3WYW

Structural characterization of catalytic site of a Nilaparvata lugens delta-class glutathione transferase

PDB DOI: https://doi.org/10.2210/pdb3WYW/pdb

Classification: TRANSFERASE
Organism(s): Nilaparvata lugens
Mutation(s): No

Deposited: 2014-09-09 Released: 2015-01-14
Deposition Author(s): Yamamoto, K., Higashiura, A., Nakagawa, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.217
R-Value Work: 0.175
R-Value Observed: 0.177

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Structural characterization of the catalytic site of a Nilaparvata lugens delta-class glutathione transferase.

Yamamoto, K., Higashiura, A., Hossain, M.T., Yamada, N., Shiotsuki, T., Nakagawa, A.

(2014) Arch Biochem Biophys 566C: 36-42

PubMed: 25497345 Search on PubMed
DOI: https://doi.org/10.1016/j.abb.2014.12.001
Primary Citation of Related Structures:
3WYW

PubMed Abstract:
Glutathione transferases (GSTs) are a major class of detoxification enzymes that play a central role in the defense against environmental toxicants and oxidative stress. Here, we studied the crystal structure of a delta-class glutathione transferase from Nilaparvata lugens, nlGSTD, to gain insights into its catalytic mechanism. The structure of nlGSTD in complex with glutathione, determined at a resolution of 1.7Å, revealed that it exists as a dimer and its secondary and tertiary structures are similar to those of other delta-class GSTs. Analysis of a complex between nlGSTD and glutathione showed that the bound glutathione was localized to the glutathione-binding site. Site-directed mutagenesis of nlGSTD mutants indicated that amino acid residues Ser11, His52, Glu66, and Phe119 contribute to catalytic activity.

Organizational Affiliation

Faculty of Agriculture, Kyushu University Graduate School, 6-10-1 Hakozaki, Higashi-ku, Fukuoka 812-8581, Japan. Electronic address: yamamok@agr.kyushu-u.ac.jp.

Macromolecule Content

Total Structure Weight: 48.62 kDa
Atom Count: 3,795
Modelled Residue Count: 427
Deposited Residue Count: 432
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutathione S-transferase	A, B	216	Nilaparvata lugens	Mutation(s): 0
UniProt
Find proteins for Q8N0B3 (Nilaparvata lugens) Explore Q8N0B3 Go to UniProtKB: Q8N0B3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8N0B3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GSH Query on GSH Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain F [auth B] MOL2 format, chain C [auth A] MOL2 format, chain F [auth B]	C [auth A], F [auth B]	GLUTATHIONE C₁₀ H₁₇ N₃ O₆ S RWSXRVCMGQZWBV-WDSKDSINSA-N		Interactions Focus chain C [auth A] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain F [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain G [auth B] SDF format, chain H [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B]	D [auth A], E [auth A], G [auth B], H [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain G [auth B] Focus chain H [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain G [auth B] Focus chain H [auth B]