Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 56.93 kDa 
• Atom Count: 4221 
• Modelled Residue Count: 476 
• Deposited Residue Count: 501 
• Unique protein chains: 1

4G26

Crystal Structure of proteinaceous RNase P 1 (PRORP1) from A. thaliana with Ca

• PDB DOI: 10.2210/pdb4G26/pdb

• Classification: RNA BINDING PROTEIN
• Organism(s): Arabidopsis thaliana
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-07-11 Released: 2012-09-26 
• Deposition Author(s): Koutmos, M., Howard, M.J., Fierke, C.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.209 
• R-Value Work: 0.162 
• R-Value Observed: 0.165 

Literature

Mitochondrial ribonuclease P structure provides insight into the evolution of catalytic strategies for precursor-tRNA 5' processing.

Howard, M.J., Lim, W.H., Fierke, C.A., Koutmos, M.

(2012) Proc Natl Acad Sci U S A 109: 16149-16154

• PubMed: 22991464 
• DOI: 10.1073/pnas.1209062109
• Primary Citation of Related Structures:  
  4G23, 4G24, 4G25, 4G26


• PubMed Abstract: 
  

Ribonuclease P (RNase P) catalyzes the maturation of the 5' end of tRNA precursors. Typically these enzymes are ribonucleoproteins with a conserved RNA component responsible for catalysis. However, protein-only RNase P (PRORP) enzymes process precursor tRNAs in human mitochondria and in all tRNA-using compartments of Arabidopsis thaliana. PRORP enzymes are nuclear encoded and conserved among many eukaryotes, having evolved recently as yeast mitochondrial genomes encode an RNase P RNA. Here we report the crystal structure of PRORP1 from A. thaliana at 1.75 Å resolution, revealing a prototypical metallonuclease domain tethered to a pentatricopeptide repeat (PPR) domain by a structural zinc-binding domain. The metallonuclease domain is a unique high-resolution structure of a Nedd4-BP1, YacP Nucleases (NYN) domain that is a member of the PIN domain-like fold superfamily, including the FLAP nuclease family. The structural similarity between PRORP1 and the FLAP nuclease family suggests that they evolved from a common ancestor. Biochemical data reveal that conserved aspartate residues in PRORP1 are important for catalytic activity and metal binding and that the PPR domain also enhances activity, likely through an interaction with pre-tRNA. These results provide a foundation for understanding tRNA maturation in organelles. Furthermore, these studies allow for a molecular-level comparison of the catalytic strategies used by the only known naturally evolved protein and RNA-based catalysts that perform the same biological function, pre-tRNA maturation, thereby providing insight into the differences between the prebiotic RNA world and the present protein-dominated world.

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Organizational Affiliation: 

Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pentatricopeptide repeat-containing protein At2g32230, mitochondrial	A	501	Arabidopsis thaliana	Mutation(s): 0  Gene Names: At2g32230, F22D22.2, PRORP1 EC: 3.1.26.5
UniProt
Find proteins for Q66GI4 (Arabidopsis thaliana) Explore Q66GI4  Go to UniProtKB:  Q66GI4

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.209 
• R-Value Work: 0.162 
• R-Value Observed: 0.165 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.79	α = 90
b = 111.883	β = 90
c = 140.073	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-07-11 
• Released Date: 2012-09-26 
Deposition Author(s): Koutmos, M., Howard, M.J., Fierke, C.A.

Revision History  

• Version 1.0: 2012-09-26
  Type: Initial release
  
• Version 1.1: 2012-11-14
  Changes: Database references