1. GOTTESMAN, S., SQUIRES, C., PICHERSKY, E., CARRINGTON, M., HOBBS, M.,
MATTICK, J.S., DALRYMPLE, B., KURAMITSU, H., SHIROZA, T., FOSTER, T.,
CLARK, W.P., ROSS, B., SQUIRES, C.L. AND MAURIZI, M.R.
Conservation of the regulatory subunit for the CLP ATP-dependent protease
in prokaryotes and eukaryotes.
PROC.NATL.ACAD.SCI.U.S.A. 87 3513-3517 (1990).
2. PARSELL, D.A., SANCHEZ, Y., STITZEL, J.D. AND LINDQUIST, S.
HSP104 is a highly conserved protein with 2 essential nucleotide-
NATURE 353 270-273 (1991).
An evolutionary relationship has been demonstrated in a group of ATP-
binding proteins that includes the regulatory subunit of the ATP-dependent
protease clpA; heat shock proteins clpB, 104 and 78; and chloroplast
proteins CD4a and CD4b [1,2]. The proteins are thought to protect cells
from stress by controlling the aggregation and denaturation of vital
cellular structures. They vary in size, but share 2 conserved 200-amino
acid domains, each of which contains an ATP-binding site.
CLPPROTEASEA is a 4-element fingerprint that provides a signature for ATP-
dependent CLP protease ATP-binding subunits. The fingerprint was derived
from an initial alignment of 4 sequences: the motifs were drawn from
the second domain, in the region of the ATP-binding site (cf. PROSITE
patterns CLPAB_1 (PS00870) and CLPAB_2 (PS00871)). Two iterations on
OWL24.0 were required to reach convergence, at which point a true set
comprising 18 sequences was identified. Amongst the partial matches was
the hypothetical protein of the putative ATP operon from Mycobacterium
leprae, which is a fragment lacking the last motif; and strong matches
with motif 1 were also made by a transmembrane ATPase from L.lactis, and
DNA polymerase III, which contains an ATP-binding site.
An update on SPTR37_9f identified a true set of 59 sequences, and 1