Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 62.44 kDa 
• Atom Count: 4,375 
• Modelled Residue Count: 470 
• Deposited Residue Count: 470 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

 2ZHB

Complex structure of AFCCA with tRNAminiDUC

• PDB DOI:  https://doi.org/10.2210/pdb2ZHB/pdb
• NDB: PR0328

• Classification: TRANSFERASE/RNA
• Organism(s): Archaeoglobus fulgidus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-02-01 Released: 2008-08-05 
• Deposition Author(s): Toh, Y., Tomita, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.05 Å
• R-Value Free: 0.265 
• R-Value Work: 0.226 
• R-Value Observed: 0.226 

Literature

Molecular basis for maintenance of fidelity during the CCA-adding reaction by a CCA-adding enzyme

Toh, Y., Numata, T., Watanabe, K., Takeshita, D., Nureki, O., Tomita, K.

(2008) EMBO J 27: 1944-1952

• PubMed: 18583961 
• DOI: https://doi.org/10.1038/emboj.2008.124
• Primary Citation of Related Structures:  
  2ZH1, 2ZH2, 2ZH3, 2ZH4, 2ZH5, 2ZH6, 2ZH7, 2ZH8, 2ZH9, 2ZHA, 2ZHB


• PubMed Abstract: 
  

CCA-adding enzyme builds the 3'-end CCA of tRNA without a nucleic acid template. The mechanism for the maintenance of fidelity during the CCA-adding reaction remains elusive. Here, we present almost a dozen complex structures of the class I CCA-adding enzyme and tRNA mini-helices (mini-D(73)N(74), mini-D(73)N(74)C(75) and mini-D(73)C(74)N(75); D(73) is a discriminator nucleotide and N is either A, G, or U). The mini-D(73)N(74) complexes adopt catalytically inactive open forms, and CTP shifts the enzymes to the active closed forms and allows N(74) to flip for CMP incorporation. In contrast, unlike the catalytically active closed form of the mini-D(73)C(74)C(75) complex, the mini-D(73)N(74)C(75) and mini-D(73)C(74)N(75) complexes adopt inactive open forms. Only the mini-D(73)C(74)U(75) accepts AMP to a similar extent as mini-D(73)C(74)C(75), and ATP shifts the enzyme to a closed, active form and allows U(75) to flip for AMP incorporation. These findings suggest that the 3'-region of RNA is proofread, after two nucleotide additions, in the closed, active form of the complex at the AMP incorporation stage. This proofreading is a prerequisite for the maintenance of fidelity for complete CCA synthesis.

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Organizational Affiliation: 

Institute of Biological Resources and Functions, National Institute of Advanced Industrial Science and Technology (AIST), Ibaraki, Japan.

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
CCA-adding enzyme	B [auth A]	436	Archaeoglobus fulgidus	Mutation(s): 0  EC: 2.7.7.25 (PDB Primary Data), 2.7.7.21 (PDB Primary Data), 2.7.7.72 (UniProt)
UniProt
Find proteins for O28126 (Archaeoglobus fulgidus (strain ATCC 49558 / DSM 4304 / JCM 9628 / NBRC 100126 / VC-16)) Explore O28126  Go to UniProtKB:  O28126

Entity ID: 1
Molecule	Chains	Length	Organism	Image
tRNA (34-MER)	A [auth B]	34	N/A

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.05 Å
• R-Value Free: 0.265 
• R-Value Work: 0.226 
• R-Value Observed: 0.226 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.139	α = 90
b = 58.139	β = 90
c = 443.483	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
ADSC	data collection
HKL-2000	data reduction
HKL-2000	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-08-05 
Deposition Author(s): Toh, Y., Tomita, K.

Revision History  

• Version 1.0: 2008-08-05
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance