1VGJ

Crystal structure of 2'-5' RNA ligase from Pyrococcus horikoshii


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.216 

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This is version 1.2 of the entry. See complete history


Literature

The structure of Pyrococcus horikoshii 2'-5' RNA ligase at 1.94 A resolution reveals a possible open form with a wider active-site cleft

Gao, Y.G.Yao, M.Okada, A.Tanaka, I.

(2006) Acta Crystallogr Sect F Struct Biol Cryst Commun 62: 1196-1200

  • DOI: 10.1107/S1744309106046616
  • Primary Citation of Related Structures:  
    1VGJ

  • PubMed Abstract: 
  • Bacterial and archaeal 2'-5' RNA ligases, members of the 2H phosphoesterase superfamily, catalyze the linkage of the 5' and 3' exons via a 2'-5'-phosphodiester bond during tRNA-precursor splicing. The crystal structure of the 2'-5' RNA ligase PH0099 from Pyrococcus horikoshii OT3 was solved at 1 ...

    Bacterial and archaeal 2'-5' RNA ligases, members of the 2H phosphoesterase superfamily, catalyze the linkage of the 5' and 3' exons via a 2'-5'-phosphodiester bond during tRNA-precursor splicing. The crystal structure of the 2'-5' RNA ligase PH0099 from Pyrococcus horikoshii OT3 was solved at 1.94 A resolution (PDB code 1vgj). The molecule has a bilobal alpha+beta arrangement with two antiparallel beta-sheets constituting a V-shaped active-site cleft, as found in other members of the 2H phosphoesterase superfamily. The present structure was significantly different from that determined previously at 2.4 A resolution (PDB code 1vdx) in the active-site cleft; the entrance to the cleft is wider and the active site is easily accessible to the substrate (RNA precursor) in our structure. Structural comparison with the 2'-5' RNA ligase from Thermus thermophilus HB8 also revealed differences in the RNA precursor-binding region. The structural differences in the active-site residues (tetrapeptide motifs H-X-T/S-X) between the members of the 2H phosphoesterase superfamily are discussed.


    Organizational Affiliation

    Faculty of Advanced Life Sciences, Graduate School of Life Sciences, Hokkaido University, Sapporo 060-0810, Japan.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Hypothetical protein PH0099A184Pyrococcus horikoshiiMutation(s): 3 
Gene Names: PH0099
EC: 3.1.4.58
UniProt
Find proteins for O57823 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3))
Explore O57823 
Go to UniProtKB:  O57823
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO57823
Protein Feature View
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.216 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.5α = 90
b = 45.7β = 90
c = 97.6γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-06-07
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance