4QJL

Crystal structure of M. ulcerans phosphopantetheinyl transferase MuPPT

• PDB DOI: https://doi.org/10.2210/pdb4QJL/pdb

• Classification: TRANSFERASE
• Organism(s): Mycobacterium ulcerans Agy99
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-06-04 Released: 2014-07-16 
• Deposition Author(s): Noel, J.P., Burkart, M.D., Vickery, C.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.208 
• R-Value Work: 0.160 
• R-Value Observed: 0.162 

Literature

Structure, biochemistry, and inhibition of essential 4'-phosphopantetheinyl transferases from two species of mycobacteria.

Vickery, C.R., Kosa, N.M., Casavant, E.P., Duan, S., Noel, J.P., Burkart, M.D.

(2014) ACS Chem Biol 9: 1939-1944

• PubMed: 24963544 
• DOI: https://doi.org/10.1021/cb500263p
• Primary Citation of Related Structures:  
  4QJK, 4QJL


• PubMed Abstract: 
  

  4'-Phosphopantetheinyl transferases (PPTase) post-translationally modify carrier proteins with a phosphopantetheine moiety, an essential reaction in all three domains of life. In the bacterial genus Mycobacteria, the Sfp-type PPTase activates pathways necessary for the biosynthesis of cell wall components and small molecule virulence factors. We solved the X-ray crystal structures and biochemically characterized the Sfp-type PPTases from two of the most prevalent Mycobacterial pathogens, PptT of M. tuberculosis and MuPPT of M. ulcerans. Structural analyses reveal significant differences in cofactor binding and active site composition when compared to previously characterized Sfp-type PPTases. Functional analyses including the efficacy of Sfp-type PPTase-specific inhibitors also suggest that the Mycobacterial Sfp-type PPTases can serve as therapeutic targets against Mycobacterial infections.

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Organizational Affiliation: 

Department of Chemistry and Biochemistry, University of California, San Diego , 9500 Gilman Drive, La Jolla, California 92093-0358, United States.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 26.53 kDa 
• Atom Count: 2,039 
• Modelled Residue Count: 228 
• Deposited Residue Count: 235 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphopantetheinyl transferase, PptII	A	235	Mycobacterium ulcerans Agy99	Mutation(s): 0  Gene Names: MUL_2141, MuPPT, pptII, YP_906028 EC: 2.7.8.7
UniProt
Find proteins for A0PQD8 (Mycobacterium ulcerans (strain Agy99)) Explore A0PQD8  Go to UniProtKB:  A0PQD8

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
COA	B [auth A]	COENZYME A C21 H36 N7 O16 P3 S RGJOEKWQDUBAIZ-IBOSZNHHSA-N
MG	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.208 
• R-Value Work: 0.160 
• R-Value Observed: 0.162 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.02	α = 90
b = 59.75	β = 90
c = 74.48	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
BOS	data collection
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-07-16 
Deposition Author(s): Noel, J.P., Burkart, M.D., Vickery, C.R.

Revision History  

• Version 1.0: 2014-07-16
  Type: Initial release
  
• Version 1.1: 2014-10-01
  Changes: Database references
• Version 1.2: 2017-11-22
  Changes: Refinement description
• Version 1.3: 2024-02-28
  Changes: Data collection, Database references, Derived calculations