6CT5 | pdb_00006ct5

PptT PAP(CoA) 8918 complex

• PDB DOI: https://doi.org/10.2210/pdb6CT5/pdb

• Classification: TRANSFERASE/INHIBITOR
• Organism(s): Mycobacterium tuberculosis
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2018-03-22 Released: 2019-02-06 
• Deposition Author(s): Mosior, J., Sacchettini, J., TB Structural Genomics Consortium (TBSGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free: 
  0.198 (Depositor), 0.203 (DCC) 
• R-Value Work: 
  0.160 (Depositor) 
• R-Value Observed: 
  0.162 (Depositor) 

Starting Models: experimental

Literature

Opposing reactions in coenzyme A metabolism sensitizeMycobacterium tuberculosisto enzyme inhibition.

Ballinger, E., Mosior, J., Hartman, T., Burns-Huang, K., Gold, B., Morris, R., Goullieux, L., Blanc, I., Vaubourgeix, J., Lagrange, S., Fraisse, L., Sans, S., Couturier, C., Bacque, E., Rhee, K., Scarry, S.M., Aube, J., Yang, G., Ouerfelli, O., Schnappinger, D., Ioerger, T.R., Engelhart, C.A., McConnell, J.A., McAulay, K., Fay, A., Roubert, C., Sacchettini, J., Nathan, C.

(2019) Science 363

• PubMed: 30705156 
• DOI: https://doi.org/10.1126/science.aau8959
• Primary Citation Related Structures: 
  6CT5


• PubMed Abstract: 
  

  Mycobacterium tuberculosis (Mtb) is the leading infectious cause of death in humans. Synthesis of lipids critical for Mtb's cell wall and virulence depends on phosphopantetheinyl transferase (PptT), an enzyme that transfers 4'-phosphopantetheine (Ppt) from coenzyme A (CoA) to diverse acyl carrier proteins. We identified a compound that kills Mtb by binding and partially inhibiting PptT. Killing of Mtb by the compound is potentiated by another enzyme encoded in the same operon, Ppt hydrolase (PptH), that undoes the PptT reaction. Thus, loss-of-function mutants of PptH displayed antimicrobial resistance. Our PptT-inhibitor cocrystal structure may aid further development of antimycobacterial agents against this long-sought target. The opposing reactions of PptT and PptH uncover a regulatory pathway in CoA physiology.

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Organizational Affiliation: 
• Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY, USA.
Departments of Biochemistry and Biophysics, Texas Agricultural and Mechanical University, College Station, TX, USA.
Department of Medicine, Weill Cornell Medicine, New York, NY, USA.
Infectious Diseases Therapeutic Area, Sanofi, Marcy-l'Étoile, France.
Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, USA.
Organic Synthesis Core, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
Departments of Biochemistry and Biophysics, Texas Agricultural and Mechanical University, College Station, TX, USA. [e-mail] [e-mail].
Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY, USA. [e-mail] [e-mail].

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

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

Macromolecule Content 

• Total Structure Weight: 56.98 kDa 
• Atom Count: 4,059 
• Modeled Residue Count: 442 
• Deposited Residue Count: 488 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
4'-phosphopantetheinyl transferase	A, B	244	Mycobacterium tuberculosis	Mutation(s): 0  Gene Names: CRX58_05810, ERS124361_01504 EC: 2.7.8.7
UniProt
Find proteins for O33336 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore O33336  Go to UniProtKB:  O33336

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
COA	C [auth A], O [auth B]	COENZYME A C21 H36 N7 O16 P3 S RGJOEKWQDUBAIZ-IBOSZNHHSA-N
FD7 (Subject of Investigation/LOI)	D [auth A], E [auth A], P [auth B]	N-(2,6-diethylphenyl)-N'-(N-ethylcarbamimidoyl)urea C14 H22 N4 O VHGRQUGTHVVVTE-UHFFFAOYSA-N
GOL	I [auth A], J [auth A], K [auth A], T [auth B], U [auth B], V [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
DMS	L [auth A], M [auth A], N [auth A], W [auth B], X [auth B], Y [auth B], Z [auth B]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
MG	F [auth A], G [auth A], H [auth A], Q [auth B], R [auth B], S [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free:  0.198 (Depositor), 0.203 (DCC) 
• R-Value Work:  0.160 (Depositor) 
• R-Value Observed: 0.162 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 134.863	α = 90
b = 63.408	β = 123.149
c = 79.267	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-02-06 
Deposition Author(s): Mosior, J., Sacchettini, J., TB Structural Genomics Consortium (TBSGC)

Revision History  

• Version 1.0: 2019-02-06
  Type: Initial release
  
• Version 1.1: 2019-02-13
  Changes: Data collection, Database references
• Version 1.2: 2023-10-04
  Changes: Data collection, Database references, Derived calculations, Refinement description