Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 36.69 kDa 
• Atom Count: 2853 
• Modelled Residue Count: 314 
• Deposited Residue Count: 318 
• Unique protein chains: 1

1B6T

PHOSPHOPANTETHEINE ADENYLYLTRANSFERASE IN COMPLEX WITH 3'-DEPHOSPHO-COA FROM ESCHERICHIA COLI

• PDB DOI: 10.2210/pdb1B6T/pdb

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


• Deposited: 1999-01-18 Released: 2000-04-19 
• Deposition Author(s): Izard, T.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.235 
• R-Value Work: 0.205 
• R-Value Observed: 0.222 

Literature

The crystal structure of a novel bacterial adenylyltransferase reveals half of sites reactivity.

Izard, T., Geerlof, A.

(1999) EMBO J 18: 2021-2030

• PubMed: 10205156 
• DOI: 10.1093/emboj/18.8.2021
• Primary Citation of Related Structures:  
  1B6T


• PubMed Abstract: 
  

Phosphopantetheine adenylyltransferase (PPAT) is an essential enzyme in bacteria that catalyses a rate-limiting step in coenzyme A (CoA) biosynthesis, by transferring an adenylyl group from ATP to 4'-phosphopantetheine, yielding dephospho-CoA (dPCoA). Each phosphopantetheine adenylyltransferase (PPAT) subunit displays a dinucleotide-binding fold that is structurally similar to that in class I aminoacyl-tRNA synthetases. Superposition of bound adenylyl moieties from dPCoA in PPAT and ATP in aminoacyl-tRNA synthetases suggests nucleophilic attack by the 4'-phosphopantetheine on the alpha-phosphate of ATP. The proposed catalytic mechanism implicates transition state stabilization by PPAT without involving functional groups of the enzyme in a chemical sense in the reaction. The crystal structure of the enzyme from Escherichia coli in complex with dPCoA shows that binding at one site causes a vice-like movement of active site residues lining the active site surface. The mode of enzyme product formation is highly concerted, with only one trimer of the PPAT hexamer showing evidence of dPCoA binding. The homologous active site attachment of ATP and the structural distribution of predicted sequence-binding motifs in PPAT classify the enzyme as belonging to the nucleotidyltransferase superfamily.

---

Organizational Affiliation: 

Department of Biochemistry, University of Leicester, Leicester LE1 [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
COD	F [auth B]	DEPHOSPHO COENZYME A C21 H35 N7 O13 P2 S KDTSHFARGAKYJN-IBOSZNHHSA-N
SO4	C [auth A], D [auth B], E [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.235 
• R-Value Work: 0.205 
• R-Value Observed: 0.222 
• Space Group: I 2 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 135.5	α = 90
b = 135.5	β = 90
c = 135.5	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1999-01-18 
• Released Date: 2000-04-19 
Deposition Author(s): Izard, T.

Revision History  

• Version 1.0: 2000-04-19
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance