Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 21.27 kDa 
• Atom Count: 1529 
• Modelled Residue Count: 184 
• Deposited Residue Count: 184 
• Unique protein chains: 1

1VGJ

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

• PDB DOI: 10.2210/pdb1VGJ/pdb

• Classification: LIGASE
• Organism(s): Pyrococcus horikoshii
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2004-04-27 Released: 2005-06-07 
• Deposition Author(s): Yao, M., Morita, H., Okada, A., Tanaka, I.

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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 

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

• PubMed: 17142895 
• 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 1.94 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical protein PH0099	A	184	Pyrococcus horikoshii	Mutation(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

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

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 = 41.5	α = 90
b = 45.7	β = 90
c = 97.6	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-04-27 
• Released Date: 2005-06-07 
Deposition Author(s): Yao, M., Morita, H., Okada, A., Tanaka, I.

Revision History  

• 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