3K9W

Crystal structure of phosphopantetheine adenylyltransferase from Burkholderia pseudomallei with hydrolyzed 3'-dephospho Coenzyme A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.191 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Structures of phosphopantetheine adenylyltransferase from Burkholderia pseudomallei.

Edwards, T.E.Leibly, D.J.Bhandari, J.Statnekov, J.B.Phan, I.Dieterich, S.H.Abendroth, J.Staker, B.L.Van Voorhis, W.C.Myler, P.J.Stewart, L.J.

(2011) Acta Crystallogr.,Sect.F 67: 1032-1037

  • DOI: 10.1107/S1744309111004349
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Phosphopantetheine adenylyltransferase (PPAT) catalyzes the fourth of five steps in the coenzyme A biosynthetic pathway, reversibly transferring an adenylyl group from ATP onto 4'-phosphopantetheine to yield dephospho-coenzyme A and pyrophosphate. Bu ...

    Phosphopantetheine adenylyltransferase (PPAT) catalyzes the fourth of five steps in the coenzyme A biosynthetic pathway, reversibly transferring an adenylyl group from ATP onto 4'-phosphopantetheine to yield dephospho-coenzyme A and pyrophosphate. Burkholderia pseudomallei is a soil- and water-borne pathogenic bacterium and the etiologic agent of melioidosis, a potentially fatal systemic disease present in southeast Asia. Two crystal structures are presented of the PPAT from B. pseudomallei with the expectation that, because of the importance of the enzyme in coenzyme A biosynthesis, they will aid in the search for defenses against this pathogen. A crystal grown in ammonium sulfate yielded a 2.1 Å resolution structure that contained dephospho-coenzyme A with partial occupancy. The overall structure and ligand-binding interactions are quite similar to other bacterial PPAT crystal structures. A crystal grown at low pH in the presence of coenzyme A yielded a 1.6 Å resolution structure in the same crystal form. However, the experimental electron density was not reflective of fully ordered coenzyme A, but rather was only reflective of an ordered 4'-diphosphopantetheine moiety.


    Related Citations: 
    • Combining functional and structural genomics to sample the essential Burkholderia structome.
      Baugh, L.,Gallagher, L.A.,Patrapuvich, R.,Clifton, M.C.,Gardberg, A.S.,Edwards, T.E.,Armour, B.,Begley, D.W.,Dieterich, S.H.,Dranow, D.M.,Abendroth, J.,Fairman, J.W.,Fox, D.,Staker, B.L.,Phan, I.,Gillespie, A.,Choi, R.,Nakazawa-Hewitt, S.,Nguyen, M.T.,Napuli, A.,Barrett, L.,Buchko, G.W.,Stacy, R.,Myler, P.J.,Stewart, L.J.,Manoil, C.,Van Voorhis, W.C.
      (2013) Plos One 8: e53851


    Organizational Affiliation

    Seattle Structural Genomics Center for Infectious Disease (SSGCID), USA. tedwards@embios.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Phosphopantetheine adenylyltransferase
A
187Burkholderia pseudomallei (strain 1710b)Mutation(s): 0 
Gene Names: coaD
EC: 2.7.7.3
Find proteins for Q3JW91 (Burkholderia pseudomallei (strain 1710b))
Go to UniProtKB:  Q3JW91
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
ACT
Query on ACT

Download SDF File 
Download CCD File 
A
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
PG4
Query on PG4

Download SDF File 
Download CCD File 
A
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
 Ligand Interaction
4PS
Query on 4PS

Download SDF File 
Download CCD File 
A
4'-diphospho pantetheine
N~3~-[(2R)-2-hydroxy-4-{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}-3,3-dimethylbutanoyl]-N-(2-sulfanylethyl)-beta-alaninamide
C11 H24 N2 O10 P2 S
UQURMDBHCKDEJS-VIFPVBQESA-N
 Ligand Interaction
ADE
Query on ADE

Download SDF File 
Download CCD File 
A
ADENINE
C5 H5 N5
GFFGJBXGBJISGV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

Unit Cell:
Length (Å)Angle (°)
a = 134.431α = 90.00
b = 134.431β = 90.00
c = 134.431γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
DENZOdata reduction
PDB_EXTRACTdata extraction
HKL-2000data scaling
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-11-03
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Refinement description, Source and taxonomy, Version format compliance
  • Version 1.2: 2011-09-21
    Type: Database references
  • Version 1.3: 2013-10-30
    Type: Database references
  • Version 1.4: 2017-11-01
    Type: Refinement description