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1i3a

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[[Image:1i3a.gif|left|200px]]
 
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{{Structure
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==RNASE HII FROM ARCHAEOGLOBUS FULGIDUS WITH COBALT HEXAMMINE CHLORIDE==
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|PDB= 1i3a |SIZE=350|CAPTION= <scene name='initialview01'>1i3a</scene>, resolution 2.15&Aring;
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<StructureSection load='1i3a' size='340' side='right'caption='[[1i3a]], [[Resolution|resolution]] 2.15&Aring;' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=NCO:COBALT HEXAMMINE ION'>NCO</scene>
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<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>
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|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]
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</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>
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|GENE= RNHB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2234 Archaeoglobus fulgidus])
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<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>
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}}
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<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>
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</table>
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== Function ==
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[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]
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/i3/1i3a_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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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].
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<div style="clear:both"></div>
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'''RNASE HII FROM ARCHAEOGLOBUS FULGIDUS WITH COBALT HEXAMMINE CHLORIDE'''
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==See Also==
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*[[Ribonuclease 3D structures|Ribonuclease 3D structures]]
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__TOC__
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==Overview==
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</StructureSection>
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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.
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==About this Structure==
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1I3A 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=1I3A OCA].
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==Reference==
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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]
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[[Category: Archaeoglobus fulgidus]]
[[Category: Archaeoglobus fulgidus]]
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[[Category: Ribonuclease H]]
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[[Category: Large Structures]]
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[[Category: Single protein]]
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[[Category: Chai Q]]
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[[Category: Chai, Q.]]
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[[Category: Chapados BR]]
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[[Category: Chapados, B R.]]
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[[Category: Hosfield DJ]]
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[[Category: Hosfield, D J.]]
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[[Category: Qiu J]]
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[[Category: Qiu, J.]]
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[[Category: Shen B]]
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[[Category: Shen, B.]]
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[[Category: Tainer JA]]
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[[Category: Tainer, J A.]]
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[[Category: NCO]]
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[[Category: helix-loop-helix]]
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[[Category: mixed beta sheet]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 11:44:57 2008''
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Current revision

RNASE HII FROM ARCHAEOGLOBUS FULGIDUS WITH COBALT HEXAMMINE CHLORIDE

PDB ID 1i3a

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