39]], [[Resolution|resolution]] 1.95&Aring;' scene=''>
|SITE=  
== Structural highlights ==
|LIGAND=  
<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>
|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]] 1.95&#8491;</td></tr>
|GENE= RNHB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2234 Archaeoglobus fulgidus])
<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>
|DOMAIN=
</table>
|RELATEDENTRY=
== Function ==
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1i39 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1i39 OCA], [http://www.ebi.ac.uk/pdbsum/1i39 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1i39 RCSB]</span>
[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.


'''RNASE HII FROM ARCHAEOGLOBUS FULGIDUS'''
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&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1i39" style="background-color:#fffaf0;"></div>


==Overview==
==See Also==
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.
*[[Ribonuclease 3D structures|Ribonuclease 3D structures]]
 
== References ==
==About this Structure==
<references/>
1I39 is a [[Single protein]] structure of sequence from [http://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].
__TOC__
 
</StructureSection>
==Reference==
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:[http://www.ncbi.nlm.nih.gov/pubmed/11254381 11254381]
[[Category: Archaeoglobus fulgidus]]
[[Category: Archaeoglobus fulgidus]]
[[Category: Ribonuclease H]]
[[Category: Large Structures]]
[[Category: Single protein]]
[[Category: Chai Q]]
[[Category: Chai, Q.]]
[[Category: Chapados BR]]
[[Category: Chapados, B R.]]
[[Category: Hosfield DJ]]
[[Category: Hosfield, D J.]]
[[Category: Qiu J]]
[[Category: Qiu, J.]]
[[Category: Shen B]]
[[Category: Shen, B.]]
[[Category: Tainer JA]]
[[Category: Tainer, J A.]]
[[Category: helix-loop-helix]]
[[Category: mixed beta sheet]]
 
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