3WD6 | pdb_00003wd6

Crystal structure of Bombyx mori omega-class glutathione transferase in complex with GSH

PDB DOI: https://doi.org/10.2210/pdb3WD6/pdb

Classification: TRANSFERASE
Organism(s): Bombyx mori
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2013-06-07 Released: 2014-07-16
Deposition Author(s): Yamamoto, K., Suzuki, M., Higashiura, A., Nakagawa, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.256 (Depositor), 0.245 (DCC)
R-Value Work:
0.208 (Depositor), 0.201 (DCC)
R-Value Observed:
0.210 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Three-dimensional structure of a Bombyx mori Omega-class glutathione transferase.

Yamamoto, K., Suzuki, M., Higashiura, A., Nakagawa, A.

(2013) Biochem Biophys Res Commun 438: 588-593

PubMed: 23939046 Search on PubMed
DOI: https://doi.org/10.1016/j.bbrc.2013.08.011
Primary Citation Related Structures:
3WD6

PubMed Abstract:
Glutathione transferases (GSTs) are major phase II detoxification enzymes that play central roles in the defense against various environmental toxicants as well as oxidative stress. Here we report the crystal structure of an Omega-class glutathione transferase of Bombyx mori, bmGSTO, to gain insight into its catalytic mechanism. The structure of bmGSTO complexed with glutathione determined at a resolution of 2.5Å reveals that it exists as a dimer and is structurally similar to Omega-class GSTs with respect to its secondary and tertiary structures. Analysis of a complex between bmGSTO and glutathione showed that bound glutathione was localized to the glutathione-binding site (G-site). Site-directed mutagenesis of bmGSTO mutants indicated that amino acid residues Leu62, Lys65, Lys77, Val78, Glu91 and Ser92 in the G-site contribute to catalytic activity.

Organizational Affiliation

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

Macromolecule Content

Total Structure Weight: 121.6 kDa
Atom Count: 8,416
Modeled Residue Count: 966
Deposited Residue Count: 1,024
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Omega-class glutathione S-transferase	A, B, C, D	256	Bombyx mori	Mutation(s): 0 Gene Names: gsto, GSTo2
UniProt
Find proteins for A8R5V3 (Bombyx mori) Explore A8R5V3 Go to UniProtKB: A8R5V3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A8R5V3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GSH Query on GSH Download:Ideal Coordinates CCD File SDF format, chain X [auth D] SDF format, chain T [auth C] SDF format, chain N [auth B] SDF format, chain J [auth A] MOL2 format, chain X [auth D] MOL2 format, chain T [auth C] MOL2 format, chain N [auth B] MOL2 format, chain J [auth A] mmCIF format, chain X [auth D] mmCIF format, chain T [auth C] mmCIF format, chain N [auth B] mmCIF format, chain J [auth A]	J [auth A], N [auth B], T [auth C], X [auth D]	Glutathione C₁₀ H₁₇ N₃ O₆ S RWSXRVCMGQZWBV-WDSKDSINSA-N		Interactions Focus chain J [auth A] Focus chain N [auth B] Focus chain T [auth C] Focus chain X [auth D] Interactions & Density Focus chain J [auth A] Focus chain N [auth B] Focus chain T [auth C] Focus chain X [auth D]
IOD Query on IOD Download:Ideal Coordinates CCD File SDF format, chain U [auth D] SDF format, chain O [auth C] MOL2 format, chain U [auth D] MOL2 format, chain O [auth C] mmCIF format, chain U [auth D] mmCIF format, chain O [auth C]	O [auth C], U [auth D]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M		Interactions Focus chain O [auth C] Focus chain U [auth D] Interactions & Density Focus chain O [auth C] Focus chain U [auth D]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A] mmCIF format, chain I [auth A]	I [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain W [auth D] SDF format, chain S [auth C] SDF format, chain R [auth C] SDF format, chain M [auth B] SDF format, chain H [auth A] MOL2 format, chain W [auth D] MOL2 format, chain S [auth C] MOL2 format, chain R [auth C] MOL2 format, chain M [auth B] MOL2 format, chain H [auth A] mmCIF format, chain W [auth D] mmCIF format, chain S [auth C] mmCIF format, chain R [auth C] mmCIF format, chain M [auth B] mmCIF format, chain H [auth A]	H [auth A], M [auth B], R [auth C], S [auth C], W [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain M [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain W [auth D] Interactions & Density Focus chain H [auth A] Focus chain M [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain W [auth D]
K Query on K Download:Ideal Coordinates CCD File SDF format, chain V [auth D] SDF format, chain Q [auth C] SDF format, chain P [auth C] SDF format, chain L [auth B] SDF format, chain K [auth B] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain V [auth D] MOL2 format, chain Q [auth C] MOL2 format, chain P [auth C] MOL2 format, chain L [auth B] MOL2 format, chain K [auth B] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain V [auth D] mmCIF format, chain Q [auth C] mmCIF format, chain P [auth C] mmCIF format, chain L [auth B] mmCIF format, chain K [auth B] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A] F [auth A] G [auth A] K [auth B] L [auth B] E [auth A], F [auth A], G [auth A], K [auth B], L [auth B], P [auth C], Q [auth C], V [auth D]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain P [auth C] Focus chain Q [auth C] Focus chain V [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain P [auth C] Focus chain Q [auth C] Focus chain V [auth D]

Biologically Interesting Molecules (External Reference)

1 Unique

Entity ID: 5
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_002593 (GSH) Query on PRD_002593	J [auth A], N [auth B], T [auth C], X [auth D]	Glutathione	Peptide-like / Oxidation-reduction		Interactions Focus chain J [auth A] Focus chain N [auth B] Focus chain T [auth C] Focus chain X [auth D] Interactions & Density Focus chain J [auth A] Focus chain N [auth B] Focus chain T [auth C] Focus chain X [auth D]