2G5I

Structure of tRNA-Dependent Amidotransferase GatCAB complexed with ADP-AlF4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.35 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.233 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Ammonia channel couples glutaminase with transamidase reactions in GatCAB

Nakamura, A.Yao, M.Chimnaronk, S.Sakai, N.Tanaka, I.

(2006) Science 312: 1954-1958

  • DOI: 10.1126/science.1127156
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The formation of glutaminyl transfer RNA (Gln-tRNA(Gln)) differs among the three domains of life. Most bacteria employ an indirect pathway to produce Gln-tRNA(Gln) by a heterotrimeric glutamine amidotransferase CAB (GatCAB) that acts on the misacylat ...

    The formation of glutaminyl transfer RNA (Gln-tRNA(Gln)) differs among the three domains of life. Most bacteria employ an indirect pathway to produce Gln-tRNA(Gln) by a heterotrimeric glutamine amidotransferase CAB (GatCAB) that acts on the misacylated Glu-tRNA(Gln). Here, we describe a series of crystal structures of intact GatCAB from Staphylococcus aureus in the apo form and in the complexes with glutamine, asparagine, Mn2+, and adenosine triphosphate analog. Two identified catalytic centers for the glutaminase and transamidase reactions are markedly distant but connected by a hydrophilic ammonia channel 30 A in length. Further, we show that the first U-A base pair in the acceptor stem and the D loop of tRNA(Gln) serve as identity elements essential for discrimination by GatCAB and propose a complete model for the overall concerted reactions to synthesize Gln-tRNA(Gln).


    Organizational Affiliation

    Faculty of Advanced Life Sciences, 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 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download SDF File 
Download CCD File 
B
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
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: 3.35 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.233 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 76.860α = 90.00
b = 85.279β = 90.00
c = 183.625γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data collection
AMoREphasing
HKL-2000data reduction
CNSrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-07-18
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance