1B6T

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


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 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

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

Izard, T.Geerlof, A.

(1999) EMBO J 18: 2021-2030

  • 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 ...

    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 7RH.ti3@le.ac.uk



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (PHOSPHOPANTETHEINE ADENYLYLTRANSFERASE)A, B159Escherichia coliMutation(s): 0 
EC: 2.7.7.3
UniProt
Find proteins for P0A6I6 (Escherichia coli (strain K12))
Explore P0A6I6 
Go to UniProtKB:  P0A6I6
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
COD (Subject of Investigation/LOI)
Query on COD

Download Ideal Coordinates CCD File 
F [auth B]DEPHOSPHO COENZYME A
C21 H35 N7 O13 P2 S
KDTSHFARGAKYJN-IBOSZNHHSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A], D [auth B], E [auth B]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
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 = 135.5α = 90
b = 135.5β = 90
c = 135.5γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

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

Revision History  (Full details and data files)

  • 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