PDBsum entry 2owq

Hydrolase

PDB id: 2owq

Contents

Protein chains

216 a.a. *

Ligands

IMD ×3

GOL ×4

SO4

Metals

_CL

Waters ×146

* Residue conservation analysis

PDB id:

2owq

Name:

Hydrolase

Title:

Crystal structure of vaccinia virus uracil-DNA glycosylase

Structure:

Uracil-DNA glycosylase. Chain: a, b. Synonym: udg. Engineered: yes. Mutation: yes

Source:

Vaccinia virus western reserve. Organism_taxid: 696871. Gene: d4r, vacwr109. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.40Å R-factor: 0.244 R-free: 0.300

Authors:

N.Schormann,D.Chattopadhyay

Key ref:

N.Schormann et al. (2007). Crystal structure of vaccinia virus uracil-DNA glycosylase reveals dimeric assembly. Bmc Struct Biol, 7, 45. PubMed id: 17605817

Date:

16-Feb-07 Release date: 24-Jul-07

Protein chains

P04303  (UNG_VACCW) -  Uracil-DNA glycosylase from Vaccinia virus (strain Western Reserve)

Seq: 218 a.a.

Struc: 216 a.a.*

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

Enzyme reactions

• Enzyme class: E.C.3.2.2.27 - uracil-DNA glycosylase.

Bmc Struct Biol 7:45 (2007)

PubMed id: 17605817

Crystal structure of vaccinia virus uracil-DNA glycosylase reveals dimeric assembly.

N.Schormann, A.Grigorian, A.Samal, R.Krishnan, L.DeLucas, D.Chattopadhyay.

ABSTRACT

BACKGROUND: Uracil-DNA glycosylases (UDGs) catalyze excision of uracil from DNA. Vaccinia virus, which is the prototype of poxviruses, encodes a UDG (vvUDG) that is significantly different from the UDGs of other organisms in primary, secondary and tertiary structure and characteristic motifs. It adopted a novel catalysis-independent role in DNA replication that involves interaction with a viral protein, A20, to form the processivity factor. UDG:A20 association is essential for assembling of the processive DNA polymerase complex. The structure of the protein must have provisions for such interactions with A20. This paper provides the first glimpse into the structure of a poxvirus UDG. RESULTS: Results of dynamic light scattering experiments and native size exclusion chromatography showed that vvUDG is a dimer in solution. The dimeric assembly is also maintained in two crystal forms. The core of vvUDG is reasonably well conserved but the structure contains one additional beta-sheet at each terminus. A glycerol molecule is found in the active site of the enzyme in both crystal forms. Interaction of this glycerol molecule with the protein possibly mimics the enzyme-substrate (uracil) interactions. CONCLUSION: The crystal structures reveal several distinctive features of vvUDG. The new structural features may have evolved for adopting novel functions in the replication machinery of poxviruses. The mode of interaction between the subunits in the dimers suggests a possible model for binding to its partner and the nature of the processivity factor in the polymerase complex.