1A79

CRYSTAL STRUCTURE OF THE TRNA SPLICING ENDONUCLEASE FROM METHANOCOCCUS JANNASCHII

• PDB DOI: https://doi.org/10.2210/pdb1A79/pdb

• Classification: ENDONUCLEASE
• Organism(s): Methanocaldococcus jannaschii
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1998-03-23 Released: 1999-06-01 
• Deposition Author(s): Li, H., Trotta, C.R., Abelson, J.N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.28 Å
• R-Value Free: 0.267 
• R-Value Work: 0.200 
• R-Value Observed: 0.200 

Literature

Crystal structure and evolution of a transfer RNA splicing enzyme.

Li, H., Trotta, C.R., Abelson, J.

(1998) Science 280: 279-284

• PubMed: 9535656 
• DOI: https://doi.org/10.1126/science.280.5361.279
• Primary Citation of Related Structures:  
  1A79


• PubMed Abstract: 
  

  The splicing of transfer RNA precursors is similar in Eucarya and Archaea. In both kingdoms an endonuclease recognizes the splice sites and releases the intron, but the mechanism of splice site recognition is different in each kingdom. The crystal structure of the endonuclease from the archaeon Methanococcus jannaschii was determined to a resolution of 2.3 angstroms. The structure indicates that the cleavage reaction is similar to that of ribonuclease A and the arrangement of the active sites is conserved between the archaeal and eucaryal enzymes. These results suggest an evolutionary pathway for splice site recognition.

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Organizational Affiliation: 

Division of Biology, Mail Code 147-75, California Institute of Technology, Pasadena, CA 91125, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 79.96 kDa 
• Atom Count: 5,651 
• Modelled Residue Count: 684 
• Deposited Residue Count: 684 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TRNA ENDONUCLEASE	A, B, C, D	171	Methanocaldococcus jannaschii	Mutation(s): 0
UniProt
Find proteins for Q58819 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)) Explore Q58819  Go to UniProtKB:  Q58819

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AU	F [auth A], G [auth B], I [auth C], J [auth D]	GOLD ION Au ZBKIUFWVEIBQRT-UHFFFAOYSA-N
SO4	E [auth A], H [auth C]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.28 Å
• R-Value Free: 0.267 
• R-Value Work: 0.200 
• R-Value Observed: 0.200 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.95	α = 90
b = 80.04	β = 90
c = 193.59	γ = 90

Software Package:

Software Name	Purpose
CCP4	model building
X-PLOR	refinement
HKL	data reduction
HKL	data scaling
CCP4	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1999-06-01 
Deposition Author(s): Li, H., Trotta, C.R., Abelson, J.N.

Revision History  

• Version 1.0: 1999-06-01
  Type: Initial release
  
• Version 1.1: 2008-03-03
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-02-07
  Changes: Data collection, Database references, Derived calculations, Other