2J8X

Epstein-Barr virus uracil-DNA glycosylase in complex with Ugi from PBS-2

Summary for 2J8X

• Entry DOI: 10.2210/pdb2j8x/pdb
• Related: 1EUI 1LQG 1LQM 1UDI 1UGH 1UGI 1UUG 2UGI 2UUG
• Descriptor: URACIL-DNA GLYCOSYLASE, URACIL-DNA GLYCOSYLASE INHIBITOR, UREA, ... (4 entities in total)
• Functional Keywords: hydrolase-inhibitor complex, ebv, dna repair, lytic protein, epstein-barr virus, uracil- dna glycosylase, hydrolase, uracil-dna glycosylase inhibitor, hydrolase/inhibitor
• Biological source: EPSTEIN-BARR VIRUS (HHV-4); More
• Total number of polymer chains: 4
• Total formula weight: 70602.79

Authors

Geoui, T.,Buisson, M.,Tarbouriech, N.,Burmeister, W.P. (deposition date: 2006-10-31, release date: 2006-12-13, Last modification date: 2023-12-13)

Primary citation

Geoui, T.,Buisson, M.,Tarbouriech, N.,Burmeister, W.P.
New Insights on the Role of the Gamma-Herpesvirus Uracil-DNA Glycosylase Leucine Loop Revealed by the Structure of the Epstein-Barr Virus Enzyme in Complex with an Inhibitor Protein.
J.Mol.Biol., 366:117-, 2007

PubMed Abstract: Epstein-Barr virus (EBV) is a human gamma-herpesvirus. Within its 86 open reading frame containing genome, two enzymes avoiding uracil incorporation into DNA can be found: uracil triphosphate hydrolase and uracil-DNA glycosylase (UNG). The latter one excises uracil bases that are due to cytosine deamination or uracil misincorporation from double-stranded DNA substrates. The EBV enzyme belongs to family 1 UNGs. We solved the three-dimensional structure of EBV UNG in complex with the uracil-DNA glycosylase inhibitor protein (Ugi) from bacteriophage PBS-2 at a resolution of 2.3 A by X-ray crystallography. The structure of EBV UNG encoded by the BKRF3 reading frame shows the excellent global structural conservation within the solved examples of family 1 enzymes. Four out of the five catalytic motifs are completely conserved, whereas the fifth one, the leucine loop, carries a seven residue insertion. Despite this insertion, catalytic constants of EBV UNG are similar to those of other UNGs. Modelling of the EBV UNG-DNA complex shows that the longer leucine loop still contacts DNA and is likely to fulfil its role of DNA binding and deformation differently than the enzymes with previously solved structures. We could show that despite the evolutionary distance of EBV UNG from the natural host protein, bacteriophage Ugi binds with an inhibitory constant of 8 nM to UNG. This is due to an excellent specificity of Ugi for conserved elements of UNG, four of them corresponding to catalytic motifs and a fifth one corresponding to an important beta-turn structuring the catalytic site.

PubMed: 17157317
DOI: 10.1016/J.JMB.2006.11.007

Experimental method

X-RAY DIFFRACTION (2.3 Å)