1H1T | pdb_00001h1t

PHOSPHOPANTETHEINE ADENYLYLTRANSFERASE IN COMPLEX WITH Coenzyme A FROM ESCHERICHIA COLI

• PDB DOI: https://doi.org/10.2210/pdb1H1T/pdb

• Classification: TRANSFERASE
• Organism(s): Escherichia coli
• Mutation(s): No 


• Deposited: 2002-07-21 Released: 2003-07-07 
• Deposition Author(s): Izard, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.78 Å
• R-Value Free: 
  0.241 (Depositor) 
• R-Value Work: 
  0.218 (Depositor) 
• R-Value Observed: 
  0.218 (Depositor) 

Starting Model: experimental

Literature

A Novel Adenylate Binding Site Confers Phosphopantetheine Adenylyltransferase Interactions with Coenzyme A

Izard, T.

(2003) J Bacteriol 185: 4074

• PubMed: 12837781 
• DOI: https://doi.org/10.1128/JB.185.14.4074-4080.2003
• Primary Citation Related Structures: 
  1H1T


• PubMed Abstract: 
  

  Phosphopantetheine adenylyltransferase (PPAT) regulates the key penultimate step in the essential coenzyme A (CoA) biosynthetic pathway. PPAT catalyzes the reversible transfer of an adenylyl group from Mg(2+):ATP to 4'-phosphopantetheine to form 3'-dephospho-CoA (dPCoA) and pyrophosphate. The high-resolution crystal structure of PPAT complexed with CoA has been determined. Remarkably, CoA and the product dPCoA bind to the active site in distinct ways. Although the phosphate moiety within the phosphopantetheine arm overlaps, the pantetheine arm binds to the same pocket in two distinct conformations, and the adenylyl moieties of these two ligands have distinct binding sites. Moreover, the PPAT:CoA crystal structure confirms the asymmetry of binding to the two trimers within the hexameric enzyme. Specifically, the pantetheine arm of CoA bound to one protomer within the asymmetric unit displays the dPCoA-like conformation with the adenylyl moiety disordered, whereas CoA binds the twofold-related protomer in an ordered and unique fashion.

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Organizational Affiliation: 
• Department of Hematology-Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105-2794, USA. [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 PQS (software)

Macromolecule Content 

• Total Structure Weight: 37.23 kDa 
• Atom Count: 2,857 
• Modeled Residue Count: 315 
• Deposited Residue Count: 318 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PHOSPHOPANTETHEINE ADENYLYLTRANSFERASE	A, B	159	Escherichia coli	Mutation(s): 0  EC: 2.7.7.3
UniProt
Find proteins for P0A6I6 (Escherichia coli (strain K12)) Explore P0A6I6  Go to UniProtKB:  P0A6I6

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
COA	C [auth A]	COENZYME A C21 H36 N7 O16 P3 S RGJOEKWQDUBAIZ-IBOSZNHHSA-N
PNS	H [auth B]	4'-PHOSPHOPANTETHEINE C11 H23 N2 O7 P S JDMUPRLRUUMCTL-VIFPVBQESA-N
SO4	D [auth A], E [auth B], F [auth B], G [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.78 Å
• R-Value Free:  0.241 (Depositor) 
• R-Value Work:  0.218 (Depositor) 
• R-Value Observed: 0.218 (Depositor) 

Space Group: I 2 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 135.426	α = 90
b = 135.426	β = 90
c = 135.426	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-07-07 
Deposition Author(s): Izard, T.

Revision History  

• Version 1.0: 2003-07-07
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-06-28
  Changes: Data collection
• Version 1.4: 2023-12-13
  Changes: Data collection, Database references, Refinement description