8C32 | pdb_00008c32

Dark state 2.2 Angstrom crystal structure of cobalamin binding domain belonging to a light-dependent transcription regulator TtCarH obtained under anaerobic condition


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 
    0.223 (Depositor), 0.221 (DCC) 
  • R-Value Work: 
    0.179 (Depositor) 
  • R-Value Observed: 
    0.181 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 8C32

Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Redox driven B 12 -ligand switch drives CarH photoresponse.

Poddar, H.Rios-Santacruz, R.Heyes, D.J.Shanmugam, M.Brookfield, A.Johannissen, L.O.Levy, C.W.Jeffreys, L.N.Zhang, S.Sakuma, M.Colletier, J.P.Hay, S.Schiro, G.Weik, M.Scrutton, N.S.Leys, D.

(2023) Nat Commun 14: 5082-5082

  • DOI: https://doi.org/10.1038/s41467-023-40817-6
  • Primary Citation Related Structures: 
    8C31, 8C32, 8C33, 8C34, 8C35, 8C36, 8C37, 8C73, 8C76

  • PubMed Abstract: 

    CarH is a coenzyme B 12 -dependent photoreceptor involved in regulating carotenoid biosynthesis. How light-triggered cleavage of the B 12 Co-C bond culminates in CarH tetramer dissociation to initiate transcription remains unclear. Here, a series of crystal structures of the CarH B 12 -binding domain after illumination suggest formation of unforeseen intermediate states prior to tetramer dissociation. Unexpectedly, in the absence of oxygen, Co-C bond cleavage is followed by reorientation of the corrin ring and a switch from a lower to upper histidine-Co ligation, corresponding to a pentacoordinate state. Under aerobic conditions, rapid flash-cooling of crystals prior to deterioration upon illumination confirm a similar B 12 -ligand switch occurs. Removal of the upper His-ligating residue prevents monomer formation upon illumination. Combined with detailed solution spectroscopy and computational studies, these data demonstrate the CarH photoresponse integrates B 12 photo- and redox-chemistry to drive large-scale conformational changes through stepwise Co-ligation changes.


  • Organizational Affiliation
    • Manchester Institute of Biotechnology, Department of Chemistry, University of Manchester, Manchester, UK.

Macromolecule Content 

  • Total Structure Weight: 99.45 kDa 
  • Atom Count: 6,750 
  • Modeled Residue Count: 782 
  • Deposited Residue Count: 860 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Probable transcriptional regulator
A, B, C, D
215Thermus thermophilus HB27Mutation(s): 0 
Gene Names: TT_P0056
UniProt
Find proteins for Q746J7 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27))
Explore Q746J7 
Go to UniProtKB:  Q746J7
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ746J7
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
B12
(Subject of Investigation/LOI)

Query on B12



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

Query on 5AD



Download:Ideal Coordinates CCD File
G [auth A],
I [auth B],
K [auth C],
M [auth D]
5'-DEOXYADENOSINE
C10 H13 N5 O3
XGYIMTFOTBMPFP-KQYNXXCUSA-N
BR

Query on BR



Download:Ideal Coordinates CCD File
E [auth A]BROMIDE ION
Br
CPELXLSAUQHCOX-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free:  0.223 (Depositor), 0.221 (DCC) 
  • R-Value Work:  0.179 (Depositor) 
  • R-Value Observed: 0.181 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.73α = 90
b = 69.39β = 90
c = 204.14γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DIALSdata reduction
DIALSdata 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: 2023-08-16
    Type: Initial release
  • Version 1.1: 2023-08-23
    Changes: Refinement description
  • Version 1.2: 2023-08-30
    Changes: Database references