7JTA | pdb_00007jta

Crystal structure of a putative nuclease with anti-Cas9 activity from an uncultured Clostridia bacterium

PDB DOI: https://doi.org/10.2210/pdb7JTA/pdb

Classification: UNKNOWN FUNCTION
Organism(s): Clostridia bacterium
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2020-08-17 Released: 2021-09-22
Deposition Author(s): Werther, R., Forsberg, K.J., Stoddard, B.L.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free:
0.246 (Depositor), 0.250 (DCC)
R-Value Work:
0.222 (Depositor), 0.220 (DCC)
R-Value Observed:
0.225 (Depositor)

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

This is version 1.3 of the entry. See complete history.

Literature

The novel anti-CRISPR AcrIIA22 relieves DNA torsion in target plasmids and impairs SpyCas9 activity.

Forsberg, K.J., Schmidtke, D.T., Werther, R., Uribe, R.V., Hausman, D., Sommer, M.O.A., Stoddard, B.L., Kaiser, B.K., Malik, H.S.

(2021) PLoS Biol 19: e3001428-e3001428

PubMed: 34644300 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1371/journal.pbio.3001428
Primary Citation of Related Structures:
7JTA

PubMed Abstract:
To overcome CRISPR-Cas defense systems, many phages and mobile genetic elements (MGEs) encode CRISPR-Cas inhibitors called anti-CRISPRs (Acrs). Nearly all characterized Acrs directly bind Cas proteins to inactivate CRISPR immunity. Here, using functional metagenomic selection, we describe AcrIIA22, an unconventional Acr found in hypervariable genomic regions of clostridial bacteria and their prophages from human gut microbiomes. AcrIIA22 does not bind strongly to SpyCas9 but nonetheless potently inhibits its activity against plasmids. To gain insight into its mechanism, we obtained an X-ray crystal structure of AcrIIA22, which revealed homology to PC4-like nucleic acid-binding proteins. Based on mutational analyses and functional assays, we deduced that acrIIA22 encodes a DNA nickase that relieves torsional stress in supercoiled plasmids. This may render them less susceptible to SpyCas9, which uses free energy from negative supercoils to form stable R-loops. Modifying DNA topology may provide an additional route to CRISPR-Cas resistance in phages and MGEs.

Organizational Affiliation

Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America.

Macromolecule Content

Total Structure Weight: 13.34 kDa
Atom Count: 849
Modeled Residue Count: 112
Deposited Residue Count: 118
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NTF2-like nuclease/anti-CRISPR	A, B	59	Clostridia bacterium	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MPD Query on MPD Download Ideal Coordinates CCD File SDF format, chain J [auth B] MOL2 format, chain J [auth B] mmCIF format, chain J [auth B]	J [auth B]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain J [auth B] Interactions & Density Focus chain J [auth B]
NO3 Query on NO3 Download Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain H [auth B] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain I [auth B] MOL2 format, chain H [auth B] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain I [auth B] mmCIF format, chain H [auth B] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A] D [auth A] E [auth A] F [auth A] G [auth A] C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth B], I [auth B]	NITRATE ION N O₃ NHNBFGGVMKEFGY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth B] Focus chain I [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth B] Focus chain I [auth B]