7E48 | pdb_00007e48

Crystal structure of InhA in complex with 3-nitropropanoic acid inhibitor

PDB DOI: https://doi.org/10.2210/pdb7E48/pdb

Classification: OXIDOREDUCTASE
Organism(s): Mycobacterium tuberculosis H37Rv
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2021-02-10 Released: 2021-11-24
Deposition Author(s): Songsiriritthigul, C., Hanwarinroj, C., Suttipanta, N., Kamsri, P., Kittakoop, P., Pungpo, P.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.220 (Depositor), 0.227 (DCC)
R-Value Work:
0.185 (Depositor), 0.190 (DCC)

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

Inhibition of Mycobacterium tuberculosis InhA by 3-nitropropanoic acid.

Songsiriritthigul, C., Hanwarinroj, C., Pakamwong, B., Srimanote, P., Suttipanta, N., Sureram, S., Suttisintong, K., Kamsri, P., Punkvang, A., Spencer, J., Kittakoop, P., Pungpo, P.

(2022) Proteins 90: 898-904

PubMed: 34677871 Search on PubMed
DOI: https://doi.org/10.1002/prot.26268
Primary Citation Related Structures:
7E48

PubMed Abstract:
3-Nitropropanoic acid (3NP), a bioactive fungal natural product, was previously demonstrated to inhibit growth of Mycobacterium tuberculosis. Here we demonstrate that 3NP inhibits the 2-trans-enoyl-acyl carrier protein reductase (InhA) from Mycobacterium tuberculosis with an IC ₅₀ value of 71 μM, and present the crystal structure of the ternary InhA-NAD ⁺ -3NP complex. The complex contains the InhA substrate-binding loop in an ordered, open conformation with Tyr158, a catalytically important residue whose orientation defines different InhA substrate/inhibitor complex conformations, in the "out" position. 3NP occupies a hydrophobic binding site adjacent to the NAD ⁺ cofactor and close to that utilized by the diphenyl ether triclosan, but binds predominantly via electrostatic and water-mediated hydrogen-bonding interactions with the protein backbone and NAD ⁺ cofactor. The identified mode of 3NP binding provides opportunities to improve inhibitory activity toward InhA.

Organizational Affiliation

Synchrotron Light Research Institute (Public Organization), Nakhon Ratchasima, Thailand.

Macromolecule Content

Total Structure Weight: 117.44 kDa
Atom Count: 8,594
Modeled Residue Count: 1,068
Deposited Residue Count: 1,076
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Enoyl-[acyl-carrier-protein] reductase [NADH]	A, B, C, D	269	Mycobacterium tuberculosis H37Rv	Mutation(s): 0 Gene Names: inhA, Rv1484, MTCY277.05 EC: 1.3.1.9
UniProt
Find proteins for P9WGR1 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WGR1 Go to UniProtKB: P9WGR1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P9WGR1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD Query on NAD Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth B] SDF format, chain J [auth C] SDF format, chain L [auth D] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain J [auth C] MOL2 format, chain L [auth D] mmCIF format, chain E [auth A] mmCIF format, chain G [auth B] mmCIF format, chain J [auth C] mmCIF format, chain L [auth D]	E [auth A], G [auth B], J [auth C], L [auth D]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain J [auth C] Focus chain L [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain J [auth C] Focus chain L [auth D]
3NP Query on 3NP Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain K [auth C] SDF format, chain M [auth D] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain K [auth C] MOL2 format, chain M [auth D] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain K [auth C] mmCIF format, chain M [auth D]	F [auth A], H [auth B], K [auth C], M [auth D]	3-NITROPROPANOIC ACID C₃ H₅ N O₄ WBLZUCOIBUDNBV-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain M [auth D] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain M [auth D]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain I [auth B] MOL2 format, chain I [auth B] mmCIF format, chain I [auth B]	I [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain I [auth B] Interactions & Density Focus chain I [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.220 (Depositor), 0.227 (DCC)
R-Value Work: 0.185 (Depositor), 0.190 (DCC)

Space Group: P 3₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.39	α = 90
b = 96.39	β = 90
c = 139.5	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2021-11-24

Deposition Author(s):

Songsiriritthigul, C.

Revision History (Full details and data files)

Version 1.0: 2021-11-24
Type: Initial release
Version 1.1: 2022-02-23
Changes: Database references
Version 1.2: 2023-11-29
Changes: Data collection, Derived calculations, Refinement description