8OFW | pdb_00008ofw

Crystal structure of the full-length dihydroorotate dehydrogenase from Mycobacterium tuberculosis

• PDB DOI: https://doi.org/10.2210/pdb8OFW/pdb

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


• Deposited: 2023-03-17 Released: 2023-09-06 
• Deposition Author(s): Alberti, M., Ferraris, D.M., Miggiano, R.
• Funding Organization(s): Ministero dell Universita e della Ricerca

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.80 Å
• R-Value Free: 
  0.328 (Depositor), 0.331 (DCC) 
• R-Value Work: 
  0.255 (Depositor), 0.257 (DCC) 

Starting Model: in silico

Literature

Biochemical characterization of Mycobacterium tuberculosis dihydroorotate dehydrogenase and identification of a selective inhibitor.

Alberti, M., Sainas, S., Ronchi, E., Lolli, M.L., Boschi, D., Rizzi, M., Ferraris, D.M., Miggiano, R.

(2023) FEBS Lett 597: 2119-2132

• PubMed: 37278160 
• DOI: https://doi.org/10.1002/1873-3468.14680
• Primary Citation Related Structures: 
  8OFW


• PubMed Abstract: 
  

  Mycobacterium tuberculosis (MTB) is the etiologic agent of tuberculosis (TB), an ancient disease which causes 1.5 million deaths worldwide. Dihydroorotate dehydrogenase (DHODH) is a key enzyme of the MTB de novo pyrimidine biosynthesis pathway, and it is essential for MTB growth in vitro, hence representing a promising drug target. We present: (i) the biochemical characterization of the full-length MTB DHODH, including the analysis of the kinetic parameters, and (ii) the previously unreleased crystal structure of the protein that allowed us to rationally screen our in-house chemical library and identify the first selective inhibitor of mycobacterial DHODH. The inhibitor has fluorescence properties, potentially instrumental to in cellulo imaging studies, and exhibits an IC ₅₀ value of 43 μm, paving the way to hit-to-lead process.

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Organizational Affiliation: 
• Department of Pharmaceutical Sciences, University of Eastern Piedmont, Novara, Italy.
Department of Sciences and Drug Technology, University of Turin, Torino, Italy.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 81.35 kDa 
• Atom Count: 5,254 
• Modeled Residue Count: 692 
• Deposited Residue Count: 754 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydroorotate dehydrogenase (quinone)	A, B	377	Mycobacterium tuberculosis	Mutation(s): 0  Gene Names: pyrD, Rv2139, MTCY270.29c EC: 1.3.5.2
UniProt
Find proteins for P9WHL1 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WHL1  Go to UniProtKB:  P9WHL1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FMN (Subject of Investigation/LOI)	C [auth A], D [auth B]	FLAVIN MONONUCLEOTIDE C17 H21 N4 O9 P FVTCRASFADXXNN-SCRDCRAPSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.80 Å
• R-Value Free:  0.328 (Depositor), 0.331 (DCC) 
• R-Value Work:  0.255 (Depositor), 0.257 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.05	α = 90
b = 85.215	β = 90
c = 181.005	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-09-06 
Deposition Author(s): Alberti, M., Ferraris, D.M., Miggiano, R.

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Funding Organization	Location	Grant Number
Ministero dell Universita e della Ricerca	Italy	--

Revision History  

• Version 1.0: 2023-09-06
  Type: Initial release