5HP4 image
Entry Detail
PDB ID:
5HP4
Keywords:
Title:
Crystal structure bacteriohage T5 D15 flap endonuclease (D155K) pseudo-enzyme-product complex with DNA and metal ions
Biological Source:
Host Organism:
PDB Version:
Deposition Date:
2016-01-20
Release Date:
2016-06-01
Method Details:
Experimental Method:
Resolution:
1.86 Å
R-Value Free:
0.18
R-Value Work:
0.15
R-Value Observed:
0.15
Space Group:
P 43 21 2
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:Exodeoxyribonuclease
Mutations:Asp155Lys
Chain IDs:B (auth: A)
Chain Length:272
Number of Molecules:1
Biological Source:Escherichia phage T5
Polymer Type:polydeoxyribonucleotide
Description:DNA (5'-D(*GP*AP*TP*CP*TP*AP*TP*AP*TP*GP*CP*CP*AP*TP*CP*GP*G)-3')
Chain IDs:A (auth: X)
Chain Length:17
Number of Molecules:1
Biological Source:synthetic construct
Primary Citation
Direct observation of DNA threading in flap endonuclease complexes.
Nat.Struct.Mol.Biol. 23 640 646 (2016)
PMID: 27273516 DOI: 10.1038/nsmb.3241

Abstact

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.

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