2NQJ

Crystal structure of Escherichia coli endonuclease IV (Endo IV) E261Q mutant bound to damaged DNA

Summary for 2NQJ

• Entry DOI: 10.2210/pdb2nqj/pdb
• Related: 2NQ9 2NQH
• Descriptor: 5'-D(*GP*CP*GP*TP*CP*CP*(3DR)P*CP*GP*AP*CP*GP*AP*CP*G)-3', 5'-D(*CP*GP*TP*CP*GP*TP*CP*GP*GP*GP*GP*AP*CP*GP*C)-3', Endonuclease 4, ... (5 entities in total)
• Functional Keywords: tim_barrel, trinuclear zinc site, hydrolase
• Biological source: Escherichia coli
• Total number of polymer chains: 4
• Total formula weight: 72370.51

Authors

Garcin-Hosfield, E.D.,Hosfield, D.J.,Tainer, J.A. (deposition date: 2006-10-31, release date: 2007-11-06, 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 (2.45 Å)