Structural basis for the hydrolysis of ATP by a nucleotide binding subunit of an amino acid ABC transporter from Thermus thermophilus

J Struct Biol. 2015 Jun;190(3):367-72. doi: 10.1016/j.jsb.2015.04.012. Epub 2015 Apr 24.


ATP-binding cassette (ABC) transporters are a major family of small molecule transporter proteins, and their deregulation is associated with several diseases, including cancer. Here, we report the crystal structure of the nucleotide binding domain (NBD) of an amino acid ABC transporter from Thermus thermophilus (TTHA1159) in its apo form and as a complex with ADP along with functional studies. TTHA1159 is a putative arginine ABC transporter. The apo-TTHA1159 was crystallized in dimeric form, a hitherto unreported form of an apo NBD. Structural comparison of the apo and ADP-Mg(2+) complexes revealed that Phe14 of TTHA1159 undergoes a significant conformational change to accommodate ADP, and that the bound ADP interacts with the P-loop (Gly40-Thr45). Modeling of ATP-Mg(2+):TTHA1159 complex revealed that Gln86 and Glu164 are involved in water-mediated hydrogen bonding contacts and Asp163 in Mg(2+) ion-mediated hydrogen bonding contacts with the γ-phosphate of ATP, consistent with the findings of other ABC transporters. Mutational studies confirmed the necessity of each of these residues, and a comparison of the apo/ADP Mg(2+):TTHA1159 with its ATP-complex model suggests the likelihood of a key conformational change to the Gln86 side chain for ATP hydrolysis.

Keywords: ADP; ATP; Crystal structure; TTHA1159; Thermus thermophilus; Transporters.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • ATP-Binding Cassette Transporters / chemistry*
  • ATP-Binding Cassette Transporters / metabolism*
  • Adenosine Diphosphate / chemistry
  • Adenosine Diphosphate / metabolism
  • Adenosine Triphosphate / chemistry*
  • Adenosine Triphosphate / metabolism*
  • Amino Acids / chemistry
  • Amino Acids / metabolism
  • Bacterial Proteins / chemistry*
  • Bacterial Proteins / metabolism*
  • Binding Sites / physiology
  • Hydrogen Bonding
  • Hydrolysis
  • Magnesium / chemistry
  • Magnesium / metabolism
  • Models, Molecular
  • Nucleotides / chemistry
  • Nucleotides / metabolism
  • Protein Binding / physiology
  • Protein Conformation
  • Thermus thermophilus / metabolism*


  • ATP-Binding Cassette Transporters
  • Amino Acids
  • Bacterial Proteins
  • Nucleotides
  • Adenosine Diphosphate
  • Adenosine Triphosphate
  • Magnesium

Associated data

  • PDB/4U00
  • PDB/4U02