6AJO

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.269 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.192 

wwPDB Validation 3D Report Full Report


This is version 1.0 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: 10.1038/s41589-019-0289-3
  • Primary Citation of Related Structures:  

  • 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 f ...

    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.,Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea. ejwoo@kribb.re.kr.,Creative Research Initiative Center for Chemical Dynamics in Living Cells, Department of Chemistry, Chung-Ang University, Seoul, Korea.,Department of Biological Sciences, KAIST Institute for the Biocentury, Korea Advanced Institute of Science and Technology, Daejeon, Korea.,Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India. varshney@iisc.ac.in.,University of Science and Technology, Daejeon, Republic of Korea. ejwoo@kribb.re.kr.,Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Uracil DNA glycosylase superfamily protein
A
209Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Find proteins for A0QP43 (Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0QP43
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(P*(ORP)P*TP*T)-3')F5Mycolicibacterium smegmatis
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

Download SDF File 
Download CCD File 
A
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
PO4
Query on PO4

Download SDF File 
Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
URA
Query on URA

Download SDF File 
Download CCD File 
A
URACIL
C4 H4 N2 O2
ISAKRJDGNUQOIC-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
ORP
Query on ORP
F
SACCHARIDEC5 H11 O7 P

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.269 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.192 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 36.829α = 90.00
b = 64.450β = 90.00
c = 82.900γ = 90.00
Software Package:
Software NamePurpose
PHENIXphasing
HKL-2000data scaling
PHENIXrefinement
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


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

Revision History 

  • Version 1.0: 2019-05-29
    Type: Initial release