4YIG

vaccinia virus D4/A20(1-50) in complex with dsDNA containing an abasic site and free uracyl

Summary for 4YIG

• Entry DOI: 10.2210/pdb4yig/pdb
• Descriptor: Uracil-DNA glycosylase, DNA polymerase processivity factor component A20, DNA (5'-D(*CP*TP*GP*TP*(ORP)P*AP*TP*CP*TP*T)-3'), ... (6 entities in total)
• Functional Keywords: uracyl dna glycosylase, dna complex, virus replication, hydrolase
• Biological source: Vaccinia virus (strain Copenhagen) (VACV); More
• Total number of polymer chains: 12
• Total formula weight: 115794.24

Authors

tarbouriech, N.,burmeister, W.P.,iseni, F. (deposition date: 2015-03-02, release date: 2015-06-10, Last modification date: 2024-01-10)

Primary citation

Burmeister, W.P.,Tarbouriech, N.,Fender, P.,Contesto-Richefeu, C.,Peyrefitte, C.N.,Iseni, F.
Crystal Structure of the Vaccinia Virus Uracil-DNA Glycosylase in Complex with DNA.
J.Biol.Chem., 290:17923-17934, 2015

PubMed 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.

PubMed: 26045555
DOI: 10.1074/jbc.M115.648352

Experimental method

X-RAY DIFFRACTION (2.7 Å)