3F3M | pdb_00003f3m

Six Crystal Structures of Two Phosphopantetheine Adenylyltransferases Reveal an Alternative Ligand Binding Mode and an Associated Structural Change

• PDB DOI: https://doi.org/10.2210/pdb3F3M/pdb

• Classification: TRANSFERASE
• Organism(s): Staphylococcus aureus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-10-31 Released: 2009-10-20 
• Deposition Author(s): Lee, H.H., Yoon, H.J., Suh, S.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.250 (Depositor), 0.277 (DCC) 
• R-Value Work: 
  0.211 (Depositor) 

Starting Model: experimental

Literature

The structure of Staphylococcus aureus phosphopantetheine adenylyltransferase in complex with 3'-phosphoadenosine 5'-phosphosulfate reveals a new ligand-binding mode

Lee, H.H., Yoon, H.J., Kang, J.Y., Park, J.H., Kim, D.J., Choi, K.H., Lee, S.K., Song, J., Kim, H.J., Suh, S.W.

(2009) Acta Crystallogr Sect F Struct Biol Cryst Commun 65: 987-991

• PubMed: 19851003 
• DOI: https://doi.org/10.1107/S1744309109036616
• Primary Citation Related Structures: 
  3F3M


• PubMed Abstract: 
  

  Bacterial phosphopantetheine adenylyltransferase (PPAT) catalyzes the penultimate step in the coenzyme A (CoA) biosynthetic pathway. It catalyzes the reversible transfer of an adenylyl group from ATP to 4'-phosphopantetheine (Ppant) to form dephospho-CoA (dPCoA) and pyrophosphate. Previous structural studies have revealed how several ligands are recognized by bacterial PPATs. ATP, ADP, Ppant and dPCoA bind to the same binding site in a highly similar manner, while CoA binds to a partially overlapping site in a different mode. To provide further structural insights into ligand binding, the crystal structure of Staphylococcus aureus PPAT was solved in a binary complex with 3'-phosphoadenosine 5'-phosphosulfate (PAPS). This study unexpectedly revealed a new mode of ligand binding to PPAT, thus providing potentially useful information for structure-based discovery of inhibitors of bacterial PPATs.

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Organizational Affiliation: 
• Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul 151-742, Republic of Korea.

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: 19.98 kDa 
• Atom Count: 1,323 
• Modeled Residue Count: 155 
• Deposited Residue Count: 168 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphopantetheine adenylyltransferase	A	168	Staphylococcus aureus	Mutation(s): 0  Gene Names: coaD EC: 2.7.7.3
UniProt
Find proteins for P63820 (Staphylococcus aureus (strain MW2)) Explore P63820  Go to UniProtKB:  P63820

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PPS	B [auth A]	3'-PHOSPHATE-ADENOSINE-5'-PHOSPHATE SULFATE C10 H15 N5 O13 P2 S GACDQMDRPRGCTN-KQYNXXCUSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.250 (Depositor), 0.277 (DCC) 
• R-Value Work:  0.211 (Depositor) 

Space Group: P 6₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.774	α = 90
b = 66.774	β = 90
c = 124.134	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-10-20 
Deposition Author(s): Lee, H.H., Yoon, H.J., Suh, S.W.

Revision History  

• Version 1.0: 2009-10-20
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2012-04-25
  Changes: Database references
• Version 1.3: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description