Biological Assembly 1  

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

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

Biological Assembly Evidence: light scattering

Macromolecule Content

• Total Structure Weight: 21.59 kDa 
• Atom Count: 1,802 
• Modelled Residue Count: 183 
• Deposited Residue Count: 183 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

 6N6C

Vibrio cholerae Oligoribonuclease bound to pAA

• PDB DOI:  https://doi.org/10.2210/pdb6N6C/pdb
• NDB: 6N6C

• Classification: rna binding protein/rna
• Organism(s): Vibrio cholerae, synthetic construct
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2018-11-26 Released: 2019-06-12 
• Deposition Author(s): Lormand, J.D., Sondermann, H.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.62 Å
• R-Value Free: 0.155 
• R-Value Work: 0.146 
• R-Value Observed: 0.147 

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

• PubMed: 31225796 
• DOI: https://doi.org/10.7554/eLife.46313
• Primary Citation of Related Structures:  
  6N6A, 6N6C, 6N6D, 6N6E, 6N6F, 6N6G, 6N6H, 6N6I, 6N6J, 6N6K


• 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 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.

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Organizational Affiliation: 

Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, United States.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA exonuclease 2 homolog,Small fragment nuclease	A	181	Vibrio cholerae	Mutation(s): 0  Gene Names: orn, VC0395_A2743, VC395_0384 EC: 3.1 (PDB Primary Data), 3.1.15 (UniProt)
UniProt
Find proteins for Q9KV17 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)) Explore Q9KV17  Go to UniProtKB:  Q9KV17

Entity ID: 2
Molecule	Chains	Length	Organism	Image
RNA (5'-R(P*AP*A)-3')	B [auth D]	2	synthetic construct

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NA	C [auth D]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.62 Å
• R-Value Free: 0.155 
• R-Value Work: 0.146 
• R-Value Observed: 0.147 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.375	α = 90
b = 89.375	β = 90
c = 59.451	γ = 120

Software Package:

Software Name	Purpose
XDS	data reduction
SCALA	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-06-12 
Deposition Author(s): Lormand, J.D., Sondermann, H.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01GM123609

Revision History  

• Version 1.0: 2019-06-12
  Type: Initial release
  
• Version 1.1: 2019-10-16
  Changes: Data collection, Database references
• Version 1.2: 2020-01-01
  Changes: Author supporting evidence