3Q8M image
Deposition Date 2011-01-06
Release Date 2011-04-27
Last Version Date 2023-09-13
Entry Detail
PDB ID:
3Q8M
Keywords:
HYDROLASE/DNA
Title:
Crystal Structure of Human Flap Endonuclease FEN1 (D181A) in complex with substrate 5'-flap DNA 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:
2.60 Å
R-Value Free:
0.27
R-Value Work:
0.21
R-Value Observed:
0.21
Space Group:
P 1 21 1
3Q8M validation report
Macromolecular Entities
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Flap endonuclease 1
Gene (Uniprot):FEN1
Chain IDs:A, B
Chain Length:341
Number of Molecules:2
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:C (auth: D), F (auth: G)
Chain Length:18
Number of Molecules:2
Biological Source:
Polymer Type:polydeoxyribonucleotide
Molecule:DNA (5'-D(*TP*TP*GP*AP*GP*GP*CP*AP*GP*AP*GP*T)-3')
Chain IDs:D (auth: E), G (auth: H)
Chain Length:12
Number of Molecules:2
Biological Source:
Polymer Type:polydeoxyribonucleotide
Molecule:DNA (5'-D(*AP*CP*CP*GP*TP*CP*C)-3')
Chain IDs:E (auth: F), H (auth: I)
Chain Length:7
Number of Molecules:2
Biological Source:
Ligand Molecules
K
Primary Citation
Human Flap Endonuclease Structures, DNA Double-Base Flipping, and a Unified Understanding of the FEN1 Superfamily.
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.

Legend

Protein

Chemical

Disease

Primary Citation of related structures
3Q8K
3Q8L