6A4D

pNP-TMP bound Oligoribonuclease (ORN) from Colwellia psychrerythraea strain 34H


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.19 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.205 

wwPDB Validation 3D Report Full Report


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Literature

Structural basis of small RNA hydrolysis by oligoribonuclease (CpsORN) from Colwellia psychrerythraea strain 34H.

Lee, C.W.Park, S.H.Jeong, C.S.Cha, S.S.Park, H.Lee, J.H.

(2019) Sci Rep 9: 2649-2649

  • DOI: 10.1038/s41598-019-39641-0
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Cells regulate their intracellular mRNA levels by using specific ribonucleases. Oligoribonuclease (ORN) is a 3'-5' exoribonuclease for small RNA molecules, important in RNA degradation and re-utilisation. However, there is no structural information o ...

    Cells regulate their intracellular mRNA levels by using specific ribonucleases. Oligoribonuclease (ORN) is a 3'-5' exoribonuclease for small RNA molecules, important in RNA degradation and re-utilisation. However, there is no structural information on the ligand-binding form of ORNs. In this study, the crystal structures of oligoribonuclease from Colwellia psychrerythraea strain 34H (CpsORN) were determined in four different forms: unliganded-structure, thymidine 5'-monophosphate p-nitrophenyl ester (pNP-TMP)-bound, two separated uridine-bound, and two linked uridine (U-U)-bound forms. The crystal structures show that CpsORN is a tight dimer, with two separated active sites and one divalent metal cation ion in each active site. These structures represent several snapshots of the enzymatic reaction process, which allowed us to suggest a possible one-metal-dependent reaction mechanism for CpsORN. Moreover, the biochemical data support our suggested mechanism and identified the key residues responsible for enzymatic catalysis of CpsORN.


    Organizational Affiliation

    Unit of Polar Genomics, Korea Polar Research Institute, Incheon, 21990, Republic of Korea.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Oligoribonuclease
A, B
184Colwellia psychrerythraea (strain 34H / ATCC BAA-681)Mutation(s): 1 
Gene Names: orn
EC: 3.1.-.-
Find proteins for Q47VZ4 (Colwellia psychrerythraea (strain 34H / ATCC BAA-681))
Go to UniProtKB:  Q47VZ4
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
9RC
Query on 9RC

Download SDF File 
Download CCD File 
A, B
5'-O-[(S)-hydroxy(4-nitrophenoxy)phosphoryl]thymidine
PNP-TMP
C16 H18 N3 O10 P
RWOAVOYBVRQNIZ-BFHYXJOUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.19 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.205 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 59.532α = 90.00
b = 59.532β = 90.00
c = 236.269γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
MxDCdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-03-13
    Type: Initial release