5HNK: Crystal Structure Of T5fen In Complex Intact Substrate And Metal Ions

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 A. 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.
PDB ID: 5HNKDownload
MMDB ID: 139755
PDB Deposition Date: 2016/1/18
Updated in MMDB: 2016/07
Experimental Method:
x-ray diffraction
Resolution: 2.22  Å
Source Organism:
synthetic construct
Similar Structures:
Biological Unit for 5HNK: trimeric; determined by author and by software (PISA)
Molecular Components in 5HNK
Label Count Molecule
Protein (1 molecule)
Exodeoxyribonuclease(Gene symbol: D15)
Molecule annotation
Nucleotide(1 molecule)
DNA (5'-d(*ap*ap*ap*ap*gp*cp*gp*tp*ap*cp*gp*c)-3')
Molecule annotation
Chemicals (4 molecules)
* Click molecule labels to explore molecular sequence information.

Citing MMDB