6QYG

4'-phosphopantetheinyl transferase PptAb from Mycobacterium abscessus at pH 8.5 with Mg2+ and CoA.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.181 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Conformational flexibility of coenzyme A and its impact on the post-translational modification of acyl carrier proteins by 4'-phosphopantetheinyl transferases.

Nguyen, M.C.Saurel, O.Carivenc, C.Gavalda, S.Saitta, S.Tran, M.P.Milon, A.Chalut, C.Guilhot, C.Mourey, L.Pedelacq, J.D.

(2020) Febs J. --: --

  • DOI: 10.1111/febs.15273
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • One central question surrounding the biosynthesis of fatty acids and polyketide-derived natural products is how the 4'-phosphopantetheinyl transferase (PPTase) interrogates the essential acyl carrier protein (ACP) domain to fulfill the initial activa ...

    One central question surrounding the biosynthesis of fatty acids and polyketide-derived natural products is how the 4'-phosphopantetheinyl transferase (PPTase) interrogates the essential acyl carrier protein (ACP) domain to fulfill the initial activation step. The triggering factor of this study was the lack of structural information on PPTases at physiological pH, which could bias our comprehension of the mechanism of action of these important enzymes. Structural and functional studies on the family II PPTase PptAb of Mycobacterium abscessus show that pH has a profound effect on the coordination of metal ions and on the conformation of endogenously bound coenzyme A (CoA). The observed conformational flexibility of CoA at physiological pH is accompanied with a disordered 4'-phosphopantetheine (Ppant) moiety. Finally, structural and dynamical information on an isolated mycobacterial ACP domain, in its apo form and in complex with the activator PptAb, suggests an alternate mechanism for the post-translational modification of modular megasynthases.


    Organizational Affiliation

    Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Possible 4'-phosphopantetheinyl transferase
A
232Mycobacteroides abscessus (strain ATCC 19977 / DSM 44196 / CIP 104536 / JCM 13569 / NCTC 13031 / TMC 1543)Mutation(s): 0 
Find proteins for B1MD73 (Mycobacteroides abscessus (strain ATCC 19977 / DSM 44196 / CIP 104536 / JCM 13569 / NCTC 13031 / TMC 1543))
Go to UniProtKB:  B1MD73
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
COA
Query on COA

Download SDF File 
Download CCD File 
A
COENZYME A
C21 H36 N7 O16 P3 S
RGJOEKWQDUBAIZ-IBOSZNHHSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.181 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 55.422α = 90.00
b = 60.334β = 90.00
c = 66.078γ = 90.00
Software Package:
Software NamePurpose
XDSdata scaling
PHASERphasing
TRUNCATEdata reduction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Union (EU)Netherlands10559
French National Research AgencyFranceANR-16-CE18-0011-01

Revision History 

  • Version 1.0: 2020-03-25
    Type: Initial release