5H6N

DNA targeting ADP-ribosyltransferase Pierisin-1, autoinhibitory form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.225 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural basis of autoinhibition and activation of the DNA-targeting ADP-ribosyltransferase pierisin-1

Oda, T.Hirabayashi, H.Shikauchi, G.Takamura, R.Hiraga, K.Minami, H.Hashimoto, H.Yamamoto, M.Wakabayashi, K.Shimizu, T.Sato, M.

(2017) J Biol Chem 292: 15445-15455

  • DOI: 10.1074/jbc.M117.776641
  • Primary Citation of Related Structures:  
    5H6J, 5H6K, 5H6L, 5H6M, 5H6N

  • PubMed Abstract: 
  • ADP-ribosyltransferases transfer the ADP-ribose moiety of βNAD + to an acceptor molecule, usually a protein that modulates the function of the acceptor. Pierisin-1 is an ADP-ribosyltransferase from the cabbage butterfly Pieris rapae and is composed of N-terminal catalytic and C-terminal ricin B-like domains ...

    ADP-ribosyltransferases transfer the ADP-ribose moiety of βNAD + to an acceptor molecule, usually a protein that modulates the function of the acceptor. Pierisin-1 is an ADP-ribosyltransferase from the cabbage butterfly Pieris rapae and is composed of N-terminal catalytic and C-terminal ricin B-like domains. Curiously, it ADP-ribosylates the DNA duplex, resulting in apoptosis of various cancer cells, which has raised interest in pierisin-1 as an anti-cancer agent. However, both the structure and the mechanism of DNA ADP-ribosylation are unclear. Here, we report the crystal structures of the N-terminal catalytic domain of pierisin-1, its complex with βNAD + , and the catalytic domain with the linker connecting it to the ricin B-like domains. We found that the catalytic domain possesses a defined, positively charged region on the molecular surface but that its overall structure is otherwise similar to those of protein-targeting ADP-ribosyltransferases. Electrophoretic mobility shift assays and site-directed mutagenesis indicated that pierisin-1 binds double-stranded but not single-stranded DNA and that Lys 122 , Lys 123 , and Lys 124 , which are found in a loop, and Arg 181 and Arg 187 , located in a basic cleft near the loop, are required for DNA binding. Furthermore, the structure of the catalytic domain with the linker revealed an autoinhibitory mechanism in which the linker occupies and blocks both the βNAD + - and DNA-binding sites, suggesting that proteolytic cleavage to remove the linker is necessary for enzyme catalysis. Our study provides a structural basis for the DNA-acceptor specificity of pierisin-1 and reveals that a self-regulatory mechanism is required for its activity.


    Organizational Affiliation

    From the Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan, msato@tsurumi.yokohama-cu.ac.jp.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Pierisin-1A, B, C, D275Pieris rapaeMutation(s): 1 
EC: 2.4.2
UniProt
Find proteins for Q9U8Q4 (Pieris rapae)
Explore Q9U8Q4 
Go to UniProtKB:  Q9U8Q4
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.225 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.07α = 90
b = 110.5β = 91.2
c = 133.64γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-08-09
    Type: Initial release
  • Version 1.1: 2017-09-27
    Changes: Database references