5NNH

KSHV uracil-DNA glycosylase, apo form

Summary for 5NNH

• Entry DOI: 10.2210/pdb5nnh/pdb
• Related: 5NN7 5NNU
• Descriptor: Uracil-DNA glycosylase, SULFATE ION (3 entities in total)
• Functional Keywords: uracil-dna glycosylase, hydrolase
• Biological source: Human herpesvirus 8 (HHV-8)
• Total number of polymer chains: 1
• Total formula weight: 27322.24

Authors

Earl, C.,Bagneris, C.,Cole, A.R.,Barrett, T.,Savva, R. (deposition date: 2017-04-09, release date: 2018-03-21, Last modification date: 2024-01-17)

Primary citation

Earl, C.,Bagneris, C.,Zeman, K.,Cole, A.,Barrett, T.,Savva, R.
A structurally conserved motif in gamma-herpesvirus uracil-DNA glycosylases elicits duplex nucleotide-flipping.
Nucleic Acids Res., 46:4286-4300, 2018

PubMed Abstract: Efficient γ-herpesvirus lytic phase replication requires a virally encoded UNG-type uracil-DNA glycosylase as a structural element of the viral replisome. Uniquely, γ-herpesvirus UNGs carry a seven or eight residue insertion of variable sequence in the otherwise highly conserved minor-groove DNA binding loop. In Epstein-Barr Virus [HHV-4] UNG, this motif forms a disc-shaped loop structure of unclear significance. To ascertain the biological role of the loop insertion, we determined the crystal structure of Kaposi's sarcoma-associated herpesvirus [HHV-8] UNG (kUNG) in its product complex with a uracil-containing dsDNA, as well as two structures of kUNG in its apo state. We find the disc-like conformation is conserved, but only when the kUNG DNA-binding cleft is occupied. Surprisingly, kUNG uses this structure to flip the orphaned partner base of the substrate deoxyuridine out of the DNA duplex while retaining canonical UNG deoxyuridine-flipping and catalysis. The orphan base is stably posed in the DNA major groove which, due to DNA backbone manipulation by kUNG, is more open than in other UNG-dsDNA structures. Mutagenesis suggests a model in which the kUNG loop is pinned outside the DNA-binding cleft until DNA docking promotes rigid structuring of the loop and duplex nucleotide flipping, a novel observation for UNGs.

PubMed: 29596604
DOI: 10.1093/nar/gky217

Experimental method

X-RAY DIFFRACTION (2.2 Å)