9GAB | pdb_00009gab

Structure and catalytic mechanism of SAM-AMP lyase in Clostridium botulinum CorA-associated type III CRISPR system

PDB DOI: https://doi.org/10.2210/pdb9GAB/pdb

Classification: LYASE
Organism(s): Clostridium botulinum
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-07-26 Released: 2025-07-02
Deposition Author(s): McMahon, S.A., Chi, H., Gloster, T.M., White, M.F., Graham, S.
Funding Organization(s): Biotechnology and Biological Sciences Research Council (BBSRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free:
0.224 (Depositor), 0.236 (DCC)
R-Value Work:
0.189 (Depositor), 0.201 (DCC)
R-Value Observed:
0.191 (Depositor)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

SAM-AMP lyases in type III CRISPR defence.

Chi, H., McMahon, S., Daniel-Pedersen, L., Graham, S., Gloster, T.M., White, M.F.

(2025) Nucleic Acids Res 53

PubMed: 40650973 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1093/nar/gkaf655
Primary Citation of Related Structures:
9GAB, 9GAD

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.

Organizational Affiliation

School of Biology, University of St Andrews, St Andrews, Fife KY16 9ST, United Kingdom.

Macromolecule Content

Total Structure Weight: 93.3 kDa
Atom Count: 6,813
Modeled Residue Count: 750
Deposited Residue Count: 786
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SAM-AMP Lyase	A [auth D] B [auth A] C [auth B] D [auth C] E A [auth D], B [auth A], C [auth B], D [auth C], E, F	131	Clostridium botulinum	Mutation(s): 0 Gene Names: CBO2178
UniProt
Find proteins for A5I3U9 (Clostridium botulinum (strain Hall / ATCC 3502 / NCTC 13319 / Type A)) Explore A5I3U9 Go to UniProtKB: A5I3U9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A5I3U9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1IJB (Subject of Investigation/LOI) Query on A1IJB Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain L [auth C] SDF format, chain M [auth F] SDF format, chain K [auth B] SDF format, chain J [auth A] SDF format, chain G [auth D] MOL2 format, chain I [auth A] MOL2 format, chain L [auth C] MOL2 format, chain M [auth F] MOL2 format, chain K [auth B] MOL2 format, chain J [auth A] MOL2 format, chain G [auth D] mmCIF format, chain I [auth A] mmCIF format, chain L [auth C] mmCIF format, chain M [auth F] mmCIF format, chain K [auth B] mmCIF format, chain J [auth A] mmCIF format, chain G [auth D]	G [auth D] I [auth A] J [auth A] K [auth B] L [auth C] G [auth D], I [auth A], J [auth A], K [auth B], L [auth C], M [auth F]	[(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 C₂₁ H₂₇ N₁₀ O₉ P S NNWVUANIXUHJMY-NAGRZYTCSA-N		Interactions Focus chain G [auth D] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth B] Focus chain L [auth C] Focus chain M [auth F] Interactions & Density Focus chain G [auth D] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth B] Focus chain L [auth C] Focus chain M [auth F]
MPD Query on MPD Download Ideal Coordinates CCD File SDF format, chain N [auth F] SDF format, chain H [auth A] MOL2 format, chain N [auth F] MOL2 format, chain H [auth A] mmCIF format, chain N [auth F] mmCIF format, chain H [auth A]	H [auth A], N [auth F]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain H [auth A] Focus chain N [auth F] Interactions & Density Focus chain H [auth A] Focus chain N [auth F]