5X3G : The WT UNG crystal structure from Nitratifractor salsuginis

Description

Experimental Technique/Method:X-RAY DIFFRACTION Resolution:2.02 Classification:DNA BINDING PROTEIN Release Date:2017-10-18 Deposition Date:2017-02-06 Revision Date:2017-12-13 Molecular Weight:30833.29 Macromolecule Type:Protein Residue Count:263 Atom Site Count:1967 DOI:10.2210/pdb5x3g/pdb Abstract: The uracil DNA glycosylase superfamily consists of at least six families with a diverse specificity toward DNA base damage. Family 1 uracil N-glycosylase (UNG) exhibits exclusive specificity on uracil-containing DNA. Here, we report a family 1 UNG homolog from Nitratifractor salsuginis with distinct biochemical features that differentiate it from conventional family 1 UNGs. Globally, the crystal structure of N. salsuginisUNG shows a few additional secondary structural elements. Biochemical and enzyme kinetic analysis, coupled with structural determination, molecular modeling, and molecular dynamics simulations, shows that N. salsuginisUNG contains a salt bridge network that plays an important role in DNA backbone interactions. Disruption of the amino acid residues involved in the salt bridges greatly impedes the enzymatic activity. A tyrosine residue in motif 1 (GQDPY) is one of the distinct sequence features setting family 1 UNG apart from other families. The crystal structure of Y81G mutant indicates that several subtle changes may account for its inactivity. Unlike the conventional family 1 UNG enzymes, N. salsuginisUNG is not inhibited by Ugi, a potent inhibitor specific for family 1 UNG. This study underscores the diversity of paths that a uracil DNA glycosylase may take to acquire its unique structural and biochemical properties during evolution.

Publication Date

10-18-2017

Publisher

RCSB-PDB

DOI

10.2210/pdb5x3g/pdb

Document Type

Data Set

Identifier

5X3G

Embargo Date

10-18-2017

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