5XNW

Crystal structure of ExoY, a unique nucleotidyl cyclase toxin from Pseudomonas aeruginosa

PDB DOI: https://doi.org/10.2210/pdb5XNW/pdb

Classification: LYASE
Organism(s): Pseudomonas aeruginosa
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2017-05-24 Released: 2018-05-30
Deposition Author(s): Khanppnavar, B., Datta, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.228
R-Value Work: 0.190
R-Value Observed: 0.194

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure and substrate specificity of ExoY, a unique T3SS mediated secreted nucleotidyl cyclase toxin from Pseudomonas aeruginosa

Khanppnavar, B., Datta, S.

(2018) Biochim Biophys Acta 1862: 2090-2103

PubMed: 29859257 Search on PubMed
DOI: https://doi.org/10.1016/j.bbagen.2018.05.021
Primary Citation of Related Structures:
5XNW

PubMed Abstract:
The nucleotidyl cyclase toxin ExoY is an important virulence determinant of Pseudomonas aeruginosa that causes severe acute and chronic infections in immune-compromised individuals. Additionally, this unique T3SS effector shows a striking preference for cUMP, a newly identified non-canonical secondary messenger. Thereby, ExoY is also considered as a potential tool to study unexplored cUMP signaling pathways.

Organizational Affiliation

Department of Structural Biology and Bioinformatics, CSIR-Indian Institute of Chemical Biology (CSIR-IICB), Kolkata, India; Academy of Scientific and Innovative Research (AcSIR), India.

Macromolecule Content

Total Structure Weight: 42.07 kDa
Atom Count: 2,267
Modelled Residue Count: 271
Deposited Residue Count: 378
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Adenylate cyclase ExoY	A	378	Pseudomonas aeruginosa	Mutation(s): 0 Gene Names: exoY, PA2191
UniProt
Find proteins for Q9I1S4 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore Q9I1S4 Go to UniProtKB: Q9I1S4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9I1S4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A]	D [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A]	B [auth A], C [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.228
R-Value Work: 0.190
R-Value Observed: 0.194
Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.621	α = 90
b = 92.621	β = 90
c = 66.022	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
HKL-2000	data reduction
MR-Rosetta	phasing
PDB_EXTRACT	data extraction
HKL	data scaling

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2018-05-30

Deposition Author(s):

Khanppnavar, B.

Datta, S.

Funding Organization	Location	Grant Number
	India	--
	India	--

Revision History (Full details and data files)

Version 1.0: 2018-05-30
Type: Initial release
Version 1.1: 2018-06-20
Changes: Data collection, Database references
Version 1.2: 2018-08-01
Changes: Data collection, Database references
Version 1.3: 2023-11-22
Changes: Data collection, Database references, Refinement description