3IP4

The high resolution structure of GatCAB


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 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
  • Primary Citation of Related Structures:  
    3IP4

  • 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-dependent amidotransferase (AdT) ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Glutamyl-tRNA(Gln) amidotransferase subunit AA485Staphylococcus aureus subsp. aureus Mu50Mutation(s): 0 
Gene Names: gatASAV1900
EC: 6.3.5 (PDB Primary Data), 6.3.5.7 (UniProt)
UniProt
Find proteins for P63488 (Staphylococcus aureus (strain Mu50 / ATCC 700699))
Explore P63488 
Go to UniProtKB:  P63488
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit BB483Staphylococcus aureus subsp. aureus Mu50Mutation(s): 0 
Gene Names: gatBSAV1899
EC: 6.3.5
UniProt
Find proteins for P64201 (Staphylococcus aureus (strain Mu50 / ATCC 700699))
Explore P64201 
Go to UniProtKB:  P64201
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit CC100Staphylococcus aureus subsp. aureus Mu50Mutation(s): 0 
Gene Names: gatCSAV1901
EC: 6.3.5
UniProt
Find proteins for P68807 (Staphylococcus aureus (strain Mu50 / ATCC 700699))
Explore P68807 
Go to UniProtKB:  P68807
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 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
b = 92.726β = 90
c = 180.356γ = 90
Software Package:
Software NamePurpose
AMoREphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

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