Thermophilic RNA Ligase from Palaeococcus pacificus K92A

Experimental Data Snapshot

  • Resolution: 1.86 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.209 

Starting Model: experimental
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Characterisation and engineering of a thermophilic RNA ligase from Palaeococcus pacificus.

Rousseau, M.Oulavallickal, T.Williamson, A.Arcus, V.Patrick, W.M.Hicks, J.

(2024) Nucleic Acids Res 52: 3924-3937

  • DOI: https://doi.org/10.1093/nar/gkae149
  • Primary Citation of Related Structures:  
    8UCE, 8UCF, 8UCG, 8UCH, 8UCI

  • PubMed Abstract: 

    RNA ligases are important enzymes in molecular biology and are highly useful for the manipulation and analysis of nucleic acids, including adapter ligation in next-generation sequencing of microRNAs. Thermophilic RNA ligases belonging to the RNA ligase 3 family are gaining attention for their use in molecular biology, for example a thermophilic RNA ligase from Methanobacterium thermoautotrophicum is commercially available for the adenylation of nucleic acids. Here we extensively characterise a newly identified RNA ligase from the thermophilic archaeon Palaeococcus pacificus (PpaRnl). PpaRnl exhibited significant substrate adenylation activity but low ligation activity across a range of oligonucleotide substrates. Mutation of Lys92 in motif I to alanine, resulted in an enzyme that lacked adenylation activity, but demonstrated improved ligation activity with pre-adenylated substrates (ATP-independent ligation). Subsequent structural characterisation revealed that in this mutant enzyme Lys238 was found in two alternate positions for coordination of the phosphate tail of ATP. In contrast mutation of Lys238 in motif V to glycine via structure-guided engineering enhanced ATP-dependent ligation activity via an arginine residue compensating for the absence of Lys238. Ligation activity for both mutations was higher than the wild-type, with activity observed across a range of oligonucleotide substrates with varying sequence and secondary structure.

  • Organizational Affiliation

    School of Science, The University of Waikato, Hamilton 3216, New Zealand.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ATP dependent DNA ligase
A, B
402Palaeococcus pacificus DY20341Mutation(s): 1 
Gene Names: PAP_02190
Find proteins for A0A075LQ94 (Palaeococcus pacificus DY20341)
Explore A0A075LQ94 
Go to UniProtKB:  A0A075LQ94
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A075LQ94
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on GOL

Download Ideal Coordinates CCD File 
G [auth B],
H [auth B]
C3 H8 O3
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
E [auth A]
F [auth A]
J [auth B]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
J [auth B],
K [auth B],
L [auth B]
NA (Subject of Investigation/LOI)
Query on NA

Download Ideal Coordinates CCD File 
Experimental Data & Validation

Experimental Data

  • Resolution: 1.86 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.209 
  • Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.793α = 90
b = 99.699β = 90
c = 142.477γ = 90
Software Package:
Software NamePurpose
Zanudadata reduction
XDSdata scaling

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Ministry of Business, Innovation and Employment (New Zealand)New ZealandRTVU1807

Revision History  (Full details and data files)

  • Version 1.0: 2024-02-21
    Type: Initial release
  • Version 1.1: 2024-03-13
    Changes: Database references
  • Version 1.2: 2024-05-08
    Changes: Database references