9F38 | pdb_00009f38

BsmI (wild-type) crystallized with Ca2+ and cognate dsDNA

PDB DOI: https://doi.org/10.2210/pdb9F38/pdb
NAKB: 9F38

Classification: HYDROLASE
Organism(s): Geobacillus stearothermophilus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-04-25 Released: 2025-04-02
Deposition Author(s): Sieskind, R., Missoury, S., Madru, C., Commenge, I., Niogret, G., Hollenstein, M., Rondelez, Y., Haouz, A., Sauguet, L., Legrand, P., Delarue, M.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.85 Å
R-Value Free:
0.293 (Depositor), 0.290 (DCC)
R-Value Work:
0.274 (Depositor), 0.266 (DCC)
R-Value Observed:
0.275 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Crystal structures of monomeric BsmI restriction endonuclease reveal coordinated sequential cleavage of two DNA strands.

Sieskind, R., Missoury, S., Madru, C., Commenge, I., Niogret, G., Hollenstein, M., Rondelez, Y., Sauguet, L., Haouz, A., Legrand, P., Delarue, M.

(2025) Commun Biol 8: 387-387

PubMed: 40055548 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s42003-025-07612-z
Primary Citation Related Structures:
9EZ5, 9EZ7, 9EZD, 9F38

PubMed Abstract:
BsmI, a thermophilic Type IIS restriction endonuclease from Bacillus stearothermophilus, presents a unique structural composition, housing two distinct active sites within a single monomer. Recognition of the non-symmetrical 5'-GAATGC-3' sequence enables precise cleavage of the top and bottom DNA strands. Synthetic biology interventions have led to the transformation of BsmI into Nb.BsmI, a nicking endonuclease. Here we introduce Nt*.BsmI, tailored for top-strand cleavage, which is inactive on standard double-stranded DNA, but active on bottom-strand nicked DNA, suggesting a sequential cleavage mechanism. Crystallographic structures of pre- and post-reactive complexes with cognate DNA show one major conformational change, a retractable loop possibly governing sequential active site accessibility. The x-ray structures reveal the position of the divalent metal ions in the active sites and the DNA:protein interactions, while the models predicted by Alphafold3 are incorrect. This comprehensive structural and functional study lays a foundation for rational enzyme redesign and potential applications in biotechnology.

Organizational Affiliation

Institut Pasteur, Université Paris Cité, CNRS UMR 3528, Unit of Architecture and Dynamics of Biological Macromolecules, 75724, Paris, France.

Macromolecule Content

Total Structure Weight: 172.8 kDa
Atom Count: 12,289
Modeled Residue Count: 1,404
Deposited Residue Count: 1,404
Unique protein chains: 1
Unique nucleic acid chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BsmI	A, F [auth Z]	676	Geobacillus stearothermophilus	Mutation(s): 0 Gene Names: bsmIR
UniProt
Find proteins for Q8RLN4 (Geobacillus stearothermophilus) Explore Q8RLN4 Go to UniProtKB: Q8RLN4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8RLN4
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by: Sequence

Molecule	Chains	Length	Organism
Entity ID: 2
DNA (Bottom strand)	B [auth E], E [auth V]	13	Geobacillus stearothermophilus
Sequence Annotations Expand
Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 3
DNA (Top strand)	C [auth F], D [auth U]	13	Geobacillus stearothermophilus
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MES Query on MES Download:Ideal Coordinates CCD File SDF format, chain M [auth Z] MOL2 format, chain M [auth Z] mmCIF format, chain M [auth Z]	M [auth Z]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C₆ H₁₃ N O₄ S SXGZJKUKBWWHRA-UHFFFAOYSA-N		Interactions Focus chain M [auth Z]
CA (Subject of Investigation/LOI) Query on CA Download:Ideal Coordinates CCD File SDF format, chain L [auth Z] SDF format, chain K [auth Z] SDF format, chain J [auth Z] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] MOL2 format, chain L [auth Z] MOL2 format, chain K [auth Z] MOL2 format, chain J [auth Z] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] mmCIF format, chain L [auth Z] mmCIF format, chain K [auth Z] mmCIF format, chain J [auth Z] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A]	G [auth A] H [auth A] I [auth A] J [auth Z] K [auth Z] G [auth A], H [auth A], I [auth A], J [auth Z], K [auth Z], L [auth Z]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth Z] Focus chain K [auth Z] Focus chain L [auth Z]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain N [auth Z] MOL2 format, chain N [auth Z] mmCIF format, chain N [auth Z]	N [auth Z]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain N [auth Z]