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 

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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 ...

    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: 

    University of Science and Technology, Daejeon, Republic of Korea. ejwoo@kribb.re.kr.



Macromolecules

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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Uracil DNA glycosylase superfamily protein209Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: MSMEG_0265
EC: 3.2.2.27
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
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsLengthOrganismImage
DNA (5'-D(P*(ORP)P*TP*T)-3')B [auth F]5Mycolicibacterium smegmatis
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4
Download Ideal Coordinates CCD File 
C [auth A]IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC		 Ligand Interaction
URA (Subject of Investigation/LOI)
Query on URA
Download Ideal Coordinates CCD File 
E [auth A]URACIL
C4 H4 N2 O2
ISAKRJDGNUQOIC-UHFFFAOYSA-N		 Ligand Interaction
PO4
Query on PO4
Download Ideal Coordinates CCD File 
D [auth A]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K		 Ligand Interaction
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

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Ligand Structure Quality Assessment 


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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