Spore photoproduct lyase

Experimental Data Snapshot

  • Resolution: 2.20 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.211 

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Ligand Structure Quality Assessment 

This is version 1.3 of the entry. See complete history


Structural insights into recognition and repair of UV-DNA damage by Spore Photoproduct Lyase, a radical SAM enzyme.

Benjdia, A.Heil, K.Barends, T.R.Carell, T.Schlichting, I.

(2012) Nucleic Acids Res 40: 9308-9318

  • DOI: https://doi.org/10.1093/nar/gks603
  • Primary Citation of Related Structures:  
    4FHC, 4FHD, 4FHE, 4FHF, 4FHG

  • PubMed Abstract: 

    Bacterial spores possess an enormous resistance to ultraviolet (UV) radiation. This is largely due to a unique DNA repair enzyme, Spore Photoproduct Lyase (SP lyase) that repairs a specific UV-induced DNA lesion, the spore photoproduct (SP), through an unprecedented radical-based mechanism. Unlike DNA photolyases, SP lyase belongs to the emerging superfamily of radical S-adenosyl-l-methionine (SAM) enzymes and uses a [4Fe-4S](1+) cluster and SAM to initiate the repair reaction. We report here the first crystal structure of this enigmatic enzyme in complex with its [4Fe-4S] cluster and its SAM cofactor, in the absence and presence of a DNA lesion, the dinucleoside SP. The high resolution structures provide fundamental insights into the active site, the DNA lesion recognition and binding which involve a β-hairpin structure. We show that SAM and a conserved cysteine residue are perfectly positioned in the active site for hydrogen atom abstraction from the dihydrothymine residue of the lesion and donation to the α-thyminyl radical moiety, respectively. Based on structural and biochemical characterizations of mutant proteins, we substantiate the role of this cysteine in the enzymatic mechanism. Our structure reveals how SP lyase combines specific features of radical SAM and DNA repair enzymes to enable a complex radical-based repair reaction to take place.

  • Organizational Affiliation

    Department of Biomolecular Mechanisms, Max-Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany. Alhosna.Benjdia@mpimf-heidelberg.mpg.de

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Spore photoproduct lyase368Geobacillus thermodenitrificans NG80-2Mutation(s): 0 
Gene Names: GTNG_2348
Find proteins for A4IQU1 (Geobacillus thermodenitrificans (strain NG80-2))
Explore A4IQU1 
Go to UniProtKB:  A4IQU1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA4IQU1
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on EEM

Download Ideal Coordinates CCD File 
C [auth A][(3S)-3-amino-4-hydroxy-4-oxo-butyl]-[[(2S,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methyl]-methyl-selanium
C15 H23 N6 O5 Se
Query on SF4

Download Ideal Coordinates CCD File 
Fe4 S4
Query on SO4

Download Ideal Coordinates CCD File 
D [auth A]
E [auth A]
F [auth A]
G [auth A]
H [auth A]
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A]
O4 S
Query on EDO

Download Ideal Coordinates CCD File 
K [auth A]1,2-ETHANEDIOL
C2 H6 O2
Experimental Data & Validation

Experimental Data

  • Resolution: 2.20 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.211 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.22α = 90
b = 63.12β = 90
c = 143.96γ = 90
Software Package:
Software NamePurpose
HEIDIdata collection
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-07-18
    Type: Initial release
  • Version 1.1: 2012-10-31
    Changes: Database references
  • Version 1.2: 2024-02-28
    Changes: Data collection, Database references, Derived calculations
  • Version 1.3: 2024-04-03
    Changes: Refinement description