title: DNA apurinic-apyrimidinic site binding and excision by endonuclease IV.
abstract: Escherichia coli endonuclease IV is an archetype for an abasic or apurinic-apyrimidinic endonuclease superfamily crucial for DNA base excision repair. Here biochemical, mutational and crystallographic characterizations reveal a three-metal ion mechanism for damage binding and incision. The 1.10-A resolution DNA-free and the 2.45-A resolution DNA-substrate complex structures capture substrate stabilization by Arg37 and reveal a distorted Zn3-ligand arrangement that reverts, after catalysis, to an ideal geometry suitable to hold rather than release cleaved DNA product. The 1.45-A resolution DNA-product complex structure shows how Tyr72 caps the active site, tunes its dielectric environment and promotes catalysis by Glu261-activated hydroxide, bound to two Zn2+ ions throughout catalysis. These structural, mutagenesis and biochemical results suggest general requirements for abasic site removal in contrast to features specific to the distinct endonuclease IV alpha-beta triose phosphate isomerase (TIM) barrel and APE1 four-layer alpha-beta folds of the apurinic-apyrimidinic endonuclease families.
authors.affiliation: Department of Molecular Biology and Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, MB4 La Jolla, California 92037, USA.
authors.forename: Elsa D
authors.initials: ED
authors.lastname: Garcin
authors.forename: David J
authors.initials: DJ
authors.lastname: Hosfield
authors.forename: Sunil A
authors.initials: SA
authors.lastname: Desai
authors.forename: Brian J
authors.initials: BJ
authors.lastname: Haas
authors.forename: Magnar
authors.initials: M
authors.lastname: Björas
authors.forename: Richard P
authors.initials: RP
authors.lastname: Cunningham
authors.forename: John A
authors.initials: JA
authors.lastname: Tainer
mesh_terms: D001665:Binding Sites; D018360:Crystallography, X-Ray; D004247:DNA / Q000378:metabolism; D043223:Deoxyribonuclease IV (Phage T4-Induced) / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D004926:Escherichia coli / Q000201:enzymology*; D057927:Hydrophobic and Hydrophilic Interactions; D007700:Kinetics; D008958:Models, Molecular; D017433:Protein Structure, Secondary
chemical_list: D004247:DNA; D043223:Deoxyribonuclease IV (Phage T4-Induced)