3O3F

T. maritima RNase H2 D107N in complex with nucleic acid substrate and magnesium ions


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.191 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal Structures of RNase H2 in Complex with Nucleic Acid Reveal the Mechanism of RNA-DNA Junction Recognition and Cleavage.

Rychlik, M.P.Chon, H.Cerritelli, S.M.Klimek, P.Crouch, R.J.Nowotny, M.

(2010) Mol.Cell 40: 658-670

  • DOI: 10.1016/j.molcel.2010.11.001
  • Primary Citation of Related Structures:  3O3G, 3O3H

  • PubMed Abstract: 
  • Two classes of RNase H hydrolyze RNA of RNA/DNA hybrids. In contrast to RNase H1 that requires four ribonucleotides for cleavage, RNase H2 can nick duplex DNAs containing a single ribonucleotide, suggesting different in vivo substrates. We report her ...

    Two classes of RNase H hydrolyze RNA of RNA/DNA hybrids. In contrast to RNase H1 that requires four ribonucleotides for cleavage, RNase H2 can nick duplex DNAs containing a single ribonucleotide, suggesting different in vivo substrates. We report here the crystal structures of a type 2 RNase H in complex with substrates containing a (5')RNA-DNA(3') junction. They revealed a unique mechanism of recognition and substrate-assisted cleavage. A conserved tyrosine residue distorts the nucleic acid at the junction, allowing the substrate to function in catalysis by participating in coordination of the active site metal ion. The biochemical and structural properties of RNase H2 explain the preference of the enzyme for junction substrates and establish the structural and mechanistic differences with RNase H1. Junction recognition is important for the removal of RNA embedded in DNA and may play an important role in DNA replication and repair.


    Organizational Affiliation

    Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, 4 Trojdena Street, 02-109 Warsaw, Poland.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ribonuclease HII
A
222Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)Gene Names: rnhB
EC: 3.1.26.4
Find proteins for Q9X017 (Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099))
Go to UniProtKB:  Q9X017
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*GP*AP*AP*TP*CP*AP*GP*GP*TP*GP*TP*C)-3')C12N/A
Entity ID: 3
MoleculeChainsLengthOrganism
DNA/RNA (5'-D(*GP*AP*CP*AP*C)-R(P*C)-D(P*TP*GP*AP*TP*TP*C)-3')D12N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A, D
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.191 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 105.062α = 90.00
b = 48.570β = 131.80
c = 78.391γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
PHASERphasing
HKL-2000data scaling
MAR345dtbdata collection
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-12-08
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance