1MIV

Crystal structure of Bacillus stearothermophilus CCA-adding enzyme

• PDB DOI: https://doi.org/10.2210/pdb1MIV/pdb

• Classification: TRANSLATION, TRANSFERASE
• Organism(s): Geobacillus stearothermophilus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2002-08-23 Released: 2002-12-13 
• Deposition Author(s): Li, F., Xiong, Y., Wang, J., Cho, H.D., Weiner, A.M., Steitz, T.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.50 Å
• R-Value Free: 0.328 
• R-Value Work: 0.289 
• R-Value Observed: 0.293 

Literature

Crystal structures of the Bacillus stearothermophilus CCA-adding enzyme and its complexes with ATP or CTP

Li, F., Xiong, Y., Wang, J., Cho, H.D., Tomita, K., Weiner, A.M., Steitz, T.A.

(2002) Cell 111: 815-824

• PubMed: 12526808 
• DOI: https://doi.org/10.1016/s0092-8674(02)01115-7
• Primary Citation of Related Structures:  
  1MIV, 1MIW, 1MIY


• PubMed Abstract: 
  

  CCA-adding enzymes polymerize CCA onto the 3' terminus of immature tRNAs without using a nucleic acid template. The 3.0 A resolution crystal structures of the CCA-adding enzyme from Bacillus stearothermophilus and its complexes with ATP or CTP reveal a seahorse-shaped subunit consisting of four domains: head, neck, body, and tail. The head is structurally homologous to the palm domain of DNA polymerase beta but has additional structural features and functions. The neck, body, and tail represent new protein folding motifs. The neck provides a specific template for the incoming ATP or CTP, whereas the body and tail may bind tRNA. Each subunit has one active site capable of switching its base specificity between ATP and CTP, an important component of the CCA-adding mechanism.

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Organizational Affiliation: 

Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 91.85 kDa 
• Atom Count: 6,264 
• Modelled Residue Count: 790 
• Deposited Residue Count: 808 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
tRNA CCA-adding enzyme	A, B	404	Geobacillus stearothermophilus	Mutation(s): 0  EC: 2.7.7.72
UniProt
Find proteins for Q7SIB1 (Geobacillus stearothermophilus) Explore Q7SIB1  Go to UniProtKB:  Q7SIB1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	C [auth A], D [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.50 Å
• R-Value Free: 0.328 
• R-Value Work: 0.289 
• R-Value Observed: 0.293 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.861	α = 90
b = 105.861	β = 90
c = 183.658	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
SCALEPACK	data scaling
MLPHARE	phasing
REFMAC	refinement
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-12-13 
Deposition Author(s): Li, F., Xiong, Y., Wang, J., Cho, H.D., Weiner, A.M., Steitz, T.A.

Revision History  

• Version 1.0: 2002-12-13
  Type: Initial release
  
• Version 1.1: 2008-04-28
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Version format compliance