1SZ1

Mechanism of CCA-adding enzymes specificity revealed by crystal structures of ternary complexes


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 6.21 Å
  • R-Value Free: 0.380 
  • R-Value Work: 0.360 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Mechanism of transfer RNA maturation by CCA-adding enzyme without using an oligonucleotide template.

Xiong, Y.Steitz, T.A.

(2004) Nature 430: 640-645

  • DOI: 10.1038/nature02711
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Transfer RNA nucleotidyltransferases (CCA-adding enzymes) are responsible for the maturation or repair of the functional 3' end of tRNAs by means of the addition of the essential nucleotides CCA. However, it is unclear how tRNA nucleotidyltransferase ...

    Transfer RNA nucleotidyltransferases (CCA-adding enzymes) are responsible for the maturation or repair of the functional 3' end of tRNAs by means of the addition of the essential nucleotides CCA. However, it is unclear how tRNA nucleotidyltransferases polymerize CCA onto the 3' terminus of immature tRNAs without using a nucleic acid template. Here we describe the crystal structure of the Archaeoglobus fulgidus tRNA nucleotidyltransferase in complex with tRNA. We also present ternary complexes of this enzyme with both RNA duplex mimics of the tRNA acceptor stem that terminate with the nucleotides C74 or C75, as well as the appropriate incoming nucleoside 5'-triphosphates. A single nucleotide-binding pocket exists whose specificity for both CTP and ATP is determined by the protein side chain of Arg 224 and backbone phosphates of the tRNA, which are non-complementary to and thus exclude UTP and GTP. Discrimination between CTP or ATP at a given addition step and at termination arises from changes in the size and shape of the nucleotide binding site that is progressively altered by the elongating 3' end of the tRNA.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
tRNA nucleotidyltransferase
A, B
437Archaeoglobus fulgidus (strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126)Mutation(s): 0 
Gene Names: cca
EC: 2.7.7.72
Find proteins for O28126 (Archaeoglobus fulgidus (strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126))
Go to UniProtKB:  O28126
Entity ID: 1
MoleculeChainsLengthOrganism
T-RNA (76-MER)E,F76N/A
Small Molecules
Modified Residues  11 Unique
IDChainsTypeFormula2D DiagramParent
PSU
Query on PSU
E, F
RNA LINKINGC9 H13 N2 O9 PU
5MC
Query on 5MC
E, F
RNA LINKINGC10 H16 N3 O8 PC
M2G
Query on M2G
E, F
RNA LINKINGC12 H18 N5 O8 PG
1MA
Query on 1MA
E, F
RNA LINKINGC11 H16 N5 O7 PA
OMC
Query on OMC
E, F
RNA LINKINGC10 H16 N3 O8 PC
2MG
Query on 2MG
E, F
RNA LINKINGC11 H16 N5 O8 PG
OMG
Query on OMG
E, F
RNA LINKINGC11 H16 N5 O8 PG
7MG
Query on 7MG
E, F
RNA LINKINGC11 H18 N5 O8 PG
YG
Query on YG
E, F
RNA LINKINGC21 H29 N6 O12 PG
5MU
Query on 5MU
E, F
RNA LINKINGC10 H15 N2 O9 PU
H2U
Query on H2U
E, F
RNA LINKINGC9 H15 N2 O9 PU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 6.21 Å
  • R-Value Free: 0.380 
  • R-Value Work: 0.360 
  • Space Group: P 3 2 1
Unit Cell:
Length (Å)Angle (°)
a = 218.403α = 90.00
b = 218.403β = 90.00
c = 170.263γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-08-10
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance