1i3a: Difference between revisions

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<StructureSection load='1i3a' size='340' side='right'caption='[[1i3a]], [[Resolution|resolution]] 2.15&Aring;' scene=''>
<StructureSection load='1i3a' size='340' side='right'caption='[[1i3a]], [[Resolution|resolution]] 2.15&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[1i3a]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1I3A OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1I3A FirstGlance]. <br>
<table><tr><td colspan='2'>[[1i3a]] 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=1I3A OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1I3A FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NCO:COBALT+HEXAMMINE(III)'>NCO</scene></td></tr>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.15&#8491;</td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1i39|1i39]]</div></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NCO:COBALT+HEXAMMINE(III)'>NCO</scene></td></tr>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Ribonuclease_H Ribonuclease H], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.26.4 3.1.26.4] </span></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=1i3a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1i3a OCA], [https://pdbe.org/1i3a PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1i3a RCSB], [https://www.ebi.ac.uk/pdbsum/1i3a PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1i3a ProSAT]</span></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=1i3a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1i3a OCA], [https://pdbe.org/1i3a PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1i3a RCSB], [https://www.ebi.ac.uk/pdbsum/1i3a PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1i3a ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== 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]  
[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 ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
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</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=1i3a ConSurf].
</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=1i3a ConSurf].
<div style="clear:both"></div>
<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&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1i3a" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
*[[Ribonuclease 3D structures|Ribonuclease 3D structures]]
*[[Ribonuclease 3D structures|Ribonuclease 3D structures]]
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Archaeoglobus fulgidus]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Ribonuclease H]]
[[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: Hydrolase]]
[[Category: Mixed beta sheet]]
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