8JBS | pdb_00008jbs

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 
    0.236 (Depositor), 0.243 (DCC) 
  • R-Value Work: 
    0.185 (Depositor), 0.198 (DCC) 
  • R-Value Observed: 
    0.188 (Depositor) 

Starting Model: in silico
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

SignatureFinder 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

  • 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Putative cobalamin binding protein
A, B
327Chloracidobacterium thermophilumMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free:  0.236 (Depositor), 0.243 (DCC) 
  • R-Value Work:  0.185 (Depositor), 0.198 (DCC) 
  • R-Value Observed: 0.188 (Depositor) 
Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 125.218α = 90
b = 125.218β = 90
c = 73.088γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
DIALSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Engineering and Physical Sciences Research CouncilUnited KingdomEP/S030336/1

Revision History  (Full details and data files)

  • Version 1.0: 2024-11-13
    Type: Initial release
  • Version 1.1: 2025-01-29
    Changes: Database references
  • Version 1.2: 2025-02-19
    Changes: Database references