5HML

Crystal Structure of T5 D15 Protein Co-crystallized with Metal Ions

Summary for 5HML

• Entry DOI: 10.2210/pdb5hml/pdb
• Descriptor: Exodeoxyribonuclease, MAGNESIUM ION, CHLORIDE ION, ... (7 entities in total)
• Functional Keywords: metal ion complex, flap endonuclease, alternative conformations, hydrolase
• Biological source: Escherichia phage T5
• Total number of polymer chains: 2
• Total formula weight: 63709.58

Authors

Flemming, C.S.,Feng, M.,Sedelnikova, S.E.,Zhang, J.,Rafferty, J.B.,Sayers, J.R.,Artymiuk, P.J. (deposition date: 2016-01-16, release date: 2016-06-01, Last modification date: 2024-01-10)

Primary citation

AlMalki, F.A.,Flemming, C.S.,Zhang, J.,Feng, M.,Sedelnikova, S.E.,Ceska, T.,Rafferty, J.B.,Sayers, J.R.,Artymiuk, P.J.
Direct observation of DNA threading in flap endonuclease complexes.
Nat.Struct.Mol.Biol., 23:640-646, 2016

PubMed 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.

PubMed: 27273516
DOI: 10.1038/nsmb.3241

Experimental method

X-RAY DIFFRACTION (1.482 Å)