8J2Y

Acidimicrobiaceae bacterium photocobilins protein, dark state


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.211 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


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
GGDEF domain-containing protein
A, B
352Acidimicrobiaceae bacteriumMutation(s): 0 
Gene Names: DCS55_04760
UniProt
Find proteins for A0A349B205 (Acidimicrobiaceae bacterium)
Explore A0A349B205 
Go to UniProtKB:  A0A349B205
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A349B205
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
B12 (Subject of Investigation/LOI)
Query on B12

Download Ideal Coordinates CCD File 
C [auth A],
H [auth B]
COBALAMIN
C62 H89 Co N13 O14 P
LKVIQTCSMMVGFU-DWSMJLPVSA-N
5AD (Subject of Investigation/LOI)
Query on 5AD

Download Ideal Coordinates CCD File 
D [auth A],
I [auth B]
5'-DEOXYADENOSINE
C10 H13 N5 O3
XGYIMTFOTBMPFP-KQYNXXCUSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
E [auth A]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
SCN
Query on SCN

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A]
THIOCYANATE ION
C N S
ZMZDMBWJUHKJPS-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.211 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 108.773α = 90
b = 125.836β = 90
c = 124.63γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DIALSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



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