ISDA

Deposition Date 2011-01-06

Release Date 2011-04-27

Last Version Date 2023-09-13

Entry Detail

PDB ID:

3Q8L

Keywords:

HYDROLASE/DNA

Title:

Crystal Structure of Human Flap Endonuclease FEN1 (WT) in complex with substrate 5'-flap DNA, SM3+, and K+

Biological Source:

Source Organism:

Homo sapiens (Taxon ID: 9606)
(Taxon ID: )

Host Organism:

Escherichia coli

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

2.32 Å

R-Value Free:

0.20

R-Value Work:

0.16

R-Value Observed:

0.16

Space Group:

P 31 2 1

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Macromolecular Entities

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Flap endonuclease 1
Gene (Uniprot):FEN1
Chain IDs:A
Chain Length:341
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P39748 Pfam ID:PF00752, PF00867 EC:3.1.99.B1

Polymer Type:polydeoxyribonucleotide
Molecule:DNA (5'-D(*AP*CP*TP*CP*TP*GP*CP*CP*TP*CP*AP*AP*GP*AP*CP*GP*GP*T)-3')
Chain IDs:B (auth: D)
Chain Length:18
Number of Molecules:1
Biological Source:

Polymer Type:polydeoxyribonucleotide
Molecule:DNA (5'-D(*TP*TP*GP*AP*GP*GP*CP*AP*GP*AP*GP*T)-3')
Chain IDs:C (auth: E)
Chain Length:12
Number of Molecules:1
Biological Source:

Polymer Type:polydeoxyribonucleotide
Molecule:DNA (5'-D(*AP*CP*CP*GP*TP*CP*C)-3')
Chain IDs:D (auth: F)
Chain Length:7
Number of Molecules:1
Biological Source:

Ligand Molecules

SO4

Primary Citation

Human Flap Endonuclease Structures, DNA Double-Base Flipping, and a Unified Understanding of the FEN1 Superfamily.

Tsutakawa, S.E, Classen, S, Chapados, B.R, Arvai, A.S, Finger, L.D, Guenther, G, Tomlinson, C.G, Thompson, P, Sarker, A.H, Shen, B, Cooper, P.K, Grasby, J.A, Tainer, J.A.Show

Cell(Cambridge,Mass.) 145 198 211 (2011)

PMID: 21496641 DOI: 10.1016/j.cell.2011.03.004

Abstact

Flap endonuclease (FEN1), essential for DNA replication and repair, removes RNA and DNA 5' flaps. FEN1 5' nuclease superfamily members acting in nucleotide excision repair (XPG), mismatch repair (EXO1), and homologous recombination (GEN1) paradoxically incise structurally distinct bubbles, ends, or Holliday junctions, respectively. Here, structural and functional analyses of human FEN1:DNA complexes show structure-specific, sequence-independent recognition for nicked dsDNA bent 100° with unpaired 3' and 5' flaps. Above the active site, a helical cap over a gateway formed by two helices enforces ssDNA threading and specificity for free 5' ends. Crystallographic analyses of product and substrate complexes reveal that dsDNA binding and bending, the ssDNA gateway, and double-base unpairing flanking the scissile phosphate control precise flap incision by the two-metal-ion active site. Superfamily conserved motifs bind and open dsDNA; direct the target region into the helical gateway, permitting only nonbase-paired oligonucleotides active site access; and support a unified understanding of superfamily substrate specificity.

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Primary Citation of related structures