3IP4

The high resolution structure of GatCAB


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.195 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Two distinct regions in Staphylococcus aureus GatCAB guarantee accurate tRNA recognition

Nakamura, A.Sheppard, K.Yamane, J.Yao, M.Soll, D.Tanaka, I.

(2010) Nucleic Acids Res. 38: 672-682

  • DOI: 10.1093/nar/gkp955

  • PubMed Abstract: 
  • In many prokaryotes the biosynthesis of the amide aminoacyl-tRNAs, Gln-tRNA(Gln) and Asn-tRNA(Asn), proceeds by an indirect route in which mischarged Glu-tRNA(Gln) or Asp-tRNA(Asn) is amidated to the correct aminoacyl-tRNA catalyzed by a tRNA-depende ...

    In many prokaryotes the biosynthesis of the amide aminoacyl-tRNAs, Gln-tRNA(Gln) and Asn-tRNA(Asn), proceeds by an indirect route in which mischarged Glu-tRNA(Gln) or Asp-tRNA(Asn) is amidated to the correct aminoacyl-tRNA catalyzed by a tRNA-dependent amidotransferase (AdT). Two types of AdTs exist: bacteria, archaea and organelles possess heterotrimeric GatCAB, while heterodimeric GatDE occurs exclusively in archaea. Bacterial GatCAB and GatDE recognize the first base pair of the acceptor stem and the D-loop of their tRNA substrates, while archaeal GatCAB recognizes the tertiary core of the tRNA, but not the first base pair. Here, we present the crystal structure of the full-length Staphylococcus aureus GatCAB. Its GatB tail domain possesses a conserved Lys rich motif that is situated close to the variable loop in a GatCAB:tRNA(Gln) docking model. This motif is also conserved in the tail domain of archaeal GatCAB, suggesting this basic region may recognize the tRNA variable loop to discriminate Asp-tRNA(Asn) from Asp-tRNA(Asp) in archaea. Furthermore, we identified a 3(10) turn in GatB that permits the bacterial GatCAB to distinguish a U1-A72 base pair from a G1-C72 pair; the absence of this element in archaeal GatCAB enables the latter enzyme to recognize aminoacyl-tRNAs with G1-C72 base pairs.


    Organizational Affiliation

    Division of Biological Sciences, Graduate School of Science, Hokkaido University, Sapporo 060-0810, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glutamyl-tRNA(Gln) amidotransferase subunit A
A
485Staphylococcus aureus (strain Mu50 / ATCC 700699)Mutation(s): 0 
Gene Names: gatA
EC: 6.3.5.7
Find proteins for P63488 (Staphylococcus aureus (strain Mu50 / ATCC 700699))
Go to UniProtKB:  P63488
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B
B
483Staphylococcus aureus (strain Mu50 / ATCC 700699)Mutation(s): 0 
Gene Names: gatB
EC: 6.3.5.-
Find proteins for P64201 (Staphylococcus aureus (strain Mu50 / ATCC 700699))
Go to UniProtKB:  P64201
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit C
C
100Staphylococcus aureus (strain Mu50 / ATCC 700699)Mutation(s): 0 
Gene Names: gatC
EC: 6.3.5.-
Find proteins for P68807 (Staphylococcus aureus (strain Mu50 / ATCC 700699))
Go to UniProtKB:  P68807
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.195 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 71.122α = 90.00
b = 92.726β = 90.00
c = 180.356γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
AMoREphasing
HKL-2000data scaling
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-11-24
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Source and taxonomy, Version format compliance
  • Version 1.2: 2013-10-16
    Type: Derived calculations
  • Version 1.3: 2014-02-05
    Type: Database references