1D8I

X-RAY CRYSTAL STRUCTURE OF YEAST RNA TRIPHOSPHATASE IN COMPLEX WITH A SULFATE ION.

• PDB DOI: https://doi.org/10.2210/pdb1D8I/pdb

• Classification: HYDROLASE
• Organism(s): Saccharomyces cerevisiae
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 1999-10-24 Released: 1999-11-29 
• Deposition Author(s): Lima, C.D., Wang, L.K., Shuman, S.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 0.270 
• R-Value Work: 0.203 

Literature

Structure and mechanism of yeast RNA triphosphatase: an essential component of the mRNA capping apparatus.

Lima, C.D., Wang, L.K., Shuman, S.

(1999) Cell 99: 533-543

• PubMed: 10589681 
• DOI: https://doi.org/10.1016/s0092-8674(00)81541-x
• Primary Citation of Related Structures:  
  1D8H, 1D8I


• PubMed Abstract: 
  

  RNA triphosphatase is an essential mRNA processing enzyme that catalyzes the first step in cap formation. The 2.05 A crystal structure of yeast RNA triphosphatase Cet1p reveals a novel active site fold whereby an eight-stranded beta barrel forms a topologically closed triphosphate tunnel. Interactions of a sulfate in the center of the tunnel with a divalent cation and basic amino acids projecting into the tunnel suggest a catalytic mechanism that is supported by mutational data. Discrete surface domains mediate Cet1p homodimerization and Cet1p binding to the guanylyltransferase component of the capping apparatus. The structure and mechanism of fungal RNA triphosphatases are completely different from those of mammalian mRNA capping enzymes. Hence, RNA triphosphatase presents an ideal target for structure-based antifungal drug discovery.

---

Organizational Affiliation: 

Biochemistry Department, Weill Medical College of Cornell University, New York, New York 10021, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 107.65 kDa 
• Atom Count: 7,329 
• Modelled Residue Count: 864 
• Deposited Residue Count: 933 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MRNA TRIPHOSPHATASE CET1	A, B, C	311	Saccharomyces cerevisiae	Mutation(s): 0  EC: 3.1.3.33 (PDB Primary Data), 3.6.1.74 (UniProt)
UniProt
Find proteins for O13297 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore O13297  Go to UniProtKB:  O13297

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	D [auth A], E [auth A], F [auth B], G [auth B], H [auth C], I [auth C]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 0.270 
• R-Value Work: 0.203 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 121.358	α = 90
b = 116.095	β = 110.25
c = 82.31	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 1999-11-29 
Deposition Author(s): Lima, C.D., Wang, L.K., Shuman, S.

Revision History  

• Version 1.0: 1999-11-29
  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: 2024-02-07
  Changes: Data collection, Database references, Derived calculations