3WFS

tRNA processing enzyme complex 3

• PDB DOI:  https://doi.org/10.2210/pdb3WFS/pdb
• NAKB: 3WFS

• Classification: Transferase/RNA
• Organism(s): Thermotoga maritima MSB8, synthetic construct, Aquifex aeolicus VF5
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-07-23 Released: 2014-01-01 
• Deposition Author(s): Yamashita, S., Takeshita, D., Tomita, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.31 Å
• R-Value Free: 0.276 
• R-Value Work: 0.229 
• R-Value Observed: 0.231 

Literature

Translocation and rotation of tRNA during template-independent RNA polymerization by tRNA nucleotidyltransferase

Yamashita, S., Takeshita, D., Tomita, K.

(2014) Structure 22: 315-325

• PubMed: 24389024 
• DOI: https://doi.org/10.1016/j.str.2013.12.002
• Primary Citation of Related Structures:  
  3WFO, 3WFP, 3WFQ, 3WFR, 3WFS


• PubMed Abstract: 
  

The 3'-terminal CCA (CCA-3' at positions 74-76) of tRNA is synthesized by CCA-adding enzyme using CTP and ATP as substrates, without a nucleic acid template. In Aquifex aeolicus, CC-adding and A-adding enzymes collaboratively synthesize the CCA-3'. The mechanism of CCA-3' synthesis by these two enzymes remained obscure. We now present crystal structures representing CC addition onto tRNA by A. aeolicus CC-adding enzyme. After C₇₄ addition in an enclosed active pocket and pyrophosphate release, the tRNA translocates and rotates relative to the enzyme, and C₇₅ addition occurs in the same active pocket as C₇₄ addition. At both the C₇₄-adding and C₇₅-adding stages, CTP is selected by Watson-Crick-like hydrogen bonds between the cytosine of CTP and conserved Asp and Arg residues in the pocket. After C₇₄C₇₅ addition and pyrophosphate release, the tRNA translocates further and drops off the enzyme, and the CC-adding enzyme terminates RNA polymerization.

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Organizational Affiliation: 

Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1, Higashi, Tsukuba, Ibaraki 305-8566, Japan. Electronic address: [e-mail].

Biological Assembly 1  

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

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

Biological Assembly 2  

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

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

Macromolecule Content

• Total Structure Weight: 161.97 kDa 
• Atom Count: 10,171 
• Modelled Residue Count: 1,029 
• Deposited Residue Count: 1,172 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Poly A polymerase	C, D	512	synthetic construct, Aquifex aeolicus VF5	Mutation(s): 0  Gene Names: pcnB2 EC: 2.7.7.72 (PDB Primary Data), 2.7.7 (UniProt)
UniProt
Find proteins for O67911 (Aquifex aeolicus (strain VF5)) Explore O67911  Go to UniProtKB:  O67911

Entity ID: 1
Molecule	Chains	Length	Organism	Image
RNA (74-MER)	A, B	74	Thermotoga maritima MSB8

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.31 Å
• R-Value Free: 0.276 
• R-Value Work: 0.229 
• R-Value Observed: 0.231 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 177.21	α = 90
b = 148.11	β = 98.54
c = 92.25	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-01-01 
Deposition Author(s): Yamashita, S., Takeshita, D., Tomita, K.

Revision History  

• Version 1.0: 2014-01-01
  Type: Initial release
  
• Version 1.1: 2014-08-13
  Changes: Database references
• Version 1.2: 2017-06-28
  Changes: Source and taxonomy