2IHN

Co-crystal of Bacteriophage T4 RNase H with a fork DNA substrate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.222 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal structure of bacteriophage T4 5' nuclease in complex with a branched DNA reveals how FEN-1 family nucleases bind their substrates.

Devos, J.M.Tomanicek, S.J.Jones, C.E.Nossal, N.G.Mueser, T.C.

(2007) J.Biol.Chem. 282: 31713-31724

  • DOI: 10.1074/jbc.M703209200

  • PubMed Abstract: 
  • Bacteriophage T4 RNase H, a flap endonuclease-1 family nuclease, removes RNA primers from lagging strand fragments. It has both 5' nuclease and flap endonuclease activities. Our previous structure of native T4 RNase H (PDB code 1TFR) revealed an acti ...

    Bacteriophage T4 RNase H, a flap endonuclease-1 family nuclease, removes RNA primers from lagging strand fragments. It has both 5' nuclease and flap endonuclease activities. Our previous structure of native T4 RNase H (PDB code 1TFR) revealed an active site composed of highly conserved Asp residues and two bound hydrated magnesium ions. Here, we report the crystal structure of T4 RNase H in complex with a fork DNA substrate bound in its active site. This is the first structure of a flap endonuclease-1 family protein with its complete branched substrate. The fork duplex interacts with an extended loop of the helix-hairpin-helix motif class 2. The 5' arm crosses over the active site, extending below the bridge (helical arch) region. Cleavage assays of this DNA substrate identify a primary cut site 7-bases in from the 5' arm. The scissile phosphate, the first bond in the duplex DNA adjacent to the 5' arm, lies above a magnesium binding site. The less ordered 3' arm reaches toward the C and N termini of the enzyme, which are binding sites for T4 32 protein and T4 45 clamp, respectively. In the crystal structure, the scissile bond is located within the double-stranded DNA, between the first two duplex nucleotides next to the 5' arm, and lies above a magnesium binding site. This complex provides important insight into substrate recognition and specificity of the flap endonuclease-1 enzymes.


    Organizational Affiliation

    Department of Chemistry, The University of Toledo, Toledo, Ohio 43606, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Ribonuclease H
A
305Enterobacteria phage T4Gene Names: rnh (33.2, das)
EC: 3.1.26.4
Find proteins for P13319 (Enterobacteria phage T4)
Go to UniProtKB:  P13319
Entity ID: 1
MoleculeChainsLengthOrganism
5'-D(*CP*TP*AP*AP*CP*TP*TP*TP*GP*AP*GP*GP*CP*AP*GP*AP*CP*C)-3'C18N/A
Entity ID: 2
MoleculeChainsLengthOrganism
5'-D(*GP*GP*TP*CP*TP*GP*CP*CP*TP*CP*AP*AP*GP*AP*CP*GP*GP*TP*AP*GP*TP*CP*AP*A)-3'D24N/A
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.222 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 68.160α = 90.00
b = 84.990β = 90.00
c = 89.290γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
CrystalCleardata reduction
REFMACrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-08-21
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance