2IHN

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

Summary for 2IHN

• Entry DOI: 10.2210/pdb2ihn/pdb
• Related: 1TFR
• Descriptor: 5'-D(*CP*TP*AP*AP*CP*TP*TP*TP*GP*AP*GP*GP*CP*AP*GP*AP*CP*C)-3', 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', Ribonuclease H, ... (4 entities in total)
• Functional Keywords: bpt4 rnase h, protein:dna complex, 5'-3' exonuclease, hydrolase (nucleic acid), helix-hairpin-helix motif type 2 (hhh2), fork dna, hydrolase-dna complex, hydrolase/dna
• Biological source: Enterobacteria phage T4; More
• Total number of polymer chains: 3
• Total formula weight: 48505.29

Authors

Devos, J.M.,Mueser, T.C. (deposition date: 2006-09-26, release date: 2007-08-21, Last modification date: 2023-08-30)

Primary citation

Devos, J.M.,Tomanicek, S.J.,Jones, C.E.,Nossal, N.G.,Mueser, T.C.
Crystal structure of bacteriophage T4 5' nuclease in complex with a branched DNA reveals how FEN-1 family nucleases bind their substrates.
J.Biol.Chem., 282:31713-31724, 2007

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 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.

PubMed: 17693399
DOI: 10.1074/jbc.M703209200

Experimental method

X-RAY DIFFRACTION (3 Å)