8J2X

Saccharothrix syringae photocobilins protein, light state


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.184 

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Literature

Photocobilins integrate B12 and bilin photochemistry for enzyme control.

Zhang, S.Jeffreys, L.N.Poddar, H.Yu, Y.Liu, C.Patel, K.Johannissen, L.O.Zhu, L.Cliff, M.J.Yan, C.Schiro, G.Weik, M.Sakuma, M.Levy, C.W.Leys, D.Heyes, D.J.Scrutton, N.S.

(2024) Nat Commun 15: 2740-2740

  • DOI: https://doi.org/10.1038/s41467-024-46995-1
  • Primary Citation of Related Structures:  
    8J2W, 8J2X, 8J2Y

  • PubMed Abstract: 

    Photoreceptor proteins utilise chromophores to sense light and trigger a biological response. The discovery that adenosylcobalamin (or coenzyme B 12 ) can act as a light-sensing chromophore heralded a new field of B 12 -photobiology. Although microbial genome analysis indicates that photoactive B 12 -binding domains form part of more complex protein architectures, regulating a range of molecular-cellular functions in response to light, experimental evidence is lacking. Here we identify and characterise a sub-family of multi-centre photoreceptors, termed photocobilins, that use B 12 and biliverdin (BV) to sense light across the visible spectrum. Crystal structures reveal close juxtaposition of the B 12 and BV chromophores, an arrangement that facilitates optical coupling. Light-triggered conversion of the B 12 affects quaternary structure, in turn leading to light-activation of associated enzyme domains. The apparent widespread nature of photocobilins implies involvement in light regulation of a wider array of biochemical processes, and thus expands the scope for B 12 photobiology. Their characterisation provides inspiration for the design of broad-spectrum optogenetic tools and next generation bio-photocatalysts.


  • Organizational Affiliation

    Manchester Institute of Biotechnology and Department of Chemistry, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK. shaowei.zhang@nudt.edu.cn.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cobalamin-binding protein341Saccharothrix syringaeMutation(s): 0 
Gene Names: EKG83_22740
UniProt
Find proteins for A0A5Q0H231 (Saccharothrix syringae)
Explore A0A5Q0H231 
Go to UniProtKB:  A0A5Q0H231
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A5Q0H231
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.184 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 109.667α = 90
b = 109.667β = 90
c = 98.074γ = 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: 2024-04-10
    Type: Initial release