5H9W

Crystal structure of Regnase PIN domain, form II


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.191 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structural basis for the regulation of enzymatic activity of Regnase-1 by domain-domain interactions

Yokogawa, M.Tsushima, T.Noda, N.N.Kumeta, H.Enokizono, Y.Yamashita, K.Standley, D.M.Takeuchi, O.Akira, S.Inagaki, F.

(2016) Sci Rep 6: 22324-22324

  • DOI: 10.1038/srep22324
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Regnase-1 is an RNase that directly cleaves mRNAs of inflammatory genes such as IL-6 and IL-12p40, and negatively regulates cellular inflammatory responses. Here, we report the structures of four domains of Regnase-1 from Mus musculus-the N-terminal ...

    Regnase-1 is an RNase that directly cleaves mRNAs of inflammatory genes such as IL-6 and IL-12p40, and negatively regulates cellular inflammatory responses. Here, we report the structures of four domains of Regnase-1 from Mus musculus-the N-terminal domain (NTD), PilT N-terminus like (PIN) domain, zinc finger (ZF) domain and C-terminal domain (CTD). The PIN domain harbors the RNase catalytic center; however, it is insufficient for enzymatic activity. We found that the NTD associates with the PIN domain and significantly enhances its RNase activity. The PIN domain forms a head-to-tail oligomer and the dimer interface overlaps with the NTD binding site. Interestingly, mutations blocking PIN oligomerization had no RNase activity, indicating that both oligomerization and NTD binding are crucial for RNase activity in vitro. These results suggest that Regnase-1 RNase activity is tightly controlled by both intramolecular (NTD-PIN) and intermolecular (PIN-PIN) interactions.


    Organizational Affiliation

    Faculty of Advanced Life Science, Hokkaido University, Sapporo 001-0021, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ribonuclease ZC3H12A
A, B
210Mus musculusMutation(s): 0 
Gene Names: Zc3h12a (Mcpip, Mcpip1)
EC: 3.1.-.-
Find proteins for Q5D1E7 (Mus musculus)
Go to UniProtKB:  Q5D1E7
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A, B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.191 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 113.333α = 90.00
b = 113.333β = 90.00
c = 78.373γ = 120.00
Software Package:
Software NamePurpose
CNSphasing
HKL-2000data reduction
HKL-2000data scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
JSPSJapan--

Revision History 

  • Version 1.0: 2016-03-16
    Type: Initial release