8EVN | pdb_00008evn

Sulfatase from Mycobacterium tuberculosis (Rv3406) in complex with N-oxalylglycine (NOG)

PDB DOI: https://doi.org/10.2210/pdb8EVN/pdb

Classification: OXIDOREDUCTASE/INHIBITOR
Organism(s): Mycobacterium tuberculosis
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2022-10-20 Released: 2023-10-25
Deposition Author(s): Juan, T.-J., Leung, I., Squire, C.J.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.64 Å
R-Value Free:
0.299 (Depositor), 0.314 (DCC)
R-Value Work:
0.250 (Depositor), 0.267 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structural remodelling of the 2OG oxygenase Rv3406 enables sulfur-scavenging in Mycobacterium tuberculosis.

Juan, V.T., Bajan, P., Eurtivong, C., Liu, T., Squire, C.J., Huang, E.Y., Leung, I.K.H.

(2025) Chem Commun (Camb) 61: 19020-19023

PubMed: 41178574 Search on PubMed
DOI: https://doi.org/10.1039/d5cc05573c
Primary Citation Related Structures:
8EVN

PubMed Abstract:
Rv3406 evolved from the ubiquitous taurine-catabolising enzyme TauD and functions as a sulfur-scavenging protein in Mycobacterium tuberculosis . Structural and biochemical analyses reveal specific changes that shape its chemical environment for ligand interaction and explain its broad substrate range. These findings show how amino acid substitutions redefine protein function and drive adaptation to the unique metabolic context of Mycobacteria.

Organizational Affiliation

School of Chemical Sciences, The University of Auckland, Auckland, 1142, New Zealand.

Macromolecule Content

Total Structure Weight: 132.55 kDa
Atom Count: 7,292
Modeled Residue Count: 943
Deposited Residue Count: 1,192
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha-ketoglutarate-dependent sulfate ester dioxygenase	A, B, C, D	298	Mycobacterium tuberculosis	Mutation(s): 0 Gene Names: Rv3406, MTCY78.22c EC: 1.14.11 (PDB Primary Data), 1.14.11.77 (UniProt)
UniProt
Find proteins for P9WKZ1 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WKZ1 Go to UniProtKB: P9WKZ1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P9WKZ1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
OGA (Subject of Investigation/LOI) Query on OGA Download:Ideal Coordinates CCD File SDF format, chain K [auth D] SDF format, chain I [auth C] SDF format, chain G [auth B] SDF format, chain E [auth A] MOL2 format, chain K [auth D] MOL2 format, chain I [auth C] MOL2 format, chain G [auth B] MOL2 format, chain E [auth A] mmCIF format, chain K [auth D] mmCIF format, chain I [auth C] mmCIF format, chain G [auth B] mmCIF format, chain E [auth A]	E [auth A], G [auth B], I [auth C], K [auth D]	N-OXALYLGLYCINE C₄ H₅ N O₅ BIMZLRFONYSTPT-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D]
TRS Query on TRS Download:Ideal Coordinates CCD File SDF format, chain L [auth D] MOL2 format, chain L [auth D] mmCIF format, chain L [auth D]	L [auth D]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain L [auth D] Interactions & Density Focus chain L [auth D]
NI Query on NI Download:Ideal Coordinates CCD File SDF format, chain M [auth D] SDF format, chain J [auth C] SDF format, chain H [auth B] SDF format, chain F [auth A] MOL2 format, chain M [auth D] MOL2 format, chain J [auth C] MOL2 format, chain H [auth B] MOL2 format, chain F [auth A] mmCIF format, chain M [auth D] mmCIF format, chain J [auth C] mmCIF format, chain H [auth B] mmCIF format, chain F [auth A]	F [auth A], H [auth B], J [auth C], M [auth D]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain M [auth D] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain M [auth D]