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New page: left|200px {{Structure |PDB= 3bsu |SIZE=350|CAPTION= <scene name='initialview01'>3bsu</scene>, resolution 2.10Å |SITE= <scene name='pdbsite=AC1:Mg+Binding+Site+F...
 
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[[Image:3bsu.jpg|left|200px]]


{{Structure
==Hybrid-binding domain of human RNase H1 in complex with 12-mer RNA/DNA==
|PDB= 3bsu |SIZE=350|CAPTION= <scene name='initialview01'>3bsu</scene>, resolution 2.10&Aring;
<StructureSection load='3bsu' size='340' side='right'caption='[[3bsu]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
|SITE= <scene name='pdbsite=AC1:Mg+Binding+Site+For+Residue+C+502'>AC1</scene>
== Structural highlights ==
|LIGAND= <scene name='pdbligand=5IU:5-IODO-2&#39;-DEOXYURIDINE-5&#39;-MONOPHOSPHATE'>5IU</scene>, <scene name='pdbligand=A:ADENOSINE-5&#39;-MONOPHOSPHATE'>A</scene>, <scene name='pdbligand=C:CYTIDINE-5&#39;-MONOPHOSPHATE'>C</scene>, <scene name='pdbligand=DA:2&#39;-DEOXYADENOSINE-5&#39;-MONOPHOSPHATE'>DA</scene>, <scene name='pdbligand=DC:2&#39;-DEOXYCYTIDINE-5&#39;-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DG:2&#39;-DEOXYGUANOSINE-5&#39;-MONOPHOSPHATE'>DG</scene>, <scene name='pdbligand=DT:THYMIDINE-5&#39;-MONOPHOSPHATE'>DT</scene>, <scene name='pdbligand=G:GUANOSINE-5&#39;-MONOPHOSPHATE'>G</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=U:URIDINE-5&#39;-MONOPHOSPHATE'>U</scene>
<table><tr><td colspan='2'>[[3bsu]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BSU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3BSU 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]] 2.1&#8491;</td></tr>
|GENE= RNASEH1, RNH1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5IU:5-IODO-2-DEOXYURIDINE-5-MONOPHOSPHATE'>5IU</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
|DOMAIN=<span class='plainlinks'>[http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=COG3341 COG3341]</span>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3bsu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bsu OCA], [https://pdbe.org/3bsu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3bsu RCSB], [https://www.ebi.ac.uk/pdbsum/3bsu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3bsu ProSAT]</span></td></tr>
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3bsu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bsu OCA], [http://www.ebi.ac.uk/pdbsum/3bsu PDBsum], [http://www.fli-leibniz.de/cgi-bin/ImgLib.pl?CODE=1kfv JenaLib], [http://www.rcsb.org/pdb/explore.do?structureId=3bsu RCSB]</span>
</table>
}}
== Function ==
[https://www.uniprot.org/uniprot/RNH1_HUMAN RNH1_HUMAN] 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/bs/3bsu_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=3bsu ConSurf].
<div style="clear:both"></div>


'''Hybrid-binding domain of human RNase H1 in complex with 12-mer RNA/DNA'''
==See Also==
 
*[[Ribonuclease 3D structures|Ribonuclease 3D structures]]
 
__TOC__
==Overview==
</StructureSection>
Human RNase H1 contains an N-terminal domain known as dsRHbd for binding both dsRNA and RNA/DNA hybrid. We find that dsRHbd binds preferentially to RNA/DNA hybrids by over 25-fold and rename it as hybrid binding domain (HBD). The crystal structure of HBD complexed with a 12 bp RNA/DNA hybrid reveals that the RNA strand is recognized by a protein loop, which forms hydrogen bonds with the 2'-OH groups. The DNA interface is highly specific and contains polar residues that interact with the phosphate groups and an aromatic patch that appears selective for binding deoxyriboses. HBD is unique relative to non-sequence-specific dsDNA- and dsRNA-binding domains because it does not use positive dipoles of alpha-helices for nucleic acid binding. Characterization of full-length enzymes with defective HBDs indicates that this domain dramatically enhances both the specific activity and processivity of RNase H1. Similar activity enhancement by small substrate-binding domains linked to the catalytic domain likely occurs in other nucleic acid enzymes.
 
==About this Structure==
3BSU is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BSU OCA].
 
==Reference==
Specific recognition of RNA/DNA hybrid and enhancement of human RNase H1 activity by HBD., Nowotny M, Cerritelli SM, Ghirlando R, Gaidamakov SA, Crouch RJ, Yang W, EMBO J. 2008 Mar 13;. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18337749 18337749]
[[Category: Homo sapiens]]
[[Category: Homo sapiens]]
[[Category: Ribonuclease H]]
[[Category: Large Structures]]
[[Category: Single protein]]
[[Category: Cerritelli SM]]
[[Category: Cerritelli, S M.]]
[[Category: Crouch RJ]]
[[Category: Crouch, R J.]]
[[Category: Gaidamakov SA]]
[[Category: Gaidamakov, S A.]]
[[Category: Ghirlando R]]
[[Category: Ghirlando, R.]]
[[Category: Nowotny M]]
[[Category: Nowotny, M.]]
[[Category: Yang W]]
[[Category: Yang, W.]]
[[Category: dsrna]]
[[Category: hydrolase/rna/dna complex]]
[[Category: rnase h,rna/dna hybrid]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Mar 26 09:56:35 2008''

Latest revision as of 09:31, 21 February 2024

Hybrid-binding domain of human RNase H1 in complex with 12-mer RNA/DNA

3bsu, resolution 2.10Å

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