{PDOC51903}
{PS51903; CLP_R}
{BEGIN}
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* Clp repeat (R) domain profile *
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Molecular chaperones  recognize  unfolded  or misfolded proteins by binding to
hydrophobic surface  patches  not  normally  exposed  in  the native proteins.
Members of  the  Clp/Hsp100 family of chaperones are present in eubacteria and
within organelles  of all eukaryotes, promoting disaggregation and disassembly
of protein   complexes   and   participating   in   energy-dependent   protein
degradation. The  ClpA,  ClpB,  and ClpC subfamilies of the Clp/Hsp100 ATPases
contain a  conserved  N-terminal  domain  of  ~150  amino acids, which in turn
consists of  two  repeats  of ~75 residues. Although the Clp repeat (R) domain
contains two   approximate   sequence   repeats,   it   behaves  as  a  single
cooperatively folded  unit. The Clp R domain is thought to provide a means for
regulating the  specificity  of and to enlarge the substrate pool available to
Clp/Hsp100 chaperone  or  protease  complexes.  These  roles  can  be assisted
through the  binding of an adaptor protein. Adaptor proteins bind to the Clp R
domain, modulate  the  target  specificity  of  the  Clp/Hsp100  complex  to a
particular substrate  of  interest,  and may also regulate the activity of the
complex [1,2,3,4,5,6].

The Clp  R  domain  is  monomeric  and partially alpha helical. It is a single
folding unit  with pseudo 2-fold symmetry. The Clp R domain structure consists
of two four-helix bundles connected by a flexible loop [2,3,4].

The profile we developed covers the entire Clp R domain.

-Sequences known to belong to this class detected by the profile: ALL.
-Other sequence(s) detected in Swiss-Prot: NONE.
-Last update: August 2019 / First entry.

[ 1] Lo J.H., Baker T.A., Sauer R.T.
     "Characterization of the N-terminal repeat domain of Escherichia coli
     ClpA-A class I Clp/HSP100 ATPase."
     Protein. Sci. 10:551-559(2001).
     PubMed=11344323; DOI=10.1110/ps.41401
[ 2] Xia D., Esser L., Singh S.K., Guo F., Maurizi M.R.
     "Crystallographic investigation of peptide binding sites in the
     N-domain of the ClpA chaperone."
     J. Struct. Biol. 146:166-179(2004).
     PubMed=15037248; DOI=10.1016/j.jsb.2003.11.025
[ 3] Wang P., Li J., Weaver C., Lucius A., Sha B.
     "Crystal structures of Hsp104 N-terminal domains from Saccharomyces
     cerevisiae and Candida albicans suggest the mechanism for the function
     of Hsp104 in dissolving prions."
     Acta Crystallogr. D. Struct. Biol. 73:365-372(2017).
     PubMed=28375147; DOI=10.1107/S2059798317002662
[ 4] Kojetin D.J., McLaughlin P.D., Thompson R.J., Dubnau D., Prepiak P.,
     Rance M., Cavanagh J.
     "Structural and motional contributions of the Bacillus subtilis ClpC
     N-domain to adaptor protein interactions."
     J. Mol. Biol. 387:639-652(2009).
     PubMed=19361434; DOI=10.1016/j.jmb.2009.01.046
[ 5] Kim J., Kimber M.S., Nishimura K., Friso G., Schultz L., Ponnala L.,
     van Wijk K.J.
     "Structures, Functions, and Interactions of ClpT1 and ClpT2 in the Clp
     Protease System of Arabidopsis Chloroplasts."
     Plant. Cell. 27:1477-1496(2015).
     PubMed=25921872; DOI=10.1105/tpc.15.00106
[ 6] Liang Y., Ward S., Li P., Bennett T., Leyser O.
     "SMAX1-LIKE7 Signals from the Nucleus to Regulate Shoot Development in
     Arabidopsis via Partially EAR Motif-Independent Mechanisms."
     Plant. Cell. 28:1581-1601(2016).
     PubMed=27317673; DOI=10.1105/tpc.16.00286

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