9GAB
Structure and catalytic mechanism of SAM-AMP lyase in Clostridium botulinum CorA-associated type III CRISPR system
This is a non-PDB format compatible entry.
Summary for 9GAB
| Entry DOI | 10.2210/pdb9gab/pdb |
| Descriptor | SAM-AMP Lyase, [(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl [(2~{S},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-2-(methylsulfanylmethyl)-4-oxidanyl-oxolan-3-yl] hydrogen phosphate, (4S)-2-METHYL-2,4-PENTANEDIOL, ... (4 entities in total) |
| Functional Keywords | type iii crispr, lyase |
| Biological source | Clostridium botulinum |
| Total number of polymer chains | 6 |
| Total formula weight | 93298.52 |
| Authors | McMahon, S.A.,Chi, H.,Gloster, T.M.,White, M.F.,Graham, S. (deposition date: 2024-07-26, release date: 2025-07-02, Last modification date: 2025-07-23) |
| Primary citation | Chi, H.,McMahon, S.,Daniel-Pedersen, L.,Graham, S.,Gloster, T.M.,White, M.F. SAM-AMP lyases in type III CRISPR defence. Nucleic Acids Res., 53:-, 2025 Cited by PubMed Abstract: Type III CRISPR systems detect non-self RNA and activate the enzymatic Cas10 subunit, which generates nucleotide second messengers for activation of ancillary effectors. Although most signal via cyclic oligoadenylate, an alternative class of signalling molecule SAM-AMP, formed by conjugating ATP and S-adenosylmethionine, was described recently. SAM-AMP activates a trans-membrane effector of the CorA magnesium transporter family to provide anti-phage defence. Intriguingly, immunity also requires SAM-AMP degradation by means of a specialized CRISPR-encoded NrN family phosphodiesterase in Bacteroides fragilis. In Clostridium botulinum, the nrn gene is replaced by a gene encoding a SAM-AMP lyase. Here, we investigate the structure and activity of C. botulinum SAM-AMP lyase, which can substitute for the nrn gene to provide CorA-mediated immunity in Escherichia coli. The structure of SAM-AMP lyase bound to its reaction product 5'-methylthioadenosine-AMP reveals key details of substrate binding and turnover by this PII superfamily protein. Bioinformatic analysis revealed a phage-encoded SAM-AMP lyase that degrades SAM-AMP efficiently in vitro, consistent with an anti-CRISPR function. PubMed: 40650973DOI: 10.1093/nar/gkaf655 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.65 Å) |
Structure validation
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