6CT5

PptT PAP(CoA) 8918 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.162 

Starting Models: 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

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

  • DOI: https://doi.org/10.1126/science.aau8959
  • Primary Citation of 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.


  • Organizational Affiliation

    Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
4'-phosphopantetheinyl transferase
A, B
244Mycobacterium tuberculosisMutation(s): 0 
Gene Names: CRX58_05810ERS124361_01504
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
COA
Query on COA

Download Ideal Coordinates CCD File 
C [auth A],
O [auth B]
COENZYME A
C21 H36 N7 O16 P3 S
RGJOEKWQDUBAIZ-IBOSZNHHSA-N
FD7 (Subject of Investigation/LOI)
Query on FD7

Download Ideal Coordinates CCD File 
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
Query on GOL

Download Ideal Coordinates CCD File 
I [auth A]
J [auth A]
K [auth A]
T [auth B]
U [auth B]
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
Query on DMS

Download Ideal Coordinates CCD File 
L [auth A]
M [auth A]
N [auth A]
W [auth B]
X [auth B]
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
Query on MG

Download Ideal Coordinates CCD File 
F [auth A]
G [auth A]
H [auth A]
Q [auth B]
R [auth B]
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 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.162 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 134.863α = 90
b = 63.408β = 123.149
c = 79.267γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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