PDBsum entry 2nqh

Hydrolase

PDB id: 2nqh

Contents

Protein chain

279 a.a. *

Ligands

PO4

Metals

_ZN ×3

Waters ×326

* Residue conservation analysis

PDB id:

2nqh

Name:

Hydrolase

Title:

High resolution crystal structure of escherichia coli endonuclease iv (endo iv) e261q mutant

Structure:

Endonuclease 4. Chain: a. Synonym: endonuclease iv, endodeoxyribonuclease iv. Engineered: yes. Mutation: yes

Source:

Escherichia coli. Organism_taxid: 562. Gene: nfo. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.10Å R-factor: 0.155 R-free: 0.192

Authors:

E.D.Garcin-Hosfield,D.J.Hosfield,J.A.Tainer

Key ref:

E.D.Garcin et al. (2008). DNA apurinic-apyrimidinic site binding and excision by endonuclease IV. Nat Struct Mol Biol, 15, 515-522. PubMed id: 18408731 DOI: 10.1038/nsmb.1414

Date:

31-Oct-06 Release date: 06-Nov-07

Protein chain

P0A6C1  (END4_ECOLI) -  Endonuclease 4 from Escherichia coli (strain K12)

Seq: 285 a.a.

Struc: 279 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.3.1.21.2 - deoxyribonuclease Iv.
• Reaction: Endonucleolytic cleavage to 5'-phosphooligonucleotide end-products.

DOI no: 10.1038/nsmb.1414

Nat Struct Mol Biol 15:515-522 (2008)

PubMed id: 18408731

DNA apurinic-apyrimidinic site binding and excision by endonuclease IV.

E.D.Garcin, D.J.Hosfield, S.A.Desai, B.J.Haas, M.Björas, R.P.Cunningham, J.A.Tainer.

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.

Selected figure(s)

Figure 2.
(a) Stereoview of DNA-free structure with coordination of the active-site phosphate and three Zn^2+ ions. Omit map is contoured at 2 (light blue) and 4 (dark blue) for the bound phosphate group. (b) AP DNA complex stereoview showing the three–metal ion active site (green spheres), residues Arg37, Tyr72 and Gln261 (pink), and bound DNA substrate with both the AP-site sugar and phosphate moieties and the cognate nucleotide (orange) flipped out from the DNA base stack. The 2F[o] - F[c] electron density map is contoured at 1 (blue mesh). (c) Stereoview of DNA substrate complex binding to active-site metal ions. Omit map (contoured at 2 , pink mesh) shows the intact phosphodiester bond (black arrow) that constrains the Zn[3] to Cyt6 O[3]' distance to 2.7 Å.

Figure 3.
The structure of the Y72A mutant reveals cleaved AP DNA (a) and ordered water molecules (b) adjacent to the cleaved AP site (3 light blue and 4 dark blue contoured omit maps). Panels a and b are drawn in stereoview. (c) The structures of wild-type (left) and Y72A mutant (right) Endo IV bound to AP DNA product are virtually superimposable. Removal of the Tyr72 side chain allows increased solvation of the active site.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Mol Biol (2008, 15, 515-522) copyright 2008.

Figures were selected by the author.