PDBsum entry 4ypr

Hydrolase/DNA

PDB id: 4ypr

Contents

Protein chains

355 a.a.

DNA/RNA

Ligands

SF4 ×2

Waters ×29

PDB id:

4ypr

Name:

Hydrolase/DNA

Title:

Crystal structure of d144n muty bound to its anti-substrate

Structure:

A/g-specific adenine glycosylase. Chain: a, b. Engineered: yes. Mutation: yes. DNA (5'-d( T Gp Tp Cp Cp Ap Cp Gp Tp Cp T)-3'). Chain: c, e. Engineered: yes. DNA (5'-d( Ap Ap Gp Ap Cp (8Og)p Tp Gp Gp Ap C)-3'). Chain: d, f.

Source:

Geobacillus stearothermophilus. Organism_taxid: 1422. Expressed in: escherichia coli. Expression_system_taxid: 469008. Synthetic: yes. Synthetic construct. Organism_taxid: 32630. Organism_taxid: 32630

Resolution:

2.59Å R-factor: 0.172 R-free: 0.228

Authors:

L.Wang,S.Lee,G.L.Verdine

Key ref:

L.Wang et al. (2015). Structural Basis for Avoidance of Promutagenic DNA Repair by MutY Adenine DNA Glycosylase. J Biol Chem, 290, 17096-17105. PubMed id: 25995449 DOI: 10.1074/jbc.M115.657866

Date:

13-Mar-15 Release date: 27-May-15

Protein chains

P83847  (MUTY_GEOSE) -  Adenine DNA glycosylase from Geobacillus stearothermophilus

Seq: 366 a.a.

Struc: 355 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

DNA/RNA chains

G-T-C-C-A-C-G-T-C-T 10 bases

A-A-G-A-C-8OG-T-G-G-A-C 11 bases

G-T-C-C-A-C-G-T-C-T 10 bases

A-A-G-A-C-8OG-T-G-G-A-C 11 bases

Enzyme reactions

• Enzyme class: E.C.3.2.2.31 - adenine glycosylase.

DOI no: 10.1074/jbc.M115.657866

J Biol Chem 290:17096-17105 (2015)

PubMed id: 25995449

Structural Basis for Avoidance of Promutagenic DNA Repair by MutY Adenine DNA Glycosylase.

L.Wang, S.J.Lee, G.L.Verdine.

ABSTRACT

The highly mutagenic A:oxoG (8-oxoguanine) base pair in DNA most frequently arises by aberrant replication of the primary oxidative lesion C:oxoG. This lesion is particularly insidious because neither of its constituent nucleobases faithfully transmit genetic information from the original C:G base pair. Repair of A:oxoG is initiated by adenine DNA glycosylase, which catalyzes hydrolytic cleavage of the aberrant A nucleobase from the DNA backbone. These enzymes, MutY in bacteria and MUTYH in humans, scrupulously avoid processing of C:oxoG because cleavage of the C residue in C:oxoG would actually promote mutagenic conversion to A:oxoG. Here we analyze the structural basis for rejection of C:oxoG by MutY, using a synthetic crystallography approach to capture the enzyme in the process of inspecting the C:oxoG anti-substrate, with which it ordinarily binds only fleetingly. We find that MutY uses two distinct strategies to avoid presentation of C to the enzyme active site. Firstly, MutY possesses an exo-site that serves as a decoy for C, and secondly, repulsive forces with a key active site residue prevent stable insertion of C into the nucleobase recognition pocket within the enzyme active site.