6N6G

Vibrio cholerae Oligoribonuclease bound to pCG


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.018 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.162 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

A dedicated diribonucleotidase resolves a key bottleneck for the terminal step of RNA degradation.

Kim, S.K.Lormand, J.D.Weiss, C.A.Eger, K.A.Turdiev, H.Turdiev, A.Winkler, W.C.Sondermann, H.Lee, V.T.

(2019) Elife 8: --

  • DOI: 10.7554/eLife.46313
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Degradation of RNA polymers, an ubiquitous process in all cells, is catalyzed by specific subsets of endo- and exoribonucleases that together recycle RNA fragments into nucleotide monophosphate. In γ-proteobacteria, 3-'5' exoribonucleases comprise up ...

    Degradation of RNA polymers, an ubiquitous process in all cells, is catalyzed by specific subsets of endo- and exoribonucleases that together recycle RNA fragments into nucleotide monophosphate. In γ-proteobacteria, 3-'5' exoribonucleases comprise up to eight distinct enzymes. Among them, Oligoribonuclease (Orn) is unique as its activity is required for clearing short RNA fragments, which is important for cellular fitness. However, the molecular basis of Orn's unique cellular function remained unclear. Here, we show that Orn exhibits exquisite substrate preference for diribonucleotides. Crystal structures of substrate-bound Orn reveal an active site optimized for diribonucleotides. While other cellular RNases process oligoribonucleotides down to diribonucleotide entities, Orn is the one and only diribonucleotidase that completes the terminal step of RNA degradation. Together, our studies indicate RNA degradation as a step-wise process with a dedicated enzyme for the clearance of a specific intermediate pool, diribonucleotides, that affects cellular physiology and viability.


    Organizational Affiliation

    Department of Molecular Medicine, College of Veterinary Medicine, Cornell University, Ithaca, United States.,Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Oligoribonuclease
A
181Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)Mutation(s): 0 
Gene Names: orn
EC: 3.1.-.-
Find proteins for Q9KV17 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961))
Go to UniProtKB:  Q9KV17
Entity ID: 2
MoleculeChainsLengthOrganism
RNA (5'-R(P*CP*G)-3')D2synthetic construct
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.018 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.162 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 88.976α = 90.00
b = 88.976β = 90.00
c = 59.906γ = 120.00
Software Package:
Software NamePurpose
SCALAdata scaling
PDB_EXTRACTdata extraction
PHENIXphasing
XDSdata reduction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesR01GM123609

Revision History 

  • Version 1.0: 2019-06-12
    Type: Initial release
  • Version 1.1: 2019-10-16
    Type: Data collection, Database references