4G10 | pdb_00004g10

LigG from Sphingobium sp. SYK-6 is related to the glutathione transferase omega class

PDB DOI: https://doi.org/10.2210/pdb4G10/pdb

Classification: TRANSFERASE
Organism(s): Sphingomonas paucimobilis
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2012-07-10 Released: 2012-10-03
Deposition Author(s): Meux, E., Prosper, P., Masai, E., Mulliert Carlin, G., Dumarcay, S., Morel, M., Didierjean, C., Gelhaye, E., Favier, F.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.20 Å
R-Value Free:
0.155 (Depositor), 0.155 (DCC)
R-Value Work:
0.140 (Depositor), 0.140 (DCC)
R-Value Observed:
0.140 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Sphingobium sp. SYK-6 LigG involved in lignin degradation is structurally and biochemically related to the glutathione transferase omega class.

Meux, E., Prosper, P., Masai, E., Mulliert, G., Dumarcay, S., Morel, M., Didierjean, C., Gelhaye, E., Favier, F.

(2012) FEBS Lett 586: 3944-3950

PubMed: 23058289 Search on PubMed
DOI: https://doi.org/10.1016/j.febslet.2012.09.036
Primary Citation Related Structures:
4G10

PubMed Abstract:
SpLigG is one of the three glutathione transferases (GSTs) involved in the process of lignin breakdown in the soil bacterium Sphingobium sp. SYK-6. Sequence comparisons showed that SpLigG and several proteobacteria homologues form an independent cluster within cysteine-containing GSTs. The relationship between SpLigG and other GSTs was investigated. The X-ray structure and biochemical properties of SpLigG indicate that this enzyme belongs to the omega class of glutathione transferases. However, the hydrophilic substrate binding site of SpLigG, together with its known ability to stereoselectively deglutathionylate the physiological substrate α-glutathionyl-β-hydroxypropiovanillone, argues for broadening the definition of the omega class.

Organizational Affiliation

Université de Lorraine, IAM, UMR 1136, IFR 110 EFABA, Vandoeuvre-les-Nancy, F-54506, France.

Macromolecule Content

Total Structure Weight: 31.2 kDa
Atom Count: 2,626
Modeled Residue Count: 263
Deposited Residue Count: 265
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutathione S-transferase homolog	A	265	Sphingomonas paucimobilis	Mutation(s): 0 Gene Names: ligG
UniProt
Find proteins for Q9WXJ9 (Sphingomonas paucimobilis) Explore Q9WXJ9 Go to UniProtKB: Q9WXJ9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9WXJ9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GSH Query on GSH Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	Glutathione C₁₀ H₁₇ N₃ O₆ S RWSXRVCMGQZWBV-WDSKDSINSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF 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]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Biologically Interesting Molecules (External Reference)

1 Unique

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.20 Å
R-Value Free: 0.155 (Depositor), 0.155 (DCC)
R-Value Work: 0.140 (Depositor), 0.140 (DCC)
R-Value Observed: 0.140 (Depositor)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.801	α = 90
b = 56.801	β = 90
c = 183.73	γ = 90

Software Package:

Software Name	Purpose
X-NEMO	data collection
SHELXCD	phasing
SHELXE	model building
PHENIX	refinement
XDS	data reduction
SCALA	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2012-10-03

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-10-03
Type: Initial release
Version 1.1: 2012-12-12
Changes: Database references
Version 1.2: 2017-11-15
Changes: Refinement description
Version 1.3: 2025-03-26
Changes: Data collection, Database references, Derived calculations, Structure summary