4AL5

Crystal structure of the Csy4-crRNA product complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.183 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Csy4 Relies on an Unusual Catalytic Dyad to Position and Cleave Crispr RNA.

Haurwitz, R.E.Sternberg, S.H.Doudna, J.A.

(2012) Embo J. 31: 2824

  • DOI: 10.1038/emboj.2012.107
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • CRISPR-Cas adaptive immune systems protect prokaryotes against foreign genetic elements. crRNAs derived from CRISPR loci base pair with complementary nucleic acids, leading to their destruction. In Pseudomonas aeruginosa, crRNA biogenesis requires th ...

    CRISPR-Cas adaptive immune systems protect prokaryotes against foreign genetic elements. crRNAs derived from CRISPR loci base pair with complementary nucleic acids, leading to their destruction. In Pseudomonas aeruginosa, crRNA biogenesis requires the endoribonuclease Csy4, which binds and cleaves the repetitive sequence of the CRISPR transcript. Biochemical assays and three co-crystal structures of wild-type and mutant Csy4/RNA complexes reveal a substrate positioning and cleavage mechanism in which a histidine deprotonates the ribosyl 2'-hydroxyl pinned in place by a serine, leading to nucleophilic attack on the scissile phosphate. The active site catalytic dyad lacks a general acid to protonate the leaving group and positively charged residues to stabilize the transition state, explaining why the observed catalytic rate constant is ∼10(4)-fold slower than that of RNase A. We show that this RNA cleavage step is essential for assembly of the Csy protein-crRNA complex that facilitates target recognition. Considering that Csy4 recognizes a single cellular substrate and sequesters the cleavage product, evolutionary pressure has likely selected for substrate specificity and high-affinity crRNA interactions at the expense of rapid cleavage kinetics.


    Organizational Affiliation

    Department of Molecular and Cell Biology, University of California, Berkeley, 94720, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CSY4 ENDORIBONUCLEASE
A
191Pseudomonas aeruginosa (strain UCBPP-PA14)Mutation(s): 1 
Gene Names: cas6f (csy4)
EC: 3.1.-.-
Find proteins for Q02MM2 (Pseudomonas aeruginosa (strain UCBPP-PA14))
Go to UniProtKB:  Q02MM2
Entity ID: 2
MoleculeChainsLengthOrganism
5'-R(*UP*UP*CP*AP*CP*UP*GP*CP*CP*GP*UP*AP*UP*AP *GP*GP*CP*AP*GP*C)-3'B20Pseudomonas aeruginosa
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.183 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 60.790α = 90.00
b = 47.800β = 109.69
c = 86.570γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
XDSdata reduction
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-06-13
    Type: Initial release
  • Version 1.1: 2012-07-04
    Type: Other