4XJR

The catalytic mechanism of human parainfluenza virus type 3 haemagglutinin-neuraminidase revealed

PDB DOI: https://doi.org/10.2210/pdb4XJR/pdb

Classification: HYDROLASE
Organism(s): Human respirovirus 3
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2015-01-08 Released: 2015-02-11
Deposition Author(s): Dirr, L., El-Deeb, I., Guillon, P., Carroux, C., Chavas, L., von Itzstein, M.
Funding Organization(s): Australian Research Council (ARC), National Health and Medical Research Council (NHMRC, Australia)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free: 0.298
R-Value Work: 0.190
R-Value Observed: 0.195

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 3.1 of the entry. See complete history.

Literature

The catalytic mechanism of human parainfluenza virus type 3 haemagglutinin-neuraminidase revealed.

Dirr, L., El-Deeb, I.M., Guillon, P., Carroux, C.J., Chavas, L.M., von Itzstein, M.

(2015) Angew Chem Int Ed Engl 54: 2936-2940

PubMed: 25676091 Search on PubMed
DOI: https://doi.org/10.1002/anie.201412243
Primary Citation of Related Structures:
4XJQ, 4XJR

PubMed Abstract:
Human parainfluenza virus type 3 (hPIV-3) is one of the leading causes for lower respiratory tract disease in children, with neither an approved antiviral drug nor vaccine available to date. Understanding the catalytic mechanism of human parainfluenza virus haemagglutinin-neuraminidase (HN) protein is key to the design of specific inhibitors against this virus. Herein, we used (1) H NMR spectroscopy, X-ray crystallography, and virological assays to study the catalytic mechanism of the HN enzyme activity and have identified the conserved Tyr530 as a key amino acid involved in catalysis. A novel 2,3-difluorosialic acid derivative showed prolonged enzyme inhibition and was found to react and form a covalent bond with Tyr530. Furthermore, the novel derivative exhibited enhanced potency in virus blockade assays relative to its Neu2en analogue. These outcomes open the door for a new generation of potent inhibitors against hPIV-3 HN.

Organizational Affiliation

Institute for Glycomics, Gold Coast Campus, Griffith University, Queensland, 4222 (Australia).

Macromolecule Content

Total Structure Weight: 104.23 kDa
Atom Count: 6,869
Modelled Residue Count: 855
Deposited Residue Count: 908
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin-neuraminidase	A, B	454	Human respirovirus 3	Mutation(s): 0 EC: 3.2.1.18
UniProt
Find proteins for P08492 (Human parainfluenza 3 virus (strain Wash/47885/57)) Explore P08492 Go to UniProtKB: P08492
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P08492
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain A Focus chain B
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C	2		N-Glycosylation	Interactions Focus chain C Interactions & Density Focus chain C
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D	3		N-Glycosylation	Interactions Focus chain D Interactions & Density Focus chain D
Glycosylation Resources
GlyTouCan: G44266EX GlyCosmos: G44266EX GlyGen: G44266EX

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
OEL Query on OEL Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain K [auth B] MOL2 format, chain H [auth A] MOL2 format, chain K [auth B] mmCIF format, chain H [auth A] mmCIF format, chain K [auth B]	H [auth A], K [auth B]	(6R)-2,6-anhydro-3,4,5-trideoxy-6-[(2S)-2,3-dihydroxypropanoyl]-3-fluoro-5-[(2-methylpropanoyl)amino]-4-triaza-1,2-dien -2-ium-1-yl-L-gulonic acid C₁₃ H₂₀ F N₄ O₇ UFSBEYSJWUBWLQ-JAYUSQFOSA-O		Interactions Focus chain H [auth A] Focus chain K [auth B] Interactions & Density Focus chain H [auth A] Focus chain K [auth B]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain J [auth B] MOL2 format, chain G [auth A] MOL2 format, chain J [auth B] mmCIF format, chain G [auth A] mmCIF format, chain J [auth B]	G [auth A], J [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain G [auth A] Focus chain J [auth B] Interactions & Density Focus chain G [auth A] Focus chain J [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain L [auth B] MOL2 format, chain L [auth B] mmCIF format, chain L [auth B]	L [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain L [auth B] Interactions & Density Focus chain L [auth B]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain I [auth B] MOL2 format, chain E [auth A] MOL2 format, chain I [auth B] mmCIF format, chain E [auth A] mmCIF format, chain I [auth B]	E [auth A], I [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain I [auth B] Interactions & Density Focus chain E [auth A] Focus chain I [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free: 0.298
R-Value Work: 0.190
R-Value Observed: 0.195
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.85	α = 90
b = 98.303	β = 90
c = 103.261	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
XDS	data reduction
Aimless	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2015-02-11

Deposition Author(s):

Funding Organization	Location	Grant Number
Australian Research Council (ARC)	Australia	DP1094549
National Health and Medical Research Council (NHMRC, Australia)	Australia	ID1047824

Revision History (Full details and data files)

Version 1.0: 2015-02-11
Type: Initial release
Version 1.1: 2015-03-04
Changes: Database references
Version 2.0: 2017-09-06
Changes: Atomic model, Author supporting evidence, Data collection, Database references, Derived calculations, Source and taxonomy, Structure summary
Version 2.1: 2020-01-01
Changes: Author supporting evidence
Version 3.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
Version 3.1: 2024-11-06
Changes: Data collection, Database references, Derived calculations, Structure summary