3WUH

Qri7 and AMP complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.937 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.223 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structure of Saccharomyces cerevisiae mitochondrial Qri7 in complex with AMP

Tominaga, T.Kobayashi, K.Ishii, R.Ishitani, R.Nureki, O.

(2014) ACTA CRYSTALLOGR.,SECT.F 70: 1009-1014

  • DOI: 10.1107/S2053230X14014046

  • PubMed Abstract: 
  • N(6)-Threonylcarbamoyladenosine (t(6)A) is a modified tRNA base required for accuracy in translation. Qri7 is localized in yeast mitochondria and is involved in t(6)A biosynthesis. In t(6)A biosynthesis, threonylcarbamoyl-adenylate (TCA) is synthesiz ...

    N(6)-Threonylcarbamoyladenosine (t(6)A) is a modified tRNA base required for accuracy in translation. Qri7 is localized in yeast mitochondria and is involved in t(6)A biosynthesis. In t(6)A biosynthesis, threonylcarbamoyl-adenylate (TCA) is synthesized from threonine, bicarbonate and ATP, and the threonyl-carbamoyl group is transferred to adenine 37 of tRNA by Qri7. Qri7 alone is sufficient to catalyze the second step of the reaction, whereas the Qri7 homologues YgjD (in bacteria) and Kae1 (in archaea and eukaryotes) function as parts of multi-protein complexes. In this study, the crystal structure of Qri7 complexed with AMP (a part of TCA) has been determined at 2.94 Å resolution in a new crystal form. The manner of AMP recognition is similar, with some minor variations, among the Qri7/Kae1/YgjD family proteins. The previously reported dimer formation was also observed in this new crystal form. Furthermore, a comparison with the structure of TobZ, which catalyzes a similar reaction to t(6)A biosynthesis, revealed the presence of a flexible loop that may be involved in tRNA binding.


    Organizational Affiliation

    Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
tRNA N6-adenosine threonylcarbamoyltransferase, mitochondrial
A, B
383Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: QRI7
EC: 2.3.1.234
Find proteins for P43122 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P43122
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
AMP
Query on AMP

Download SDF File 
Download CCD File 
A, B
ADENOSINE MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.937 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.223 
  • Space Group: P 43 3 2
Unit Cell:
Length (Å)Angle (°)
a = 180.315α = 90.00
b = 180.315β = 90.00
c = 180.315γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
HKL-2000data reduction
PHENIXrefinement
HKL-2000data collection
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-09-17
    Type: Initial release