4WC2

Crystal structure of tRNA nucleotidyltransferase complexed with a primer tRNA and an incoming ATP analog


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.218 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 1VFG


Literature

Measurement of Acceptor-T Psi C Helix Length of tRNA for Terminal A76-Addition by A-Adding Enzyme.

Yamashita, S.Martinez, A.Tomita, K.

(2015) Structure 23: 830-842

  • DOI: https://doi.org/10.1016/j.str.2015.03.013
  • Primary Citation of Related Structures:  
    4WBY, 4WBZ, 4WC0, 4WC1, 4WC2, 4WC3, 4WC4, 4WC5, 4WC6, 4WC7, 4X0A, 4X0B

  • PubMed Abstract: 

    The 3'-terminal CCA (C74C75A76-3') of tRNA is required for protein synthesis. In Aquifex aeolicus, the CCA-3' is synthesized by CC-adding and A-adding enzymes, although in most organisms, CCA is synthesized by a single CCA-adding enzyme. The mechanisms by which the A-adding enzyme adds only A76, but not C74C75, onto tRNA remained elusive. The complex structures of the enzyme with various tRNAs revealed the presence of a single tRNA binding site on the enzyme, with the enzyme measuring the acceptor-TΨC helix length of tRNA. The 3'-C75 of tRNA lacking A76 can reach the active site and the size and shape of the nucleotide binding pocket at the insertion stage are suitable for ATP. The 3'-C74 of tRNA lacking C75A76 cannot reach the active site, although CTP or ATP can bind the active pocket. Thus, the A-adding enzyme adds only A76, but not C74C75, onto tRNA.


  • Organizational Affiliation

    Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1, Higashi, Tsukuba, Ibaraki 305-8566, Japan.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Poly A polymerase396Aquifex aeolicus VF5Mutation(s): 0 
Gene Names: pcnB1aq_411
EC: 2.7.7
UniProt
Find proteins for O66728 (Aquifex aeolicus (strain VF5))
Explore O66728 
Go to UniProtKB:  O66728
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO66728
Sequence Annotations
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  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains LengthOrganismImage
RNA 75-mer75Thermotoga maritima MSB8
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
APC
Query on APC

Download Ideal Coordinates CCD File 
C [auth A]DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER
C11 H18 N5 O12 P3
CAWZRIXWFRFUQB-IOSLPCCCSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
D [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.218 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.92α = 90
b = 109.48β = 90
c = 125.9γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Science and Technology Agency (JST)JapanLS135

Revision History  (Full details and data files)

  • Version 1.0: 2015-04-15
    Type: Initial release
  • Version 1.1: 2015-05-27
    Changes: Database references
  • Version 1.2: 2017-09-27
    Changes: Data collection, Database references, Derived calculations, Other, Source and taxonomy
  • Version 1.3: 2024-03-20
    Changes: Data collection, Database references, Refinement description