3Q8M

Crystal Structure of Human Flap Endonuclease FEN1 (D181A) in complex with substrate 5'-flap DNA and K+

Summary for 3Q8M

• Entry DOI: 10.2210/pdb3q8m/pdb
• Related: 3Q8K 3Q8L
• Descriptor: Flap endonuclease 1, DNA (5'-D(*AP*CP*TP*CP*TP*GP*CP*CP*TP*CP*AP*AP*GP*AP*CP*GP*GP*T)-3'), DNA (5'-D(*TP*TP*GP*AP*GP*GP*CP*AP*GP*AP*GP*T)-3'), ... (6 entities in total)
• Functional Keywords: helix-3 turn-helix, hydrophobic wedge, 3' flap binding site, hydrolase-dna complex, dna repair, replication, flap endonuclease, fen, fen1, dna, nuclease, 5' flap, ss-dsdna junction, helix-2 turn-helix, h2th, h3th, divalent cation, metal helical gateway, cap, acid block, two metal mechanism, unpaired, 5' nuclease, human, long patch base excision repair, hydrolase/dna
• Biological source: Homo sapiens (human); More
• Cellular location: Nucleus, nucleolus: P39748
• Total number of polymer chains: 8
• Total formula weight: 99567.32

Authors

Tsutakawa, S.E.,Classen, S.,Chapados, B.R.,Arvai, A.,Finger, D.L.,Guenther, G.,Tomlinson, C.G.,Thompson, P.,Sarker, A.H.,Shen, B.,Cooper, P.K.,Grasby, J.A.,Tainer, J.A. (deposition date: 2011-01-06, release date: 2011-04-27, Last modification date: 2023-09-13)

Primary citation

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.
Human Flap Endonuclease Structures, DNA Double-Base Flipping, and a Unified Understanding of the FEN1 Superfamily.
Cell(Cambridge,Mass.), 145:198-211, 2011

PubMed Abstract: 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.

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

Experimental method

X-RAY DIFFRACTION (2.6 Å)