7T6H | pdb_00007t6h

E. coli dihydroorotate dehydrogenase

• PDB DOI: https://doi.org/10.2210/pdb7T6H/pdb

• Classification: OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli B
• Mutation(s): No 


• Deposited: 2021-12-13 Released: 2022-03-02 
• Deposition Author(s): Horwitz, S.M., Ambarian, J.A., Davis, K.M.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.42 Å
• R-Value Free: 
  0.235 (Depositor), 0.234 (DCC) 
• R-Value Work: 
  0.200 (Depositor), 0.201 (DCC) 
• R-Value Observed: 
  0.202 (Depositor) 

Literature

Structural insights into inhibition of the drug target dihydroorotate dehydrogenase by bacterial hydroxyalkylquinolines.

Horwitz, S.M., Blue, T.C., Ambarian, J.A., Hoshino, S., Seyedsayamdost, M.R., Davis, K.M.

(2022) RSC Chem Biol 3: 420-425

• PubMed: 35441142 
• DOI: https://doi.org/10.1039/d1cb00255d
• Primary Citation Related Structures: 
  7T5K, 7T5Y, 7T6C, 7T6H


• PubMed Abstract: 
  

  Hydroxyalkylquinolines (HAQs) are ubiquitious natural products but their interactions with associated protein targets remain elusive. We report X-ray crystal structures of two HAQs in complex with dihydroorotate dehydrogenase (DHODH). Our results reveal the structural basis of DHODH inhibition by HAQs and open the door to downstream structure-activity relationship studies.

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Organizational Affiliation: 
• Department of Chemistry, Emory University Atlanta GA 30322 USA [e-mail].
Department of Chemistry, Princeton University Princeton NJ 08544 USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 81.8 kDa 
• Atom Count: 5,343 
• Modeled Residue Count: 670 
• Deposited Residue Count: 736 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydroorotate dehydrogenase (quinone)	A, B	368	Escherichia coli K-12	Mutation(s): 0  Gene Names: pyrD, b0945, JW0928 EC: 1.3.5.2
UniProt
Find proteins for P0A7E1 (Escherichia coli (strain K12)) Explore P0A7E1  Go to UniProtKB:  P0A7E1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FMN (Subject of Investigation/LOI)	D [auth A], F [auth B]	FLAVIN MONONUCLEOTIDE C17 H21 N4 O9 P FVTCRASFADXXNN-SCRDCRAPSA-N
ORO (Subject of Investigation/LOI)	C [auth A], E [auth B]	OROTIC ACID C5 H4 N2 O4 PXQPEWDEAKTCGB-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.42 Å
• R-Value Free:  0.235 (Depositor), 0.234 (DCC) 
• R-Value Work:  0.200 (Depositor), 0.201 (DCC) 
• R-Value Observed: 0.202 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.525	α = 90
b = 169.495	β = 90
c = 129.984	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Coot	model building
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-03-02 
Deposition Author(s): Horwitz, S.M., Ambarian, J.A., Davis, K.M.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	--

Revision History  

• Version 1.0: 2022-03-02
  Type: Initial release
  
• Version 1.1: 2022-06-29
  Changes: Database references
• Version 1.2: 2024-02-28
  Changes: Data collection