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| | <StructureSection load='1i3a' size='340' side='right'caption='[[1i3a]], [[Resolution|resolution]] 2.15Å' scene=''> | | <StructureSection load='1i3a' size='340' side='right'caption='[[1i3a]], [[Resolution|resolution]] 2.15Å' 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 [http://oca.weizmann.ac.il/oca-docs/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"><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]] 2.15Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1i39|1i39]]</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'>[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='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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1i3a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1i3a OCA], [http://pdbe.org/1i3a PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1i3a RCSB], [http://www.ebi.ac.uk/pdbsum/1i3a PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1i3a ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://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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| | <jmolCheckbox> | | <jmolCheckbox> |
| | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/i3/1i3a_consurf.spt"</scriptWhenChecked> | | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/i3/1i3a_consurf.spt"</scriptWhenChecked> |
| - | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | + | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked> |
| | <text>to colour the structure by Evolutionary Conservation</text> | | <text>to colour the structure by Evolutionary Conservation</text> |
| | </jmolCheckbox> | | </jmolCheckbox> |
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| | | | |
| | ==See Also== | | ==See Also== |
| - | *[[Ribonuclease|Ribonuclease]] | + | *[[Ribonuclease 3D structures|Ribonuclease 3D structures]] |
| - | *[[Temp|Temp]]
| + | |
| | == References == | | == References == |
| | <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]]
| + | |
| Structural highlights
Function
RNH2_ARCFU Endonuclease that specifically degrades the RNA of RNA-DNA hybrids (By similarity).[HAMAP-Rule:MF_00052_A]
Evolutionary Conservation
Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.
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[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Chapados BR, Chai Q, Hosfield DJ, Qiu J, Shen B, Tainer JA. Structural biochemistry of a type 2 RNase H: RNA primer recognition and removal during DNA replication. J Mol Biol. 2001 Mar 23;307(2):541-56. PMID:11254381 doi:10.1006/jmbi.2001.4494
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