3G8Q

A cytidine deaminase edits C-to-U in transfer RNAs in archaea

• PDB DOI: https://doi.org/10.2210/pdb3G8Q/pdb

• Classification: RNA BINDING PROTEIN
• Organism(s): Methanopyrus kandleri
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-02-12 Released: 2009-05-26 
• Deposition Author(s): Xiong, Y., Stanley, B.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.265 
• R-Value Work: 0.202 
• R-Value Observed: 0.205 

Literature

A cytidine deaminase edits C to U in transfer RNAs in Archaea

Randau, L., Stanley, B.J., Kohlway, A., Mechta, S., Xiong, Y., Soll, D.

(2009) Science 324: 657-659

• PubMed: 19407206 
• DOI: https://doi.org/10.1126/science.1170123
• Primary Citation of Related Structures:  
  3G8Q


• PubMed Abstract: 
  

  All canonical transfer RNAs (tRNAs) have a uridine at position 8, involved in maintaining tRNA tertiary structure. However, the hyperthermophilic archaeon Methanopyrus kandleri harbors 30 (out of 34) tRNA genes with cytidine at position 8. Here, we demonstrate C-to-U editing at this location in the tRNA's tertiary core, and present the crystal structure of a tRNA-specific cytidine deaminase, CDAT8, which has the cytidine deaminase domain linked to a tRNA-binding THUMP domain. CDAT8 is specific for C deamination at position 8, requires only the acceptor stem hairpin for activity, and belongs to a unique family within the "cytidine deaminase-like" superfamily. The presence of this C-to-U editing enzyme guarantees the proper folding and functionality of all M. kandleri tRNAs.

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Organizational Affiliation: 

Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 123.05 kDa 
• Atom Count: 8,787 
• Modelled Residue Count: 1,109 
• Deposited Residue Count: 1,112 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Predicted RNA-binding protein, contains THUMP domain	A, B, C, D	278	Methanopyrus kandleri	Mutation(s): 0  Gene Names: MK0935
UniProt
Find proteins for Q8TWU6 (Methanopyrus kandleri (strain AV19 / DSM 6324 / JCM 9639 / NBRC 100938)) Explore Q8TWU6  Go to UniProtKB:  Q8TWU6

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	E [auth A], G [auth B], I [auth C], L [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
NA	F [auth A], H [auth B], J [auth C], K [auth C], M [auth D], N [auth D], O [auth D]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.265 
• R-Value Work: 0.202 
• R-Value Observed: 0.205 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 184.465	α = 90
b = 77.06	β = 103.57
c = 109.082	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-05-26 
Deposition Author(s): Xiong, Y., Stanley, B.J.

Revision History  

• Version 1.0: 2009-05-26
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-02-21
  Changes: Data collection, Database references, Derived calculations