2DF4

Structure of tRNA-Dependent Amidotransferase GatCAB complexed with Mn2+


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.238 

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:  
    2DQN, 2F2A, 2G5I, 2G5H, 2DF4

  • 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
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Glutamyl-tRNA(Gln) amidotransferase subunit AA485Staphylococcus aureusMutation(s): 0 
Gene Names: gatA
EC: 6.3.5 (PDB Primary Data), 6.3.5.7 (UniProt)
Find proteins for P63488 (Staphylococcus aureus (strain Mu50 / ATCC 700699))
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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 aureusMutation(s): 0 
Gene Names: gatB
EC: 6.3.5
Find proteins for P64201 (Staphylococcus aureus (strain Mu50 / ATCC 700699))
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Go to UniProtKB:  P64201
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit CC100Staphylococcus aureusMutation(s): 0 
Gene Names: gatC
EC: 6.3.5
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
MN
Query on MN

Download CCD File 
B
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.238 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.019α = 90
b = 91.654β = 90
c = 181.302γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
HKL-2000data reduction

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-07-18
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance