3H0M

Structure of trna-dependent amidotransferase gatcab from aquifex aeolicus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.305 
  • R-Value Work: 0.254 
  • R-Value Observed: 0.256 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Insights into tRNA-Dependent Amidotransferase Evolution and Catalysis from the Structure of the Aquifex aeolicus Enzyme

Wu, J.Bu, W.Sheppard, K.Kitabatake, M.Kwon, S.T.Soll, D.Smith, J.L.

(2009) J Mol Biol 391: 703-716

  • DOI: 10.1016/j.jmb.2009.06.014
  • Primary Citation of Related Structures:  
    3H0L, 3H0M, 3H0R

  • PubMed Abstract: 
  • Many bacteria form Gln-tRNA(Gln) and Asn-tRNA(Asn) by conversion of the misacylated Glu-tRNA(Gln) and Asp-tRNA(Asn) species catalyzed by the GatCAB amidotransferase in the presence of ATP and an amide donor (glutamine or asparagine). Here, we report the crystal structures of GatCAB from the hyperthermophilic bacterium Aquifex aeolicus, complexed with glutamine, asparagine, aspartate, ADP, or ATP ...

    Many bacteria form Gln-tRNA(Gln) and Asn-tRNA(Asn) by conversion of the misacylated Glu-tRNA(Gln) and Asp-tRNA(Asn) species catalyzed by the GatCAB amidotransferase in the presence of ATP and an amide donor (glutamine or asparagine). Here, we report the crystal structures of GatCAB from the hyperthermophilic bacterium Aquifex aeolicus, complexed with glutamine, asparagine, aspartate, ADP, or ATP. In contrast to the Staphylococcus aureus GatCAB, the A. aeolicus enzyme formed acyl-enzyme intermediates with either glutamine or asparagine, in line with the equally facile use by the amidotransferase of these amino acids as amide donors in the transamidation reaction. A water-filled ammonia channel is open throughout the length of the A. aeolicus GatCAB from the GatA active site to the synthetase catalytic pocket in the B-subunit. A non-catalytic Zn(2+) site in the A. aeolicus GatB stabilizes subunit contacts and the ammonia channel. Judged from sequence conservation in the known GatCAB sequences, the Zn(2+) binding motif was likely present in the primordial GatB/E, but became lost in certain lineages (e.g., S. aureus GatB). Two divalent metal binding sites, one permanent and the other transient, are present in the catalytic pocket of the A. aeolicus GatB. The two sites enable GatCAB to first phosphorylate the misacylated tRNA substrate and then amidate the activated intermediate to form the cognate products, Gln-tRNA(Gln) or Asn-tRNA(Asn).


    Organizational Affiliation

    Life Sciences Institute, Department of Biological Chemistry, University of Michigan, Ann Arbor, 48109, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Glutamyl-tRNA(Gln) amidotransferase subunit A
A, D, G, J, M, P, S, V
A, D, G, J, M, P, S, V
478Aquifex aeolicusMutation(s): 0 
Gene Names: aq_247gatAGATCA
EC: 6.3.5 (PDB Primary Data), 6.3.5.7 (UniProt)
UniProt
Find proteins for O66610 (Aquifex aeolicus (strain VF5))
Explore O66610 
Go to UniProtKB:  O66610
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO66610
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 B
B, E, H, K, N, Q, T, W
B, E, H, K, N, Q, T, W
478Aquifex aeolicusMutation(s): 0 
Gene Names: aq_461gatB
EC: 6.3.5
UniProt
Find proteins for O66766 (Aquifex aeolicus (strain VF5))
Explore O66766 
Go to UniProtKB:  O66766
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO66766
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Glutamyl-tRNA(Gln) amidotransferase subunit C
C, F, I, L, O, R, U, X
C, F, I, L, O, R, U, X
94Aquifex aeolicusMutation(s): 0 
Gene Names: gatCaq_2149
EC: 6.3.5
UniProt
Find proteins for O67904 (Aquifex aeolicus (strain VF5))
Explore O67904 
Go to UniProtKB:  O67904
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO67904
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GLN
Query on GLN

Download Ideal Coordinates CCD File 
BA [auth D],
DA [auth G],
GA [auth J],
JA [auth M],
MA [auth P],
BA [auth D],
DA [auth G],
GA [auth J],
JA [auth M],
MA [auth P],
PA [auth S],
SA [auth V],
Y [auth A]
GLUTAMINE
C5 H10 N2 O3
ZDXPYRJPNDTMRX-VKHMYHEASA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
AA [auth B],
CA [auth E],
FA [auth H],
IA [auth K],
LA [auth N],
AA [auth B],
CA [auth E],
FA [auth H],
IA [auth K],
LA [auth N],
OA [auth Q],
RA [auth T],
UA [auth W]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
EA [auth H],
HA [auth K],
KA [auth N],
NA [auth Q],
QA [auth T],
EA [auth H],
HA [auth K],
KA [auth N],
NA [auth Q],
QA [auth T],
TA [auth W],
Z [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.305 
  • R-Value Work: 0.254 
  • R-Value Observed: 0.256 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 128.248α = 90.01
b = 129.856β = 89.96
c = 155.069γ = 90.11
Software Package:
Software NamePurpose
HKL-2000data collection
PHASESphasing
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-07-21
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance