3BSU

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.220 

wwPDB Validation 3D Report Full Report


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

  • 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 ...

    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

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Ribonuclease H1
A, B, C, F, G, H
53Homo sapiensMutation(s): 0 
Gene Names: RNASEH1 (RNH1)
EC: 3.1.26.4
Find proteins for O60930 (Homo sapiens)
Go to Gene View: RNASEH1
Go to UniProtKB:  O60930
Entity ID: 1
MoleculeChainsLengthOrganism
RNA (5'-R(*GP*AP*CP*AP*CP*CP*UP*GP*AP*UP*UP*C)-3')D,I12N/A
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*DGP*DAP*DAP*DTP*DCP*DAP*DGP*DGP*(5IU)P*DGP*DTP*DC)-3')E,J12N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG
Download SDF File 
Download CCD File 
A, C
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
5IU
Query on 5IU
E, J
DNA LINKINGC9 H12 I N2 O8 PDU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 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 = 90.00
b = 64.262β = 90.00
c = 140.322γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
XDSdata reduction
PHASERphasing
XDSdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

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