6AJO

Complex form of Uracil DNA glycosylase X and uracil-DNA.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.27 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.199 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Covalent binding of uracil DNA glycosylase UdgX to abasic DNA upon uracil excision.

Ahn, W.C.Aroli, S.Kim, J.H.Moon, J.H.Lee, G.S.Lee, M.H.Sang, P.B.Oh, B.H.Varshney, U.Woo, E.J.

(2019) Nat Chem Biol 15: 607-614

  • DOI: https://doi.org/10.1038/s41589-019-0289-3
  • Primary Citation of Related Structures:  
    6AIL, 6AJO, 6AJP, 6AJQ, 6AJR, 6AJS

  • PubMed Abstract: 

    Uracil DNA glycosylases (UDGs) are important DNA repair enzymes that excise uracil from DNA, yielding an abasic site. Recently, UdgX, an unconventional UDG with extremely tight binding to DNA containing uracil, was discovered. The structure of UdgX from Mycobacterium smegmatis in complex with DNA shows an overall similarity to that of family 4 UDGs except for a protruding loop at the entrance of the uracil-binding pocket. Surprisingly, H109 in the loop was found to make a covalent bond to the abasic site to form a stable intermediate, while the excised uracil remained in the pocket of the active site. H109 functions as a nucleophile to attack the oxocarbenium ion, substituting for the catalytic water molecule found in other UDGs. To our knowledge, this change from a catalytic water attack to a direct nucleophilic attack by the histidine residue is unprecedented. UdgX utilizes a unique mechanism of protecting cytotoxic abasic sites from exposure to the cellular environment.


  • Organizational Affiliation

    Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Uracil DNA glycosylase superfamily protein209Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: MSMEG_0265
UniProt
Find proteins for A0QP43 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Explore A0QP43 
Go to UniProtKB:  A0QP43
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0QP43
Sequence Annotations
Expand
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (5'-D(P*(ORP)P*TP*T)-3')B [auth F]5Mycolicibacterium smegmatis
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.27 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.199 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 36.829α = 90
b = 64.45β = 90
c = 82.9γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Research Foundation (Korea)Korea, Republic OfNRF-2018R1A2A2A05021648

Revision History  (Full details and data files)

  • Version 1.0: 2019-05-29
    Type: Initial release
  • Version 1.1: 2024-03-27
    Changes: Data collection, Database references, Derived calculations