3BSU

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.220 

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This is version 1.1 of the entry. See complete history. 


Literature

Specific recognition of RNA/DNA hybrid and enhancement of human RNase H1 activity by HBD.

Nowotny, M., Cerritelli, S.M., Ghirlando, R., Gaidamakov, S.A., Crouch, R.J., Yang, W.

(2008) EMBO J 27: 1172-1181

  • DOI: 10.1038/emboj.2008.44
  • Primary Citation of Related Structures:  
    3BSU

  • PubMed Abstract: 

    • 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 ...

    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.

    Organizational Affiliation: 

    Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA.



Macromolecules

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Ribonuclease H153Homo sapiensMutation(s): 0 
Gene Names: RNASEH1, RNH1
EC: 3.1.26.4
UniProt & NIH Common Fund Data Resources
Find proteins for O60930 (Homo sapiens)
Explore O60930 
Go to UniProtKB:  O60930
PHAROS:  O60930
GTEx:  ENSG00000171865 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO60930
Protein Feature View
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  • Reference Sequence

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Entity ID: 1
MoleculeChainsLengthOrganismImage
RNA (5'-R(*GP*AP*CP*AP*CP*CP*UP*GP*AP*UP*UP*C)-3')A [auth D],
C [auth I]		12N/A
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsLengthOrganismImage
DNA (5'-D(*DGP*DAP*DAP*DTP*DCP*DAP*DGP*DGP*(5IU)P*DGP*DTP*DC)-3')B [auth E],
D [auth J]		12N/A
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG
Download Ideal Coordinates CCD File 
K [auth A],
L [auth C]		MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.220 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.492α = 90
b = 64.262β = 90
c = 140.322γ = 90
Software Package:
Software NamePurpose
PHASERphasing
CNSrefinement
XDSdata reduction
XDSdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-03-25
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance