5DIZ

Crystal Structure of nuclear proteinaceous RNase P 2 (PRORP2) from A. thaliana


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.228 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Nuclear Protein-Only Ribonuclease P2 Structure and Biochemical Characterization Provide Insight into the Conserved Properties of tRNA 5' End Processing Enzymes.

Karasik, A.Shanmuganathan, A.Howard, M.J.Fierke, C.A.Koutmos, M.

(2016) J.Mol.Biol. 428: 26-40

  • DOI: 10.1016/j.jmb.2015.11.025

  • PubMed Abstract: 
  • Protein-only RNase Ps (PRORPs) are a recently discovered class of RNA processing enzymes that catalyze maturation of the 5' end of precursor tRNAs in Eukaryotes. PRORPs are found in the nucleus and/or organelles of most eukaryotic organisms. Arabidop ...

    Protein-only RNase Ps (PRORPs) are a recently discovered class of RNA processing enzymes that catalyze maturation of the 5' end of precursor tRNAs in Eukaryotes. PRORPs are found in the nucleus and/or organelles of most eukaryotic organisms. Arabidopsis thaliana is a representative organism that contains PRORP enzymes (PRORP1, PRORP2 and PRORP3) in both its nucleus and its organelles; PRORP2 and PRORP3 localize to the nucleus and PRORP1 localizes to the chloroplast and the mitochondria. Apart from their identification, almost nothing is known about the structure and function of PRORPs that act in the nucleus. Here, we use a combination of biochemical assays and X-ray crystallography to characterize A. thaliana PRORP2. We solved the crystal structure of PRORP2 (3.2Å) revealing an overall V-shaped protein and conserved metallonuclease active-site structure. Our biochemical studies indicate that PRORP2 requires Mg(2+) for catalysis and catalyzes the maturation of nuclear encoded substrates up to 10-fold faster than mitochondrial encoded precursor nad6 t-element under single-turnover conditions. We also demonstrate that PRORP2 preferentially binds precursor tRNAs containing short 5' leaders and 3' trailers; however, leader and trailer lengths do not significantly alter the observed rate constants of PRORP2 in single-turnover cleavage assays. Our data provide a biochemical and structural framework to begin understanding how nuclear localized PRORPs recognize and cleave their substrates.


    Organizational Affiliation

    Department of Biochemistry, Uniformed Services University of the Health Sciences, 4301 Jones Bridge Road, Bethesda, MD 28104, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Proteinaceous RNase P 2
A, B
531Arabidopsis thalianaMutation(s): 0 
Gene Names: PRORP2
EC: 3.1.26.5
Find proteins for Q680B9 (Arabidopsis thaliana)
Go to UniProtKB:  Q680B9
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.228 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 69.980α = 72.66
b = 76.993β = 64.11
c = 80.112γ = 77.76
Software Package:
Software NamePurpose
REFMACrefinement
PHASERphasing
HKL-2000data scaling
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-12-30
    Type: Initial release
  • Version 1.1: 2016-02-17
    Type: Database references
  • Version 1.2: 2017-11-01
    Type: Author supporting evidence, Database references, Derived calculations