2DR7

Complex structure of CCA-adding enzyme with tRNAminiDC

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.219 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

Complete crystallographic analysis of the dynamics of CCA sequence addition

Tomita, K., Ishitani, R., Fukai, S., Nureki, O.

(2006) Nature 443: 956-960

  • DOI: 10.1038/nature05204
  • Primary Citation of Related Structures:  
    2DR5, 2DR7, 2DR8, 2DR9, 2DRA, 2DRB, 2DVI

  • PubMed Abstract: 

    • CCA-adding polymerase matures the essential 3'-CCA terminus of transfer RNA without any nucleic-acid template. However, it remains unclear how the correct nucleotide triphosphate is selected in each reaction step and how the polymerization is driven by the protein and RNA dynamics ...

    CCA-adding polymerase matures the essential 3'-CCA terminus of transfer RNA without any nucleic-acid template. However, it remains unclear how the correct nucleotide triphosphate is selected in each reaction step and how the polymerization is driven by the protein and RNA dynamics. Here we present complete sequential snapshots of six complex structures of CCA-adding enzyme and four distinct RNA substrates with and without CTP (cytosine triphosphate) or ATP (adenosine triphosphate). The CCA-lacking RNA stem extends by one base pair to force the discriminator nucleoside into the active-site pocket, and then tracks back after incorporation of the first cytosine monophosphate (CMP). Accommodation of the second CTP clamps the catalytic cleft, inducing a reorientation of the turn, which flips C74 to allow CMP to be accepted. In contrast, after the second CMP is added, the polymerase and RNA primer are locked in the closed state, which directs the subsequent A addition. Between the CTP- and ATP-binding stages, the side-chain conformation of Arg 224 changes markedly; this is controlled by the global motion of the enzyme and position of the primer terminus, and is likely to achieve the CTP/ATP discrimination, depending on the polymerization stage. Throughout the CCA-adding reaction, the enzyme tail domain firmly anchors the TPsiC-loop of the tRNA, which ensures accurate polymerization and termination.

    Organizational Affiliation: 

    Institute for Biological Resources and Functions, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1, Higashi, Tsukuba-shi, Ibaragi 305-8565, Japan.



Macromolecules

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
CCA-adding enzymeB [auth A]437Archaeoglobus fulgidusMutation(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 Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO28126
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsLengthOrganismImage
tRNA (33-MER)A [auth B]33N/A
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4
Download Ideal Coordinates CCD File 
C [auth A],
D [auth A]		SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.219 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.962α = 90
b = 57.962β = 90
c = 441.72γ = 90
Software Package:
Software NamePurpose
CNSrefinement
SCALEPACKdata scaling
AMoREphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-11-14
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance