Endopeptidase Clp

Endopeptidase Clp (EC 3.4.21.92, endopeptidase Ti, caseinolytic protease, protease Ti, ATP-dependent Clp protease, ClpP, Clp protease).[1][2][3][4] This enzyme catalyses the following chemical reaction

Hydrolysis of proteins to small peptides in the presence of ATP and Mg2+.
Endopeptidase Clp
ATP-dependent Clp protease (fragment) homo14mer, Streptococcus pneumoniae
Identifiers
EC number3.4.21.92
CAS number110910-59-3
Databases
IntEnzIntEnz view
BRENDABRENDA entry
ExPASyNiceZyme view
KEGGKEGG entry
MetaCycmetabolic pathway
PRIAMprofile
PDB structuresRCSB PDB PDBe PDBsum

This bacterial enzyme contains subunits of two types, ClpP, with peptidase activity, and the protein ClpA, with AAA+ ATPase activity. ClpP and ClpA are not evolutionarily related.

A fully assembled Clp protease complex has a barrel-shaped structure in which two stacked heptameric ring of proteolytic subunits (ClpP or ClpQ) are either sandwiched between two rings or single-caped by one ring of hexameric ATPase-active chaperon subunits (ClpA, ClpC, ClpE, ClpX, ClpY, or others).[5]

ClpXP is presented in almost all bacteria while ClpA is found in the Gram-negative bacteria, ClpC in Gram-Positive bacteria and cyanobacteria. ClpAP, ClpXP and ClpYQ coexist in E. Coli while only ClpXP complex in present in humans as mitochondrial enzymes.[5] ClpYQ is another name for the HslVU complex, a heat shock protein complex thought to resemble the hypothetical ancestor of the proteasome.[6]

ATPase
ClpA/B
Identifiers
SymbolClpA/B
PfamPF02861
InterProIPR001270
ClpX
Identifiers
SymbolClpX
InterProIPR004487

The Hsp100 family of eukaryotic heat shock proteins is homologous to the ATPase-active chaperon subunits found in the Clp complex; as such the entire group is often referred to as the HSP100/Clp family. The family is usually broken into two parts, one being the ClpA/B family with two ATPase domains, and the other being ClpX and friends with only one such domain.[7] ClpA through E is put into the first group along with Hsp78/104, and ClpX and HSIU is put into the second group.[8]

Many of the proteins are not associated with a protease and have functions other than proteolysis. ClpB (human CLPB "Hsp78", yeast Hsp104) break up insoluble protein aggregates in conjunction with DnaK/Hsp70. They are thought to function by threading client proteins through a small 20 Å (2 nm) pore, thereby giving each client protein a second chance to fold.[8][9][10] A member of the ClpA/B family termed ClpV is used in the bacterial T6SS.[11]

See also

References
  1. Gottesman S, Clark WP, Maurizi MR (May 1990). "The ATP-dependent Clp protease of Escherichia coli. Sequence of clpA and identification of a Clp-specific substrate". The Journal of Biological Chemistry. 265 (14): 7886–93. PMID 2186030.
  2. Maurizi MR, Clark WP, Katayama Y, Rudikoff S, Pumphrey J, Bowers B, Gottesman S (July 1990). "Sequence and structure of Clp P, the proteolytic component of the ATP-dependent Clp protease of Escherichia coli". The Journal of Biological Chemistry. 265 (21): 12536–45. PMID 2197275.
  3. Maurizi MR, Thompson MW, Singh SK, Kim SH (1994). "Endopeptidase Clp: ATP-dependent Clp protease from Escherichia coli". Methods in Enzymology. 244: 314–31. doi:10.1016/0076-6879(94)44025-5. PMID 7845217.
  4. Kessel M, Maurizi MR, Kim B, Kocsis E, Trus BL, Singh SK, Steven AC (July 1995). "Homology in structural organization between E. coli ClpAP protease and the eukaryotic 26 S proteasome". Journal of Molecular Biology. 250 (5): 587–94. doi:10.1006/jmbi.1995.0400. PMID 7623377.
  5. Hamon MP, Bulteau AL, Friguet B (September 2015). "Mitochondrial proteases and protein quality control in ageing and longevity". Ageing Research Reviews. 23 (Pt A): 56–66. doi:10.1016/j.arr.2014.12.010. PMID 25578288. S2CID 205667759.
  6. Gille C, Goede A, Schlöetelburg C, Preissner R, Kloetzel PM, Göbel UB, Frömmel C (March 2003). "A comprehensive view on proteasomal sequences: implications for the evolution of the proteasome". Journal of Molecular Biology. 326 (5): 1437–48. doi:10.1016/s0022-2836(02)01470-5. PMID 12595256.
  7. Schirmer EC, Glover JR, Singer MA, Lindquist S (August 1996). "HSP100/Clp proteins: a common mechanism explains diverse functions". Trends in Biochemical Sciences. 21 (8): 289–96. doi:10.1016/S0968-0004(96)10038-4. PMID 8772382.
  8. Doyle SM, Wickner S (January 2009). "Hsp104 and ClpB: protein disaggregating machines". Trends in Biochemical Sciences. 34 (1): 40–8. doi:10.1016/j.tibs.2008.09.010. PMID 19008106.
  9. Horwich AL (November 2004). "Chaperoned protein disaggregation--the ClpB ring uses its central channel". Cell. 119 (5): 579–81. doi:10.1016/j.cell.2004.11.018. PMID 15550237.
  10. Weibezahn J, Tessarz P, Schlieker C, Zahn R, Maglica Z, Lee S, et al. (November 2004). "Thermotolerance requires refolding of aggregated proteins by substrate translocation through the central pore of ClpB". Cell. 119 (5): 653–65. doi:10.1016/j.cell.2004.11.027. PMID 15550247.
  11. Schlieker C, Zentgraf H, Dersch P, Mogk A (November 2005). "ClpV, a unique Hsp100/Clp member of pathogenic proteobacteria". Biological Chemistry. 386 (11): 1115–27. doi:10.1515/BC.2005.128. PMID 16307477. S2CID 34095247.
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