Crystal structure of TT0787 of thermus thermophilus HB8

Experimental Data Snapshot

  • Resolution: 2.50 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.198 

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Crystal Structure of the 2'-5' RNA Ligase from Thermus thermophilus HB8

Kato, M.Shirouzu, M.Terada, T.Yamaguchi, H.Murayama, K.Sakai, H.Kuramitsu, S.Yokoyama, S.

(2003) J Mol Biol 329: 903-911

  • DOI: https://doi.org/10.1016/s0022-2836(03)00448-0
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The 2'-5' RNA ligase family members are bacterial and archaeal RNA ligases that ligate 5' and 3' half-tRNA molecules with 2',3'-cyclic phosphate and 5'-hydroxyl termini, respectively, to the product containing the 2'-5' phosphodiester linkage. Here, the crystal structure of the 2'-5' RNA ligase protein from an extreme thermophile, Thermus thermophilus HB8, was solved at 2.5A resolution. The structure of the 2'-5' RNA ligase superimposes well on that of the Arabidopsis thaliana cyclic phosphodiesterase (CPDase), which hydrolyzes ADP-ribose 1",2"-cyclic phosphate (a product of the tRNA splicing reaction) to the monoester ADP-ribose 1"-phosphate. Although the sequence identity between the two proteins is remarkably low (9.3%), the 2'-5' RNA ligase and CPDase structures have two HX(T/S)X motifs in their corresponding positions. The HX(T/S)X motifs play important roles in the CPDase activity, and are conserved in both the CPDases and 2'-5' RNA ligases. Therefore, the catalytic mechanism of the 2'-5' RNA ligase may be similar to that of the CPDase. On the other hand, the electrostatic potential of the cavity of the 2'-5' RNA ligase is positive, but that of the CPDase is negative. Furthermore, in the CPDase, two loops with low B-factors cover the cavity. In contrast, in the 2'-5' RNA ligase, the corresponding loops form an open conformation and are flexible. These characteristics may be due to the differences in the substrates, tRNA and ADP-ribose 1",2"-cyclic phosphate.

  • Organizational Affiliation

    RIKEN Genomic Sciences Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
2'-5' RNA Ligase198Thermus thermophilusMutation(s): 0 
Find proteins for Q5SHB1 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore Q5SHB1 
Go to UniProtKB:  Q5SHB1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5SHB1
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.50 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.198 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 37.982α = 90
b = 75.816β = 90
c = 159.64γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-06-17
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-04
    Changes: Refinement description
  • Version 1.4: 2023-12-27
    Changes: Data collection, Database references