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 

wwPDB Validation 3D Report Full Report


This is version 1.0 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: 10.1038/s41589-019-0290-x
  • Primary Citation of Related Structures:  

  • 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. Howev ...

    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

    Department of Genetics and Biochemistry, Clemson University, Clemson, SC, USA.,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. xiewei6@mail.sysu.edu.cn.,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: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Phage SPO1 DNA polymerase-related protein
A, B
212Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
EC: 2.7.7.7
Find proteins for I7F541 (Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  I7F541
Entity ID: 2
MoleculeChainsLengthOrganism
DNAC,D16Mycolicibacterium smegmatis
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

Download SDF File 
Download CCD File 
A, B
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
ORP
Query on ORP
C, D
SACCHARIDEC5 H11 O7 P

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.66 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.182 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 43.805α = 90.00
b = 83.862β = 94.51
c = 122.664γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
HKL-3000data scaling
HKL-3000data reduction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2018-10-29 
  • 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 

  • Version 1.0: 2019-07-31
    Type: Initial release