2NQ9

High resolution crystal structure of Escherichia coli endonuclease IV (Endo IV) Y72A mutant bound to damaged DNA

Summary for 2NQ9

• Entry DOI: 10.2210/pdb2nq9/pdb
• Descriptor: 5'-D(*AP*TP*AP*TP*CP*T)-3', 5'-D(P*(3DR)P*AP*GP*AP*T)-3', 5'-D(*AP*TP*CP*TP*GP*AP*AP*GP*TP*AP*T)-3', ... (6 entities in total)
• Functional Keywords: tim-barrel, trinuclear zn active site, hydrolase-dna complex, hydrolase/dna
• Biological source: Escherichia coli
• Total number of polymer chains: 4
• Total formula weight: 38173.03

Authors

Garcin-Hosfield, E.D.,Hosfield, D.J.,Tainer, J.A. (deposition date: 2006-10-30, release date: 2007-11-13, Last modification date: 2023-08-30)

Primary citation

Garcin, E.D.,Hosfield, D.J.,Desai, S.A.,Haas, B.J.,Bjoras, M.,Cunningham, R.P.,Tainer, J.A.
DNA apurinic-apyrimidinic site binding and excision by endonuclease IV.
Nat.Struct.Mol.Biol., 15:515-522, 2008

PubMed 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.

PubMed: 18408731
DOI: 10.1038/nsmb.1414

Experimental method

X-RAY DIFFRACTION (1.45 Å)