4NKU

Structure of Cid1 in complex with its short product ApU


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.179 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

A critical switch in the enzymatic properties of the Cid1 protein deciphered from its product-bound crystal structure.

Munoz-Tello, P.Gabus, C.Thore, S.

(2014) Nucleic Acids Res. 42: 3372-3380

  • DOI: 10.1093/nar/gkt1278
  • Primary Citation of Related Structures:  4NKT

  • PubMed Abstract: 
  • The addition of uridine nucleotide by the poly(U) polymerase (PUP) enzymes has a demonstrated impact on various classes of RNAs such as microRNAs (miRNAs), histone-encoding RNAs and messenger RNAs. Cid1 protein is a member of the PUP family. We solve ...

    The addition of uridine nucleotide by the poly(U) polymerase (PUP) enzymes has a demonstrated impact on various classes of RNAs such as microRNAs (miRNAs), histone-encoding RNAs and messenger RNAs. Cid1 protein is a member of the PUP family. We solved the crystal structure of Cid1 in complex with non-hydrolyzable UMPNPP and a short dinucleotide compound ApU. These structures revealed new residues involved in substrate/product stabilization. In particular, one of the three catalytic aspartate residues explains the RNA dependence of its PUP activity. Moreover, other residues such as residue N165 or the β-trapdoor are shown to be critical for Cid1 activity. We finally suggest that the length and sequence of Cid1 substrate RNA influence the balance between Cid1's processive and distributive activities. We propose that particular processes regulated by PUPs require the enzymes to switch between the two types of activity as shown for the miRNA biogenesis where PUPs can either promote DICER cleavage via short U-tail or trigger miRNA degradation by adding longer poly(U) tail. The enzymatic properties of these enzymes may be critical for determining their particular function in vivo.


    Organizational Affiliation

    Department of Molecular Biology, University of Geneva, Geneva, 1211, Switzerland.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Poly(A) RNA polymerase protein cid1
A, B
341Schizosaccharomyces pombe (strain 972 / ATCC 24843)Gene Names: cid1
EC: 2.7.7.-
Find proteins for O13833 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Go to UniProtKB:  O13833
Entity ID: 2
MoleculeChainsLengthOrganism
5'-R(*AP*U)-3'D,H2N/A
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BR
Query on BR

Download SDF File 
Download CCD File 
A, B, D
BROMIDE ION
Br
CPELXLSAUQHCOX-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.179 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 54.020α = 90.00
b = 77.090β = 90.71
c = 81.830γ = 90.00
Software Package:
Software NamePurpose
XDSdata scaling
PHENIXrefinement
PHASERphasing
XDSdata reduction
ADSCdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-12-18
    Type: Initial release
  • Version 1.1: 2014-01-15
    Type: Database references
  • Version 1.2: 2014-03-26
    Type: Database references