Synchrotron protein footprinting supports substrate translocation by ClpA via ATP-induced movements of the D2 loop.
Synchrotron X-ray protein footprinting is used to study structural changes upon formation of the ClpA hexamer. Comparative solvent accessibilities between ClpA monomer and ClpA hexamer samples are in agreement throughout most of the sequence, with calculations based on two previously proposed hexameric models. The data differ substantially from the proposed models in two parts of the structure: the D1 sensor 1 domain and the D2 loop region. The results suggest that these two regions can access alternate conformations in which their solvent protection is greater than that in the structural models based on crystallographic data. In combination with previously reported structural data, the footprinting data provide support for a revised model in which the D2 loop contacts the D1 sensor 1 domain in the ATP-bound form of the complex. These data provide the first direct experimental support for the nucleotide-dependent D2 loop conformational change previously proposed to mediate substrate translocation.
Bohon
Jen
J
Center for Proteomics and Center for Synchrotron Biosciences, Case Western Reserve University, Cleveland, OH 44106, USA.
Jennings
Laura D
LD
Phillips
Christine M
CM
Licht
Stuart
S
Chance
Mark R
MR
D000255:Adenosine Triphosphate / Q000378:metabolism*; D000595:Amino Acid Sequence; D049071:Endopeptidase Clp / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D029968:Escherichia coli Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D008958:Models, Molecular; D008969:Molecular Sequence Data; D010455:Peptides / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D011487:Protein Conformation; D023302:Protein Footprinting; D016415:Sequence Alignment; D017356:Synchrotrons
D029968:Escherichia coli Proteins; D010455:Peptides; D000255:Adenosine Triphosphate; C483568:ClpA protease, E coli; D049071:Endopeptidase Clp