6IOD

The structure of UdgX in complex with single-stranded DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.66 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.184 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Suicide inactivation of the uracil DNA glycosylase UdgX by covalent complex formation.

Tu, J.Chen, R.Yang, Y.Cao, W.Xie, W.

(2019) Nat Chem Biol 15: 615-622

  • DOI: https://doi.org/10.1038/s41589-019-0290-x
  • Primary Citation of Related Structures:  
    6IO9, 6IOA, 6IOB, 6IOC, 6IOD

  • PubMed Abstract: 

    A uracil DNA glycosylase (UDG) from Mycobacterium smegmatis (MsmUdgX) shares sequence similarity with family 4 UDGs and forms exceedingly stable complexes with single-stranded uracil-containing DNAs (ssDNA-Us) that are resistant to denaturants. However, MsmUdgX has been reported to be inactive in excising uracil from ssDNA-Us and the underlying structural basis is unclear. Here, we report high-resolution crystal structures of MsmUdgX in the free, uracil- and DNA-bound forms, respectively. The structural information, supported by mutational and biochemical analyses, indicates that the conserved residue His109 located on a characteristic loop forms an irreversible covalent linkage with the deoxyribose at the apyrimidinic site of ssDNA-U, thus rendering the enzyme unable to regenerate. By proposing the catalytic pathway and molecular mechanism for MsmUdgX, our studies provide an insight into family 4 UDGs and UDGs in general.


  • Organizational Affiliation

    MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, The Sun Yat-Sen University, Guangzhou, Guangdong, China.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Phage SPO1 DNA polymerase-related protein
A, B
212Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: MSMEI_0259
EC: 2.7.7.7
UniProt
Find proteins for I7F541 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Explore I7F541 
Go to UniProtKB:  I7F541
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupI7F541
Sequence Annotations
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  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains LengthOrganismImage
DNA
C, D
16Mycolicibacterium smegmatis
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.66 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.184 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.805α = 90
b = 83.862β = 94.51
c = 122.664γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

  • Released Date: 2019-07-31 
  • Deposition Author(s): Xie, W., Tu, J.

Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina31870782
National Natural Science Foundation of ChinaChina31700657

Revision History  (Full details and data files)

  • Version 1.0: 2019-07-31
    Type: Initial release
  • Version 1.1: 2023-11-22
    Changes: Data collection, Database references, Derived calculations, Refinement description