5C8E

Crystal structure of Thermus thermophilus CarH bound to adenosylcobalamin and a 26-bp DNA segment


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.89 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.250 
  • R-Value Observed: 0.251 

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Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history


Literature

Structural basis for gene regulation by a B12-dependent photoreceptor.

Jost, M.Fernandez-Zapata, J.Polanco, M.C.Ortiz-Guerrero, J.M.Chen, P.Y.Kang, G.Padmanabhan, S.Elias-Arnanz, M.Drennan, C.L.

(2015) Nature 526: 536-541

  • DOI: https://doi.org/10.1038/nature14950
  • Primary Citation of Related Structures:  
    5C8A, 5C8D, 5C8E, 5C8F

  • PubMed Abstract: 

    Photoreceptor proteins enable organisms to sense and respond to light. The newly discovered CarH-type photoreceptors use a vitamin B12 derivative, adenosylcobalamin, as the light-sensing chromophore to mediate light-dependent gene regulation. Here we present crystal structures of Thermus thermophilus CarH in all three relevant states: in the dark, both free and bound to operator DNA, and after light exposure. These structures provide visualizations of how adenosylcobalamin mediates CarH tetramer formation in the dark, how this tetramer binds to the promoter -35 element to repress transcription, and how light exposure leads to a large-scale conformational change that activates transcription. In addition to the remarkable functional repurposing of adenosylcobalamin from an enzyme cofactor to a light sensor, we find that nature also repurposed two independent protein modules in assembling CarH. These results expand the biological role of vitamin B12 and provide fundamental insight into a new mode of light-dependent gene regulation.


  • Organizational Affiliation

    Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Light-dependent transcriptional regulator CarH
A, B, C, D, E
A, B, C, D, E, F, G, H
305Thermus 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
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Entity ID: 2
MoleculeChains LengthOrganismImage
26-mer DNA segment containing the CarH operator sequence (antisense strand)
I, K
26Thermus thermophilus HB27
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains LengthOrganismImage
26-mer DNA segment containing the CarH operator sequence (sense strand)
J, L
26Thermus thermophilus HB27
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
B12
Query on B12

Download Ideal Coordinates CCD File 
AA [auth H]
M [auth A]
O [auth B]
Q [auth C]
S [auth D]
AA [auth H],
M [auth A],
O [auth B],
Q [auth C],
S [auth D],
U [auth E],
W [auth F],
Y [auth G]
COBALAMIN
C62 H89 Co N13 O14 P
LKVIQTCSMMVGFU-DWSMJLPVSA-N
5AD
Query on 5AD

Download Ideal Coordinates CCD File 
BA [auth H]
N [auth A]
P [auth B]
R [auth C]
T [auth D]
BA [auth H],
N [auth A],
P [auth B],
R [auth C],
T [auth D],
V [auth E],
X [auth F],
Z [auth G]
5'-DEOXYADENOSINE
C10 H13 N5 O3
XGYIMTFOTBMPFP-KQYNXXCUSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.89 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.250 
  • R-Value Observed: 0.251 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 177.94α = 90
b = 141.82β = 90
c = 162.69γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
Cootmodel building

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM069857
Howard Hughes Medical Institute (HHMI)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2015-09-30
    Type: Initial release
  • Version 1.1: 2015-10-14
    Changes: Database references
  • Version 1.2: 2015-11-04
    Changes: Database references
  • Version 1.3: 2017-09-20
    Changes: Author supporting evidence, Database references, Derived calculations
  • Version 1.4: 2019-11-20
    Changes: Author supporting evidence
  • Version 1.5: 2023-09-27
    Changes: Data collection, Database references, Derived calculations, Refinement description