PDBsum entry 4yig

Hydrolase

PDB id: 4yig

Contents

Protein chains

220 a.a.

50 a.a.

DNA/RNA

Ligands

URA ×3

Waters ×54

PDB id:

4yig

Name:

Hydrolase

Title:

Vaccinia virus d4/a20(1-50) in complex with dsdna containing an abasic site and free uracyl

Structure:

Uracil-DNA glycosylase. Chain: a, e, i. Synonym: udg. Engineered: yes. DNA polymerase processivity factor component a20. Chain: b, f, j. Engineered: yes. DNA (5'-d( Cp Tp Gp Tp (Orp)p Ap Tp Cp Tp T)-3'). Chain: c, g, k.

Source:

Vaccinia virus (strain copenhagen). Vacv. Organism_taxid: 10249. Gene: ung, d4r. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Vaccinia virus. Gene: a20r. Synthetic: yes.

Resolution:

2.70Å R-factor: 0.182 R-free: 0.228

Authors:

N.Tarbouriech,W.P.Burmeister,F.Iseni

Key ref:

W.P.Burmeister et al. (2015). Crystal Structure of the Vaccinia Virus Uracil-DNA Glycosylase in Complex with DNA. J Biol Chem, 290, 17923-17934. PubMed id: 26045555 DOI: 10.1074/jbc.M115.648352

Date:

02-Mar-15 Release date: 10-Jun-15

Protein chains

P20536  (UNG_VACCC) -  Uracil-DNA glycosylase from Vaccinia virus (strain Copenhagen)

Seq: 218 a.a.

Struc: 220 a.a.

Protein chains

P20995  (A20_VACCC) -  DNA polymerase processivity factor component OPG148 from Vaccinia virus (strain Copenhagen)

Seq: 426 a.a.

Struc: 50 a.a.*

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

DNA/RNA chains

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

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

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

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

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

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

Enzyme reactions

• Enzyme class: Chains A, E, I: E.C.3.2.2.27 - uracil-DNA glycosylase.

DOI no: 10.1074/jbc.M115.648352

J Biol Chem 290:17923-17934 (2015)

PubMed id: 26045555

Crystal Structure of the Vaccinia Virus Uracil-DNA Glycosylase in Complex with DNA.

W.P.Burmeister, N.Tarbouriech, P.Fender, C.Contesto-Richefeu, C.N.Peyrefitte, F.Iseni.

ABSTRACT

Vaccinia virus polymerase holoenzyme is composed of the DNA polymerase catalytic subunit E9 associated with its heterodimeric co-factor A20·D4 required for processive genome synthesis. Although A20 has no known enzymatic activity, D4 is an active uracil-DNA glycosylase (UNG). The presence of a repair enzyme as a component of the viral replication machinery suggests that, for poxviruses, DNA synthesis and base excision repair is coupled. We present the 2.7 Å crystal structure of the complex formed by D4 and the first 50 amino acids of A20 (D4·A201-50) bound to a 10-mer DNA duplex containing an abasic site resulting from the cleavage of a uracil base. Comparison of the viral complex with its human counterpart revealed major divergences in the contacts between protein and DNA and in the enzyme orientation on the DNA. However, the conformation of the dsDNA within both structures is very similar, suggesting a dominant role of the DNA conformation for UNG function. In contrast to human UNG, D4 appears rigid, and we do not observe a conformational change upon DNA binding. We also studied the interaction of D4·A201-50 with different DNA oligomers by surface plasmon resonance. D4 binds weakly to nonspecific DNA and to uracil-containing substrates but binds abasic sites with a Kd of <1.4 μm. This second DNA complex structure of a family I UNG gives new insight into the role of D4 as a co-factor of vaccinia virus DNA polymerase and allows a better understanding of the structural determinants required for UNG action.