4Q9N | pdb_00004q9n

Crystal structure of Chlamydia trachomatis enoyl-ACP reductase (FabI) in complex with NADH and AFN-1252

• PDB DOI: https://doi.org/10.2210/pdb4Q9N/pdb

• Classification: oxidoreductase/oxidoreductase inhibitor
• Organism(s): Chlamydia trachomatis F/11-96
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-05-01 Released: 2014-06-25 
• Deposition Author(s): Yao, J., Abdelrahman, Y., Robertson, R.M., Cox, J.V., Belland, R.J., White, S.W., Rock, C.O.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.79 Å
• R-Value Free: 
  0.229 (Depositor), 0.223 (DCC) 
• R-Value Work: 
  0.186 (Depositor), 0.181 (DCC) 
• R-Value Observed: 
  0.188 (Depositor) 

Starting Model: experimental

Literature

Type II Fatty Acid Synthesis Is Essential for the Replication of Chlamydia trachomatis.

Yao, J., Abdelrahman, Y.M., Robertson, R.M., Cox, J.V., Belland, R.J., White, S.W., Rock, C.O.

(2014) J Biological Chem 289: 22365-22376

• PubMed: 24958721 
• DOI: https://doi.org/10.1074/jbc.M114.584185
• Primary Citation Related Structures: 
  4Q9N


• PubMed Abstract: 
  

  The major phospholipid classes of the obligate intracellular bacterial parasite Chlamydia trachomatis are the same as its eukaryotic host except that they also contain chlamydia-made branched-chain fatty acids in the 2-position. Genomic analysis predicts that C. trachomatis is capable of type II fatty acid synthesis (FASII). AFN-1252 was deployed as a chemical tool to specifically inhibit the enoyl-acyl carrier protein reductase (FabI) of C. trachomatis to determine whether chlamydial FASII is essential for replication within the host. The C. trachomatis FabI (CtFabI) is a homotetramer and exhibited typical FabI kinetics, and its expression complemented an Escherichia coli fabI(Ts) strain. AFN-1252 inhibited CtFabI by binding to the FabI·NADH complex with an IC50 of 0.9 μM at saturating substrate concentration. The x-ray crystal structure of the CtFabI·NADH·AFN-1252 ternary complex revealed the specific interactions between the drug, protein, and cofactor within the substrate binding site. AFN-1252 treatment of C. trachomatis-infected HeLa cells at any point in the infectious cycle caused a decrease in infectious titers that correlated with a decrease in branched-chain fatty acid biosynthesis. AFN-1252 treatment at the time of infection prevented the first cell division of C. trachomatis, although the cell morphology suggested differentiation into a metabolically active reticulate body. These results demonstrate that FASII activity is essential for C. trachomatis proliferation within its eukaryotic host and validate CtFabI as a therapeutic target against C. trachomatis.

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Organizational Affiliation: 
• From the Departments of Infectious Diseases and.
the Department of Microbiology, Immunology, and Biochemistry, University of Tennessee Health Science Center, Memphis, Tennessee 38163, and the Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo 11562, Egypt.
Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee 48105.
the Department of Microbiology, Immunology, and Biochemistry, University of Tennessee Health Science Center, Memphis, Tennessee 38163, and.
From the Departments of Infectious Diseases and [e-mail].

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Biological Assembly 2  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 264.27 kDa 
• Atom Count: 19,232 
• Modeled Residue Count: 2,360 
• Deposited Residue Count: 2,384 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Enoyl-[acyl-carrier-protein] reductase [NADH]	A, B, C, D, E, F, G, H	298	Chlamydia trachomatis F/11-96	Mutation(s): 0  Gene Names: fabI(CT104), O173_00565 EC: 1.3.1.9

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAI	I [auth A], K [auth B], M [auth C], O [auth D], Q [auth E], S [auth F], U [auth G], W [auth H]	1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE C21 H29 N7 O14 P2 BOPGDPNILDQYTO-NNYOXOHSSA-N
0WE	J [auth A], L [auth B], N [auth C], P [auth D], R [auth E], T [auth F], V [auth G], X [auth H]	N-methyl-N-[(3-methyl-1-benzofuran-2-yl)methyl]-3-(7-oxo-5,6,7,8-tetrahydro-1,8-naphthyridin-3-yl)propanamide C22 H23 N3 O3 WDNCPCMRTFYNIQ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.79 Å
• R-Value Free:  0.229 (Depositor), 0.223 (DCC) 
• R-Value Work:  0.186 (Depositor), 0.181 (DCC) 
• R-Value Observed: 0.188 (Depositor) 

Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.146	α = 90
b = 96.146	β = 90
c = 263.082	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-06-25 
Deposition Author(s): Yao, J., Abdelrahman, Y., Robertson, R.M., Cox, J.V., Belland, R.J., White, S.W., Rock, C.O.

Revision History  

• Version 1.0: 2014-06-25
  Type: Initial release
  
• Version 1.1: 2014-08-27
  Changes: Database references
• Version 1.2: 2017-11-22
  Changes: Refinement description
• Version 1.3: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description