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[[Image:1io2.jpg|left|200px]]
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{{STRUCTURE_1io2|  PDB=1io2  |  SCENE=  }}
'''CRYSTAL STRUCTURE OF TYPE 2 RIBONUCLEASE H FROM HYPERTHERMOPHILIC ARCHAEON, THERMOCOCCUS KODAKARAENSIS KOD1'''


==Crystal structure of type 2 ribonuclease h from hyperthermophilic archaeon, thermococcus kodakaraensis kod1==
<StructureSection load='1io2' size='340' side='right'caption='[[1io2]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1io2]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermococcus_kodakarensis_KOD1 Thermococcus kodakarensis KOD1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IO2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1IO2 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]] 2&#8491;</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=1io2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1io2 OCA], [https://pdbe.org/1io2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1io2 RCSB], [https://www.ebi.ac.uk/pdbsum/1io2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1io2 ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/RNH2_THEKO RNH2_THEKO] Endonuclease that specifically degrades the RNA of RNA-DNA hybrids.
== 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/io/1io2_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.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=1io2 ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The catalytic center of an archaeal Type 2 RNase H has been identified by a combination of X-ray crystallographic and mutational analyses. The crystal structure of the Type 2 RNase H from Thermococcus kodakaraensis KOD1 has revealed that the N-terminal major domain adopts the RNase H fold, despite the poor sequence similarity to the Type 1 RNase H. Mutational analyses showed that the catalytic reaction requires four acidic residues, which are well conserved in the Type 1 RNase H and the members of the polynucleotidyl transferase family. Thus, the Type 1 and Type 2 RNases H seem to share a common catalytic mechanism, except for the requirement of histidine as a general base in the former enzyme. Combined with the results from deletion mutant analyses, the structure suggests that the C-terminal domain of the Type 2 RNase H is involved in the interaction with the DNA/RNA hybrid.


==Overview==
Catalytic center of an archaeal type 2 ribonuclease H as revealed by X-ray crystallographic and mutational analyses.,Muroya A, Tsuchiya D, Ishikawa M, Haruki M, Morikawa M, Kanaya S, Morikawa K Protein Sci. 2001 Apr;10(4):707-14. PMID:11274461<ref>PMID:11274461</ref>
The catalytic center of an archaeal Type 2 RNase H has been identified by a combination of X-ray crystallographic and mutational analyses. The crystal structure of the Type 2 RNase H from Thermococcus kodakaraensis KOD1 has revealed that the N-terminal major domain adopts the RNase H fold, despite the poor sequence similarity to the Type 1 RNase H. Mutational analyses showed that the catalytic reaction requires four acidic residues, which are well conserved in the Type 1 RNase H and the members of the polynucleotidyl transferase family. Thus, the Type 1 and Type 2 RNases H seem to share a common catalytic mechanism, except for the requirement of histidine as a general base in the former enzyme. Combined with the results from deletion mutant analyses, the structure suggests that the C-terminal domain of the Type 2 RNase H is involved in the interaction with the DNA/RNA hybrid.


==About this Structure==
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
1IO2 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Thermococcus_kodakarensis Thermococcus kodakarensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IO2 OCA].
</div>
<div class="pdbe-citations 1io2" style="background-color:#fffaf0;"></div>


==Reference==
==See Also==
Catalytic center of an archaeal type 2 ribonuclease H as revealed by X-ray crystallographic and mutational analyses., Muroya A, Tsuchiya D, Ishikawa M, Haruki M, Morikawa M, Kanaya S, Morikawa K, Protein Sci. 2001 Apr;10(4):707-14. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/11274461 11274461]
*[[Ribonuclease 3D structures|Ribonuclease 3D structures]]
[[Category: Ribonuclease H]]
== References ==
[[Category: Single protein]]
<references/>
[[Category: Thermococcus kodakarensis]]
__TOC__
[[Category: Haruki, M.]]
</StructureSection>
[[Category: Ishikawa, M.]]
[[Category: Large Structures]]
[[Category: Morikawa, M.]]
[[Category: Thermococcus kodakarensis KOD1]]
[[Category: Muroya, A.]]
[[Category: Haruki M]]
[[Category: Tsuchiya, D.]]
[[Category: Ishikawa M]]
[[Category: Endonuclease]]
[[Category: Morikawa M]]
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May  2 20:12:23 2008''
[[Category: Muroya A]]
[[Category: Tsuchiya D]]

Latest revision as of 23:33, 27 December 2023

Crystal structure of type 2 ribonuclease h from hyperthermophilic archaeon, thermococcus kodakaraensis kod1

1io2, resolution 2.00Å

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