8JBT

B12-binding domain from Chloracidobacterium thermophilum MerR family protein, anaerobic light state

Summary for 8JBT

• Entry DOI: 10.2210/pdb8jbt/pdb
• Descriptor: Putative cobalamin binding protein, COBALAMIN, 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, ... (7 entities in total)
• Functional Keywords: b12-dependent transcription regulators from the merr superfamily, transcription
• Biological source: Chloracidobacterium thermophilum
• Total number of polymer chains: 2
• Total formula weight: 75723.48

Authors

Zhang, S.,Yu, Y. (deposition date: 2023-05-09, release date: 2024-11-13, Last modification date: 2025-02-19)

Primary citation

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.
SignatureFinder enables sequence mining to identify cobalamin-dependent photoreceptor proteins.
Febs J., 292:635-652, 2025

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.

PubMed: 39718193
DOI: 10.1111/febs.17377

Experimental method

X-RAY DIFFRACTION (2.3 Å)