5KCM

Crystal structure of iron-sulfur cluster containing photolyase PhrB mutant I51W


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.166 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history


Literature

Crystal Structures of Bacterial (6-4) Photolyase Mutants with Impaired DNA Repair Activity.

Zhang, F.Ma, H.Bowatte, K.Kwiatkowski, D.Mittmann, E.Qasem, H.Krau, N.Zeng, X.Ren, Z.Scheerer, P.Yang, X.Lamparter, T.

(2017) Photochem Photobiol 93: 304-314

  • DOI: https://doi.org/10.1111/php.12699
  • Primary Citation of Related Structures:  
    5KCM, 5LFA

  • PubMed Abstract: 

    PhrB from Agrobacterium fabrum is the first prokaryotic photolyase which repairs (6-4) UV DNA photoproducts. The protein harbors three cofactors: the enzymatically active FAD chromophore, a second chromophore, 6,7-dimethyl-8-ribityllumazine (DMRL) and a cubane-type Fe-S cluster. Tyr424 of PhrB is part of the DNA-binding site and could provide an electron link to the Fe-S cluster. The PhrB Y 424F mutant showed reduced binding of lesion DNA and loss of DNA repair. The mutant PhrB I 51W is characterized by the loss of the DMRL chromophore, reduced photoreduction and reduced DNA repair capacity. We have determined the crystal structures of both mutants and found that both mutations only affect local protein environments, whereas the overall fold remained unchanged. The crystal structure of PhrB Y 424F revealed a water network extending to His366, which are part of the lesion-binding site. The crystal structure of PhrB I 51W shows how the bulky Trp leads to structural rearrangements in the DMRL chromophore pocket. Spectral characterizations of PhrB I 51W suggest that DMRL serves as an antenna chromophore for photoreduction and DNA repair in the wild type. The energy transfer from DMRL to FAD could represent a phylogenetically ancient process.


  • Organizational Affiliation

    Karlsruhe Institute of Technology, Botanical Institute, Karlsruhe, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
(6-4) photolyase
A, B
518Agrobacterium fabrum str. C58Mutation(s): 1 
Gene Names: phrBAtu4765
EC: 4.1.99.13
UniProt
Find proteins for A9CH39 (Agrobacterium fabrum (strain C58 / ATCC 33970))
Explore A9CH39 
Go to UniProtKB:  A9CH39
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA9CH39
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

Download Ideal Coordinates CCD File 
C [auth A],
F [auth B]
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
SF4
Query on SF4

Download Ideal Coordinates CCD File 
D [auth A],
G [auth B]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B],
I [auth B],
J [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.166 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97.607α = 90
b = 107.243β = 90
c = 113.672γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Eye Institute (NIH/NEI)United StatesR01EY024363

Revision History  (Full details and data files)

  • Version 1.0: 2017-01-11
    Type: Initial release
  • Version 1.1: 2017-03-01
    Changes: Database references
  • Version 1.2: 2017-03-15
    Changes: Other
  • Version 1.3: 2017-09-20
    Changes: Author supporting evidence
  • Version 1.4: 2019-12-11
    Changes: Author supporting evidence, Database references
  • Version 1.5: 2023-09-27
    Changes: Data collection, Database references, Refinement description