8U3P | pdb_00008u3p

1.79 Angstrom resolution crystal structure of KatG from Mycobacterium tuberculosis with an MYW cofactor after heat incubation for 60 minutes

PDB DOI: https://doi.org/10.2210/pdb8U3P/pdb

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

Deposited: 2023-09-08 Released: 2024-09-11
Deposition Author(s): Liu, A., Li, J., Ran, D.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.79 Å
R-Value Free:
0.220 (Depositor), 0.222 (DCC)
R-Value Work:
0.179 (Depositor), 0.180 (DCC)
R-Value Observed:
0.179 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Indole N-Linked Hydroperoxyl Adduct of Protein-Derived Cofactor Modulating Catalase-Peroxidase Functions.

Li, J., Duan, R., Traore, E.S., Nguyen, R.C., Davis, I., Griffth, W.P., Goodwin, D.C., Jarzecki, A.A., Liu, A.

(2024) Angew Chem Int Ed Engl 63: e202407018-e202407018

PubMed: 39300819 Search on PubMed
DOI: https://doi.org/10.1002/anie.202407018
Primary Citation Related Structures:
8CZP, 8U3P, 8W1W, 8W1X, 8W1Y

PubMed Abstract:
Bifunctional catalase-peroxidase (KatG) features a posttranslational methionine-tyrosine-tryptophan (MYW) crosslinked cofactor crucial for its catalase function, enabling pathogens to neutralize hydrogen peroxide during infection. We discovered the presence of indole nitrogen-linked hydroperoxyl adduct (MYW-OOH) in Mycobacterium tuberculosis KatG in the solution state under ambient conditions, suggesting its natural occurrence. By isolating predominantly MYW-OOH-containing KatG protein, we investigated the chemical stability and functional impact of MYW-OOH. We discovered that MYW-OOH inhibits catalase activity, presenting a unique temporary lock. Exposure to peroxide or increased temperature removes the hydroperoxyl adduct from the protein cofactor, converting MYW-OOH to MYW and restoring the detoxifying ability of the enzyme against hydrogen peroxide. Thus, the N-linked hydroperoxyl group is releasable. KatG with MYW-OOH represents a catalase dormant, but primed, state of the enzyme. These findings provide insight into chemical strategies targeting the bifunctional enzyme KatG in pathogens, highlighting the role of N-linked hydroperoxyl modifications in enzymatic function.

Organizational Affiliation

University of Texas at San Antonio, Chemistry, UNITED STATES.

Macromolecule Content

Total Structure Weight: 327.37 kDa
Atom Count: 25,857
Modeled Residue Count: 2,868
Deposited Residue Count: 2,964
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Catalase-peroxidase	A, B, C, D	741	Mycobacterium tuberculosis	Mutation(s): 0 Gene Names: katG EC: 1.11.1.21
UniProt
Find proteins for P9WIE5 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WIE5 Go to UniProtKB: P9WIE5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P9WIE5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM (Subject of Investigation/LOI) Query on HEM Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain M [auth B] SDF format, chain V [auth C] SDF format, chain Z [auth D] MOL2 format, chain F [auth A] MOL2 format, chain M [auth B] MOL2 format, chain V [auth C] MOL2 format, chain Z [auth D] mmCIF format, chain F [auth A] mmCIF format, chain M [auth B] mmCIF format, chain V [auth C] mmCIF format, chain Z [auth D]	F [auth A], M [auth B], V [auth C], Z [auth D]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain F [auth A] Focus chain M [auth B] Focus chain V [auth C] Focus chain Z [auth D] Interactions & Density Focus chain F [auth A] Focus chain M [auth B] Focus chain V [auth C] Focus chain Z [auth D]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain BA [auth D] SDF format, chain CA [auth D] SDF format, chain DA [auth D] SDF format, chain EA [auth D] SDF format, chain FA [auth D] SDF format, chain GA [auth D] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain W [auth C] SDF format, chain X [auth C] MOL2 format, chain BA [auth D] MOL2 format, chain CA [auth D] MOL2 format, chain DA [auth D] MOL2 format, chain EA [auth D] MOL2 format, chain FA [auth D] MOL2 format, chain GA [auth D] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain W [auth C] MOL2 format, chain X [auth C] mmCIF format, chain BA [auth D] mmCIF format, chain CA [auth D] mmCIF format, chain DA [auth D] mmCIF format, chain EA [auth D] mmCIF format, chain FA [auth D] mmCIF format, chain GA [auth D] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B] mmCIF format, chain T [auth B] mmCIF format, chain W [auth C] mmCIF format, chain X [auth C]	BA [auth D] CA [auth D] DA [auth D] EA [auth D] FA [auth D] BA [auth D], CA [auth D], DA [auth D], EA [auth D], FA [auth D], GA [auth D], H [auth A], I [auth A], J [auth A], K [auth A], P [auth B], Q [auth B], R [auth B], S [auth B], T [auth B], W [auth C], X [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain BA [auth D] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain EA [auth D] Focus chain FA [auth D] Focus chain GA [auth D] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain W [auth C] Focus chain X [auth C] Interactions & Density Focus chain BA [auth D] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain EA [auth D] Focus chain FA [auth D] Focus chain GA [auth D] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain W [auth C] Focus chain X [auth C]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain G [auth A] SDF format, chain N [auth B] SDF format, chain O [auth B] MOL2 format, chain AA [auth D] MOL2 format, chain G [auth A] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] mmCIF format, chain AA [auth D] mmCIF format, chain G [auth A] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B]	AA [auth D], G [auth A], N [auth B], O [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain AA [auth D] Focus chain G [auth A] Focus chain N [auth B] Focus chain O [auth B] Interactions & Density Focus chain AA [auth D] Focus chain G [auth A] Focus chain N [auth B] Focus chain O [auth B]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain L [auth B] SDF format, chain U [auth C] SDF format, chain Y [auth D] MOL2 format, chain E [auth A] MOL2 format, chain L [auth B] MOL2 format, chain U [auth C] MOL2 format, chain Y [auth D] mmCIF format, chain E [auth A] mmCIF format, chain L [auth B] mmCIF format, chain U [auth C] mmCIF format, chain Y [auth D]	E [auth A], L [auth B], U [auth C], Y [auth D]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain L [auth B] Focus chain U [auth C] Focus chain Y [auth D] Interactions & Density Focus chain E [auth A] Focus chain L [auth B] Focus chain U [auth C] Focus chain Y [auth D]