4K9R

Spore photoproduct lyase Y98F mutant

Summary for 4K9R

• Entry DOI: 10.2210/pdb4k9r/pdb
• Related: 4FHC
• 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, ... (5 entities in total)
• Functional Keywords: partial tim barrel, dna repair, lyase
• Biological source: Geobacillus thermodenitrificans
• Total number of polymer chains: 1
• Total formula weight: 44142.14

Authors

Yang, L.,Nelson, R.S.,Benjdia, A.,Lin, G.,Telser, J.,Stoll, S.,Schlichting, I.,Li, L. (deposition date: 2013-04-20, release date: 2013-05-08, Last modification date: 2024-02-28)

Primary citation

Yang, L.,Nelson, R.S.,Benjdia, A.,Lin, G.,Telser, J.,Stoll, S.,Schlichting, I.,Li, L.
A radical transfer pathway in spore photoproduct lyase.
Biochemistry, 52:3041-3050, 2013

PubMed Abstract: Spore photoproduct lyase (SPL) repairs a covalent UV-induced thymine dimer, spore photoproduct (SP), in germinating endospores and is responsible for the strong UV resistance of endospores. SPL is a radical S-adenosyl-l-methionine (SAM) enzyme, which uses a [4Fe-4S](+) cluster to reduce SAM, generating a catalytic 5'-deoxyadenosyl radical (5'-dA(•)). This in turn abstracts a H atom from SP, generating an SP radical that undergoes β scission to form a repaired 5'-thymine and a 3'-thymine allylic radical. Recent biochemical and structural data suggest that a conserved cysteine donates a H atom to the thymine radical, resulting in a putative thiyl radical. Here we present structural and biochemical data that suggest that two conserved tyrosines are also critical in enzyme catalysis. One [Y99(Bs) in Bacillus subtilis SPL] is downstream of the cysteine, suggesting that SPL uses a novel hydrogen atom transfer (HAT) pathway with a pair of cysteine and tyrosine residues to regenerate SAM. The other tyrosine [Y97(Bs)] has a structural role to facilitate SAM binding; it may also contribute to the SAM regeneration process by interacting with the putative (•)Y99(Bs) and/or 5'-dA(•) intermediates to lower the energy barrier for the second H abstraction step. Our results indicate that SPL is the first member of the radical SAM superfamily (comprising more than 44000 members) to bear a catalytically operating HAT chain.

PubMed: 23607538
DOI: 10.1021/bi3016247

Experimental method

X-RAY DIFFRACTION (2.3 Å)