Dynamics at the serine loop underlie differential affinity of cryptochromes for CLOCK:BMAL1 to control circadian timing

Elife. 2020 Feb 26;9:e55275. doi: 10.7554/eLife.55275.


Mammalian circadian rhythms are generated by a transcription-based feedback loop in which CLOCK:BMAL1 drives transcription of its repressors (PER1/2, CRY1/2), which ultimately interact with CLOCK:BMAL1 to close the feedback loop with ~24 hr periodicity. Here we pinpoint a key difference between CRY1 and CRY2 that underlies their differential strengths as transcriptional repressors. Both cryptochromes bind the BMAL1 transactivation domain similarly to sequester it from coactivators and repress CLOCK:BMAL1 activity. However, we find that CRY1 is recruited with much higher affinity to the PAS domain core of CLOCK:BMAL1, allowing it to serve as a stronger repressor that lengthens circadian period. We discovered a dynamic serine-rich loop adjacent to the secondary pocket in the photolyase homology region (PHR) domain that regulates differential binding of cryptochromes to the PAS domain core of CLOCK:BMAL1. Notably, binding of the co-repressor PER2 remodels the serine loop of CRY2, making it more CRY1-like and enhancing its affinity for CLOCK:BMAL1.

Keywords: biochemistry; chemical biology; circadian rhythms; cryo-electron microscopy; molecular dynamics; mouse; x-ray crystallography.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • ARNTL Transcription Factors / chemistry
  • ARNTL Transcription Factors / metabolism
  • ARNTL Transcription Factors / physiology*
  • Animals
  • CLOCK Proteins / chemistry
  • CLOCK Proteins / metabolism
  • CLOCK Proteins / physiology*
  • Circadian Rhythm* / physiology
  • Cryptochromes / chemistry
  • Cryptochromes / metabolism*
  • Cryptochromes / physiology
  • Mice
  • Protein Structure, Tertiary
  • Serine / metabolism


  • ARNTL Transcription Factors
  • Arntl protein, mouse
  • Cry1 protein, mouse
  • Cry2 protein, mouse
  • Cryptochromes
  • Serine
  • CLOCK Proteins
  • Clock protein, mouse

Associated data

  • PDB/6OF7