5H1O

CRISPR-associated protein

PDB DOI: 10.2210/pdb5H1O/pdb

Classification: HYDROLASE
Organism(s): Xanthomonas albilineans GPE PC73
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2016-10-11 Released: 2017-10-18
Deposition Author(s): Ka, D., Jeong, U., Bae, E.
Funding Organization(s): Rural Development Administration

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free: 0.205
R-Value Work: 0.166
R-Value Observed: 0.168

wwPDB Validation 3D Report Full Report

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

Literature

Structural and dynamic insights into the role of conformational switching in the nuclease activity of the Xanthomonas albilineans Cas2 in CRISPR-mediated adaptive immunity

Ka, D., Hong, S., Jeong, U., Jeong, M., Suh, N., Suh, J.Y., Bae, E.

(2017) Struct Dyn 4: 054701-054701

PubMed: 28612041 Search on PubMedSearch on PubMed Central
DOI: 10.1063/1.4984052
Primary Citation of Related Structures:
5H1O, 5H1P

PubMed Abstract:

Clustered regularly interspaced short palindromic repeats (CRISPRs) and CRISPR-associated (Cas) proteins constitute a microbial, adaptive immune system countering invading nucleic acids. Cas2 is a universal Cas protein found in all types of CRISPR-Cas systems, and its role is implicated in new spacer acquisition into CRISPR loci. In subtype I-C CRISPR-Cas systems, Cas2 proteins are metal-dependent double-stranded DNA (dsDNA) nucleases, and a pH-dependent conformational transition has been proposed as a prerequisite for catalytic action. Here, we report the crystal structure of Xanthomonas albilineans Cas2 (XaCas2) and provide experimental evidence of a pH-dependent conformational change during functional activation. XaCas2 crystallized at an acidic pH represented a catalytically inactive conformational state in which two Asp8 residues were too far apart to coordinate a single catalytic metal ion. Consistently, XaCas2 exhibited dsDNA nuclease activity only under neutral and basic conditions. Despite the overall structural similarity of the two protomers, significant conformational heterogeneity was evident in the putative hinge regions, suggesting that XaCas2 engages in hinge-bending conformational switching. The presence of a Trp residue in the hinge region enabled the investigation of hinge dynamics by fluorescence spectroscopy. The pH dependence of the fluorescence intensity overlapped precisely with that of nuclease activity. Mutational analyses further suggested that conformational activation proceeded via a rigid-body hinge-bending motion as both D8E and hinge mutations significantly reduced nuclease activity. Together, our results reveal strong correlations between the conformational states, catalytic activity, and hinge dynamics of XaCas2, and provide structural and dynamic insights into the conformational activation of the nuclease function of Cas2.

Organizational Affiliation:

Department of Pharmaceutical Engineering, Soon Chun Hyang University, Asan 31538, South Korea.

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CRISPR-associated endoribonuclease Cas2	A, B	104	Xanthomonas albilineans GPE PC73	Mutation(s): 0 Gene Names: cas2, XALc_2892 EC: 3.1
UniProt
Find proteins for D2UG58 (Xanthomonas albilineans (strain GPE PC73 / CFBP 7063)) Explore D2UG58 Go to UniProtKB: D2UG58
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	D2UG58
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A]	C [auth A], D [auth A], E [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Ligand Interaction