Crystal Structure of ATP-Bound Human ABCF1 Demonstrates a Unique Conformation of ABC Proteins

Abstract

Gene translation requires the correct selection of start codon AUG in mRNA. ATP-binding cassette subfamily F member 1 (ABCF1) plays a key role in the accuracy of start codon selection. However, the function of human ABCF1 is not clearly understood. Here, we solve the crystal structure of an ATP-bound wild-type human ABCF1 at 2.3-Å resolution. The comparative studies indicate that the structure is in a pre-activation intermediate conformation. This conformation is stabilized by the interaction between ATP and protein. Thus, we propose that this conformation is an important step in the activation of ABCF1. This study extends our understanding of ABC (ATP-binding cassette) protein activation at the molecular level.

ATP-binding cassette protein ABCF1 couples gene transcription with maintenance of genome integrity in embryonic stem cells

“…ABCF1 contains two conserved nucleotide-binding domains (NBDs) and a ~ 300 amino acid N-terminal domain that is predicted to be highly disordered (Abor et al, 2018) ( Figure S5A). This is consistent with a recent structural study on ABCF1 which indicated that the Nterminal domain cannot be crystallized (Qu et al, 2018). The N-terminal domain of ABCF1 is a low-complexity region that is unusually rich in charged amino acids, of which ~40% are divided between lysine (K) and glutamic acid (E) residues (Dyson, 2016;Hansen et al, 2006;Paytubi et al, 2009) ( Figure 5A).…”

“…First, ABCF1 is unambiguously shown to be the sole constituent of SCC-B. Second, ATP binding and hydrolysis by ABCF1 are dispensable for transcription, unlike for ABCF1's role in translation (Paytubi et al, 2009;Qu et al, 2018). Third, while the entire IDR is essential for full coactivator activity, the IDR fragment by itself is not sufficient to activate transcription.…”

ABC-F proteins in mRNA translation and antibiotic resistance

“…The two tandem ABC domains in EttA (Fig. 3A) and other ABC-F proteins share the canonical structure comprising three subdomains that is present in all ABC superfamily ATPases: (i) an F1-ATPase-like / Core subdomain with a complex topology conserved in many other ATPases including F1 and the AAA+ ATPase superfamily (as noted above); (ii) an N-terminal antiparallel -sheet (ABC ) subdomain that forms a rigid ATP-binding module together with the F1-like Core subdomain, and (iii) a 60-100 residue -helical (ABC ) subdomain containing the ABC superfamily Signature Sequence, canonically LSGGQ but generally LSGGE in proteins, inserted within the primary sequence of the F1-like Core subdomain [18,23,25,75]. The Walker A motif in the F1-like Core is a phosphate-binding loop or "P-loop" that ligates the phosphates of ATP, while Walker B motif in this subdomain is a hydrophobic -strand terminating in an aspartic acid that contributes to ligating the Mg ++ cofactor of ATP [18,25,53].…”

ABC‐F translation factors: from antibiotic resistance to immune response

“…Structures have also been determined for two eukaryotic ABC-F proteins. The first is a crystal structure of human ABCF1 [46]. While its tandem ABC domains have essentially canonical structures, they are bound to ATP in the crystal structure, but they do not adopt the ATP-sandwich heterodimer conformation observed in all of the ribosome-bound ABC-F structures published to date, which is equivalent to the active ATP-bound conformations observed for a wide variety of ABC transporter transmembrane proteins [47][48][49].…”

“…The X-ray crystal structure of human ABCF1, which contains the Arm motif in ABC1, shows two protein conformations in the asymmetric unit. One of these has well-resolved electron density for the PtIM, while the Arm motif is disordered ( Figure 2B, ABCF1), and the other has weak electron density for the PtIM, while the Arm motif has well-resolved electron density [46]. These observations suggest that there is some degree of flexibility in the attachment of these structures to the ABC domains and that crystal-packing interactions possibly mimicking interactions with the ribosome control their exact orientation in the crystal lattice.…”