CLPB

Structure

Gene

The CLPB gene has 19 exons and is located at the chromosome band 11q13.4.

Protein

Skd3 has five isoforms due to alternative splicing. Isoform 1 is considered to have the 'canonical' sequence. The protein is 78.7 kDa in size and composed of 707 amino acids. It contains an N-terminal mitochondrial targeting sequence (1-92 amino acids). After processing, the mature mitochondrial protein has a theoretical pI of 7.53. Skd3 is further processed by the mitochondrial rhomboid protease PARL at amino acid 127. Skd3 has a specific C-terminal D2 domain and proteins with this domain form the sub-family of Caseinolytic peptidase (Clp) proteins, also called HSP100. The domain composition of human Skd3 is different from that of microbial or plant orthologs. Notably, the presence of ankyrin repeats replaced the first of two ATPase domains found in bacteria and fungi.

Function

Skd3 belongs to the HCLR clade of the large AAA+ superfamily. The unifying characteristic of this family is the hydrolysis of ATP through the AAA+ domain to produce energy required to catalyze protein unfolding, disassembly and disaggregation. Skd3 does not cooperate with HSP70, unlike its bacterial orthologue. The in vitro ATPase activity of Skd3 has been confirmed. Skd3 is a potent disaggregase in vitro and is activated by PARL to increase disaggregation activity by over 10-fold. Indeed, PARL-activated Skd3 is capable of disassembling alpha-synuclein fibrils in vitro. Even though the bacterial orthologue, ClpB, contributes to the thermotolerance of cells, it is yet unclear if Skd3 plays a similar role within mitochondria. The interaction with protein like HAX1 suggests that human Skd3 may be involved in apoptosis. Indeed, Skd3 solubilizes HAX1 in cells and the deletion of the CLPB gene in human cells has been shown to sensitize cells to apoptotic signals. In humans, the presence of ankyrin repeats replaced the first of two ATPase domains found in bacteria and fungi, which might have evolved to ensure more elaborate substrate recognition or to support a putative chaperone function. Either the ankyrin repeats alone or the AAA+ domain were found to be insufficient to support disaggregation activity. With only one ATPase domain, Skd3 is postulated competent in the use of ATP hydrolysis energy for threading unfolded polypeptide through the central channel of the hexamer ring. /

Clinical significance

Neonatal encephalopathy is a kind of severe neurological impairment in the newborn with no specific clinical sign at the early stage of life, and its diagnosis remains a challenge. This neonatal encephalopathy includes a heterogeneous group of 3-methylglutaconic aciduria syndromes and loss of Skd3 function is reported to be one of the causes. Knocking down the clpB gene in the zebrafish induced reduction of growth and increment of motor activity, which is similar to the signs observed in patients. Its loss may lead to a broad phenotypic spectrum encompassing intellectual disability/developmental delay, congenital neutropenia, progressive brain atrophy, movement disorder, and bilateral cataracts, with 3-methylglutaconic aciduria. Further investigation into Skd3 may shed a new light on the diagnosis of this disease.

Interactions

This protein is known to interact with:

• HAX1
• PARL
• HTRA2
• SMAC/DIABLO
• OPA1
• OPA3
• PHB2
• MICU1
• MICU2
• SLC25A25
• SLC25A13
• TIMM8A
• TIMM8B
• TIMM13
• TIMM21
• TIMM22
• TIMM23
• TIMM50
• NDUFA8
• NDUFA11
• NDUFA13
• NDUFB7
• NDUFB10
• TTC19
• COX11
• CYC1

References

References

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2. (January 1995). "Expression of a putative ATPase suppresses the growth defect of a yeast potassium transport mutant: identification of a mammalian member of the Clp/HSP104 family". Gene.
3. "Entrez Gene: CLPB ClpB caseinolytic peptidase B homolog (E. coli)".
4. (February 2015). "CLPB mutations cause 3-methylglutaconic aciduria, progressive brain atrophy, intellectual disability, congenital neutropenia, cataracts, movement disorder". American Journal of Human Genetics.
5. (February 2015). "CLPB variants associated with autosomal-recessive mitochondrial disorder with cataract, neutropenia, epilepsy, and methylglutaconic aciduria". American Journal of Human Genetics.
6. (2020-06-23). "Skd3 (human CLPB) is a potent mitochondrial protein disaggregase that is inactivated by 3-methylglutaconic aciduria-linked mutations". eLife.
7. (April 2016). "Novel CLPB mutation in a patient with 3-methylglutaconic aciduria causing severe neurological involvement and congenital neutropenia". Clinical Immunology.
8. (2021-06-11). "Heterozygous Variants of CLPB are a Cause of Severe Congenital Neutropenia". Blood.
9. "Q9H078 - CLPB_HUMAN". Uniprot.
10. (April 2017). "PARL mediates Smac proteolytic maturation in mitochondria to promote apoptosis". Nature Cell Biology.
11. (September 2006). "A camel passes through the eye of a needle: protein unfolding activity of Clp ATPases". Molecular Microbiology.
12. (2015-02-24). "Metabolic and Chaperone Gene Loss Marks the Origin of Animals: Evidence for Hsp104 and Hsp78 Chaperones Sharing Mitochondrial Enzymes as Clients". PLOS ONE.
13. (June 2004). "The ankyrin repeat as molecular architecture for protein recognition". Protein Science.
14. (December 2006). "Ankyrin repeat: a unique motif mediating protein-protein interactions". Biochemistry.
15. (2006-05-11). "Evolutionary relationships and structural mechanisms of aaa+ proteins". Annual Review of Biophysics and Biomolecular Structure.
16. (May 2015). "Disruption of CLPB is associated with congenital microcephaly, severe encephalopathy and 3-methylglutaconic aciduria". Journal of Medical Genetics.
17. (30 April 2008). "The AAA+ superfamily of functionally diverse proteins". Genome Biology.
18. (April 2020). "CLPB (caseinolytic peptidase B homolog), the first mitochondrial protein refoldase associated with human disease". Biochimica et Biophysica Acta (BBA) - General Subjects.
19. (October 1998). "Roles of the Escherichia coli small heat shock proteins IbpA and IbpB in thermal stress management: comparison with ClpA, ClpB, and HtpG In vivo". Journal of Bacteriology.
20. (July 2019). "Targeting Mitochondrial Structure Sensitizes Acute Myeloid Leukemia to Venetoclax Treatment". Cancer Discovery.
21. (November 2004). "Chaperoned protein disaggregation--the ClpB ring uses its central channel". Cell.
22. (November 2004). "Thermotolerance requires refolding of aggregated proteins by substrate translocation through the central pore of ClpB". Cell.
23. (December 2014). "ClpB chaperone passively threads soluble denatured proteins through its central pore". Genes to Cells.
24. (12 June 2016). "New perspective in diagnostics of mitochondrial disorders: two years' experience with whole-exome sequencing at a national paediatric centre". Journal of Translational Medicine.
25. (2019-09-27). "Structural Basis of Mitochondrial Scaffolds by Prohibitin Complexes: Insight into a Role of the Coiled-Coil Region". iScience.