Mechanistic and evolutionary insights into isoform-specific 'supercharging' in DCLK family kinases.
E. coli
allostery
bioinformatics
catalytic activity
computational biology
evolution
evolutionary biology
molecular biology
protein kinase
systems biology
Journal
eLife
ISSN: 2050-084X
Titre abrégé: Elife
Pays: England
ID NLM: 101579614
Informations de publication
Date de publication:
26 10 2023
26 10 2023
Historique:
medline:
27
10
2023
pubmed:
26
10
2023
entrez:
26
10
2023
Statut:
epublish
Résumé
Catalytic signaling outputs of protein kinases are dynamically regulated by an array of structural mechanisms, including allosteric interactions mediated by intrinsically disordered segments flanking the conserved catalytic domain. The doublecortin-like kinases (DCLKs) are a family of microtubule-associated proteins characterized by a flexible C-terminal autoregulatory 'tail' segment that varies in length across the various human DCLK isoforms. However, the mechanism whereby these isoform-specific variations contribute to unique modes of autoregulation is not well understood. Here, we employ a combination of statistical sequence analysis, molecular dynamics simulations, and in vitro mutational analysis to define hallmarks of DCLK family evolutionary divergence, including analysis of splice variants within the DCLK1 sub-family, which arise through alternative codon usage and serve to 'supercharge' the inhibitory potential of the DCLK1 C-tail. We identify co-conserved motifs that readily distinguish DCLKs from all other calcium calmodulin kinases (CAMKs), and a 'Swiss Army' assembly of distinct motifs that tether the C-terminal tail to conserved ATP and substrate-binding regions of the catalytic domain to generate a scaffold for autoregulation through C-tail dynamics. Consistently, deletions and mutations that alter C-terminal tail length or interfere with co-conserved interactions within the catalytic domain alter intrinsic protein stability, nucleotide/inhibitor binding, and catalytic activity, suggesting isoform-specific regulation of activity through alternative splicing. Our studies provide a detailed framework for investigating kinome-wide regulation of catalytic output through cis-regulatory events mediated by intrinsically disordered segments, opening new avenues for the design of mechanistically divergent DCLK1 modulators, stabilizers, or degraders.
Identifiants
pubmed: 37883155
doi: 10.7554/eLife.87958
pii: 87958
pmc: PMC10602587
doi:
pii:
Substances chimiques
Protein Isoforms
0
Protein Serine-Threonine Kinases
EC 2.7.11.1
Calcium, Dietary
0
DCLK1 protein, human
EC 2.7.1.11
Doublecortin-Like Kinases
EC 2.7.1.11
Banques de données
Dryad
['10.5061/dryad.8931zcrxb']
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Subventions
Organisme : NIGMS NIH HHS
ID : R35 GM139656
Pays : United States
Organisme : Biotechnology and Biological Sciences Research Council
ID : BB/S018514/1
Pays : United Kingdom
Organisme : Biotechnology and Biological Sciences Research Council
ID : BB/N021703/1
Pays : United Kingdom
Organisme : Biotechnology and Biological Sciences Research Council
ID : BB/X002780/1
Pays : United Kingdom
Commentaires et corrections
Type : UpdateOf
Informations de copyright
© 2023, Venkat, Watterson, Byrne et al.
Déclaration de conflit d'intérêts
AV, GW, DB, BO, SS, NG, EF, LD, CB, WY, IA, SK, CE, PE, NK No competing interests declared
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