4FHG

Spore photoproduct lyase C140S mutant

Summary for 4FHG

• Entry DOI: 10.2210/pdb4fhg/pdb
• Related: 4FHC 4FHD 4FHE 4FHF
• Descriptor: Spore photoproduct lyase, IRON/SULFUR CLUSTER, [(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, ... (6 entities in total)
• Functional Keywords: partial tim-barrel, dna repair, damaged dna, lyase
• Biological source: Geobacillus thermodenitrificans
• Total number of polymer chains: 1
• Total formula weight: 44204.14

Authors

Benjdia, A.,Heil, K.,Barends, T.R.M.,Carell, T.,Schlichting, I. (deposition date: 2012-06-06, release date: 2012-07-18, Last modification date: 2024-04-03)

Primary citation

Benjdia, A.,Heil, K.,Barends, T.R.,Carell, T.,Schlichting, I.
Structural insights into recognition and repair of UV-DNA damage by Spore Photoproduct Lyase, a radical SAM enzyme.
Nucleic Acids Res., 40:9308-9318, 2012

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.

PubMed: 22761404
DOI: 10.1093/nar/gks603

Experimental method

X-RAY DIFFRACTION (2 Å)