Download MendeleySignatureFinder enables sequence mining to identify cobalamin-dependent photoreceptor proteins.
Yu, Y., Jeffreys, L.N., Poddar, H., Hill, A., Johannissen, L., Dai, F., Sakuma, M., Leys, D., Heyes, D.J., Zhang, S., Scrutton, N.S.(2025) FEBS J 292: 635-652
- PubMed: 39718193
- DOI: https://doi.org/10.1111/febs.17377
- Primary Citation of Related Structures:
8JBS, 8JBT - PubMed Abstract:
Photoreceptors control cellular processes in response to light. Most photoreceptors sense blue or red light, but the recent discovery of the cobalamin-dependent photoreceptor, CarH, has expanded the wavelength range of photoreception to other regions of the electromagnetic spectrum to include the green light region. Further identification of cobalamin-dependent green light-sensitive photoreceptors has been hampered owing to poor annotation of the light responsiveness of cobalamin-binding domains (CBDs) in public databases. Here we report a computational workflow, SignatureFinder, that uses a combination of sequence and structural analyses to identify new light-responsive CBD-containing proteins. The light response of exemplar proteins containing the proposed signature were confirmed experimentally. A structural analysis of these new photoreceptors, including the crystal structure of a new CBD domain, highlights how the signature elements interact with the cobalamin chromophore to sense light. Database mining of 128 000 CBD-containing sequences using the identified signature revealed more diverse CBD-containing photoreceptors, thereby expanding the family of green-light photoreceptors. A SignatureFinder web server is available (https://enzymeevolver.com) for wider applications, including the identification of signature sequences of other biological ligands of interest.
Organizational Affiliation:
Department of Chemistry, The University of Manchester, Manchester Institute of Biotechnology, UK.
