2FYH | pdb_00002fyh

Solution structure of the 2'-5' RNA ligase-like protein from Pyrococcus furiosus

• PDB DOI: https://doi.org/10.2210/pdb2FYH/pdb

• Classification: LIGASE
• Organism(s): Pyrococcus furiosus DSM 3638
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2006-02-08 Released: 2007-02-20 
• Deposition Author(s): Okada, K., Matsuda, T., Sakamoto, T., Muto, Y., Yokoyama, S., Kanai, A., Kawai, G., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 

Literature

Characterization of a heat-stable enzyme possessing GTP-dependent RNA ligase activity from a hyperthermophilic archaeon, Pyrococcus furiosus

Kanai, A., Sato, A., Fukuda, Y., Okada, K., Matsuda, T., Sakamoto, T., Muto, Y., Yokoyama, S., Kawai, G., Tomita, M.

(2009) RNA 15: 420-431

• PubMed: 19155324 
• DOI: https://doi.org/10.1261/rna.1122109
• Primary Citation Related Structures: 
  2FYH


• PubMed Abstract: 
  

  Using an expression protein library of a hyperthermophilic archaeon, Pyrococcus furiosus, we identified a gene (PF0027) that encodes a protein with heat-stable cyclic nucleotide phosphodiesterase (CPDase) activity. The PF0027 gene encoded a 21-kDa protein and an amino acid sequence that showed approximately 27% identity to that of the 2'-5' tRNA ligase protein, ligT (20 kDa), from Escherichia coli. We found that the purified PF0027 protein possessed GTP-dependent RNA ligase activity and that synthetic tRNA halves bearing 2',3'-cyclic phosphate and 5'-OH termini were substrates for the ligation reaction in vitro. GTP hydrolysis was not required for the reaction, and GTPgammaS enhanced the tRNA ligation activity of PF0027 protein, suggesting that the ligation step is regulated by a novel mechanism. In comparison to the strong CPDase activity of the PF0027 protein, the RNA ligase activity itself was quite weak, and the ligation product was unstable during in vitro reaction. Finally, we used NMR to determine the solution structure of the PF0027 protein and discuss the implications of our results in understanding the role of the PF0027 protein.

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Organizational Affiliation: 
• Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0017, Japan. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 21.86 kDa 
• Atom Count: 1,542 
• Modeled Residue Count: 190 
• Deposited Residue Count: 190 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
putative integral membrane transport protein	A	190	Pyrococcus furiosus DSM 3638	Mutation(s): 0  Gene Names: PF0027 EC: 3.1.4.58
UniProt
Find proteins for Q8U4Q3 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)) Explore Q8U4Q3  Go to UniProtKB:  Q8U4Q3

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-02-20 
Deposition Author(s): Okada, K., Matsuda, T., Sakamoto, T., Muto, Y., Yokoyama, S., Kanai, A., Kawai, G., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2007-02-20
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-05-01
  Changes: Data collection, Database references