3UC5

Phosphopantetheine adenylyltransferase from Mycobacterium tuberculosis complexed with ATP

• PDB DOI: https://doi.org/10.2210/pdb3UC5/pdb

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


• Deposited: 2011-10-26 Released: 2012-11-07 
• Deposition Author(s): Timofeev, V.I., Smirnova, E.A., Chupova, L.A., Esipov, R.S., Kuranova, I.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.222 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.177 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.179 (Depositor) 

Starting Model: experimental

Literature

X-ray study of the conformational changes in the molecule of phosphopantetheine adenylyltransferase from Mycobacterium tuberculosis during the catalyzed reaction.

Timofeev, V., Smirnova, E., Chupova, L., Esipov, R., Kuranova, I.

(2012) Acta Crystallogr D Biol Crystallogr 68: 1660-1670

• PubMed: 23151631 
• DOI: https://doi.org/10.1107/S0907444912040206
• Primary Citation of Related Structures:  
  3UC5, 4E1A


• PubMed Abstract: 
  

  Structures of recombinant phosphopantetheine adenylyltransferase (PPAT) from Mycobacterium tuberculosis (PPATMt) in the apo form and in complex with the substrate ATP were determined at 1.62 and 1.70 Å resolution, respectively, using crystals grown in microgravity by the counter-diffusion method. The ATP molecule of the PPATMt-ATP complex was located with full occupancy in the active-site cavity. Comparison of the solved structures with previously determined structures of PPATMt complexed with the reaction product dephosphocoenzyme A (dPCoA) and the feedback inhibitor coenzyme A (CoA) was performed using superposition on C(α) atoms. The peculiarities of the arrangement of the ligands in the active-site cavity of PPATMt are described. The conformational states of the PPAT molecule in the consequent steps of the catalyzed reaction in the apo enzyme and the enzyme-substrate and enzyme-product complexes are characterized. It is shown that the binding of ATP and dPCoA induces the rearrangement of a short part of the polypeptide chain restricting the active-site cavity in the subunits of the hexameric enzyme molecule. The changes in the quaternary structure caused by this rearrangement are accompanied by a variation of the size of the inner water-filled channel which crosses the PPAT molecule along the threefold axis of the hexamer. The molecular mechanism of the observed changes is described.

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Organizational Affiliation: 

Laboratory of X-ray Analysis Methods and Synchrotron Radiation, Shubnikov Institute of Crystallography, Russian Academy of Sciences, Leninsky Prospect 59, Moscow, Russian Federation. [e-mail]

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

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

Macromolecule Content

• Total Structure Weight: 17.67 kDa 
• Atom Count: 1,309 
• Modelled Residue Count: 157 
• Deposited Residue Count: 157 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphopantetheine adenylyltransferase	A	157	Mycobacterium tuberculosis	Mutation(s): 0  Gene Names: coaD, kdtB, Rv2965c, MT3043, MTCY349.22, u0002e EC: 2.7.7.3
UniProt
Find proteins for P9WPA5 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WPA5  Go to UniProtKB:  P9WPA5

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ATP	B [auth A]	ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.222 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.177 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.179 (Depositor) 

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.909	α = 90
b = 99.909	β = 90
c = 114.419	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-11-07 
Deposition Author(s): Timofeev, V.I., Smirnova, E.A., Chupova, L.A., Esipov, R.S., Kuranova, I.P.

Revision History  

• Version 1.0: 2012-11-07
  Type: Initial release
  
• Version 1.1: 2012-11-28
  Changes: Database references
• Version 1.2: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2024-11-27
  Changes: Structure summary