6LYE

Crystal Structure of mimivirus UNG Y322F in complex with UGI


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.187 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Selective interactions between mimivirus uracil-DNA glycosylase and inhibitory proteins determined by a single amino acid.

Pathak, D.Kwon, E.Kim, D.Y.

(2020) J Struct Biol 211: 107552-107552

  • DOI: 10.1016/j.jsb.2020.107552
  • Primary Citation of Related Structures:  
    6LYD, 6LYE

  • PubMed Abstract: 
  • Uracil-N-glycosylase (UNG) is found in most organisms as well as in large DNA viruses. Its inhibitory proteins, including uracil glycosylase inhibitor (UGI) and p56, tightly bind to the active site of UNG by mimicking the DNA substrates. As the binding motifs are conserved in UNG family proteins, the inhibitory proteins bind to various UNG proteins across species ...

    Uracil-N-glycosylase (UNG) is found in most organisms as well as in large DNA viruses. Its inhibitory proteins, including uracil glycosylase inhibitor (UGI) and p56, tightly bind to the active site of UNG by mimicking the DNA substrates. As the binding motifs are conserved in UNG family proteins, the inhibitory proteins bind to various UNG proteins across species. However, the intercalation residue that penetrates the DNA minor groove during uracil excision is not conserved among UNG proteins. To understand the role of the intercalation residue in their binding to the inhibitory proteins, we prepared mutants of mimivirus UNG, measured the binding affinity between the UNG mutants and inhibitory proteins, and analyzed the interactions based on the crystal structures of mimivirus UNG mutants complexed with UGI. The results show that mimivirus UNG, which harbors Tyr as an intercalation residue, did not interact with the inhibitory proteins intrinsically, whereas mutations of the intercalation residue to Phe or Leu resulted in tight interactions with UGI and p56; mutation to Met resulted in tight interactions only with p56. The crystal structures revealed that Phe and Leu stabilize the interactions by fitting into the hydrophobic pocket of UGI. These results show that differences in size and hydrophobicity of the intercalation residues determine the interactions between UNG family proteins and the inhibitory proteins, UGI and p56.


    Organizational Affiliation

    College of pharmacy, Yeungnam University, Gyeongsan, Gyeongbuk 38541, South Korea. Electronic address: dyokim@ynu.ac.kr.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Probable uracil-DNA glycosylaseA276Acanthamoeba polyphaga mimivirusMutation(s): 1 
Gene Names: UNGMIMI_L249
EC: 3.2.2
Find proteins for Q5UPT2 (Acanthamoeba polyphaga mimivirus)
Explore Q5UPT2 
Go to UniProtKB:  Q5UPT2
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Uracil-DNA glycosylase inhibitorI83Bacillus phage PBS2Mutation(s): 0 
Gene Names: UGI
Find proteins for P14739 (Bacillus phage PBS2)
Explore P14739 
Go to UniProtKB:  P14739
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.187 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 104.23α = 90
b = 104.23β = 90
c = 83.12γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Research Foundation (NRF, Korea)Korea, Republic Of2017R1A6A3A11029218
National Research Foundation (NRF, Korea)Korea, Republic Of2017R1D1A1B03034088

Revision History 

  • Version 1.0: 2020-07-08
    Type: Initial release
  • Version 1.1: 2020-08-12
    Changes: Database references