SNAP output for PDB entry 5hnk [SNAP web server]

PDB-id

5hnk; SNAP-derived features in text and JSON formats; DNAproDB

Class

hydrolase

Method

X-ray (2.22 Å)

Summary

Crystal structure of t5fen in complex intact substrate and metal ions.

Reference

AlMalki FA, Flemming CS, Zhang J, Feng M, Sedelnikova SE, Ceska T, Rafferty JB, Sayers JR, Artymiuk PJ (2016): "Direct observation of DNA threading in flap endonuclease complexes." Nat.Struct.Mol.Biol., 23, 640-646. doi: 10.1038/nsmb.3241.

Abstract

Maintenance of genome integrity requires that branched nucleic acid molecules be accurately processed to produce double-helical DNA. Flap endonucleases are essential enzymes that trim such branched molecules generated by Okazaki-fragment synthesis during replication. Here, we report crystal structures of bacteriophage T5 flap endonuclease in complexes with intact DNA substrates and products, at resolutions of 1.9-2.2 Å. They reveal single-stranded DNA threading through a hole in the enzyme, which is enclosed by an inverted V-shaped helical arch straddling the active site. Residues lining the hole induce an unusual barb-like conformation in the DNA substrate, thereby juxtaposing the scissile phosphate and essential catalytic metal ions. A series of complexes and biochemical analyses show how the substrate's single-stranded branch approaches, threads through and finally emerges on the far side of the enzyme. Our studies suggest that substrate recognition involves an unusual 'fly-casting, thread, bend and barb' mechanism.