6DFL

WaaP in complex with acyl carrier protein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.396 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.233 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Acylated-acyl carrier protein stabilizes the Pseudomonas aeruginosa WaaP lipopolysaccharide heptose kinase.

Kreamer, N.N.K.Chopra, R.Caughlan, R.E.Fabbro, D.Fang, E.Gee, P.Hunt, I.Li, M.Leon, B.C.Muller, L.Vash, B.Woods, A.L.Stams, T.Dean, C.R.Uehara, T.

(2018) Sci Rep 8: 14124-14124

  • DOI: 10.1038/s41598-018-32379-1

  • PubMed Abstract: 
  • Phosphorylation of Pseudomonas aeruginosa lipopolysaccharide (LPS) is important for maintaining outer membrane integrity and intrinsic antibiotic resistance. We solved the crystal structure of the LPS heptose kinase WaaP, which is essential for growt ...

    Phosphorylation of Pseudomonas aeruginosa lipopolysaccharide (LPS) is important for maintaining outer membrane integrity and intrinsic antibiotic resistance. We solved the crystal structure of the LPS heptose kinase WaaP, which is essential for growth of P. aeruginosa. WaaP was structurally similar to eukaryotic protein kinases and, intriguingly, was complexed with acylated-acyl carrier protein (acyl-ACP). WaaP produced by in vitro transcription-translation was insoluble unless acyl-ACP was present. WaaP variants designed to perturb the acyl-ACP interaction were less stable in cells and exhibited reduced kinase function. Mass spectrometry identified myristyl-ACP as the likely physiological binding partner for WaaP in P. aeruginosa. Together, these results demonstrate that acyl-ACP is required for WaaP protein solubility and kinase function. To the best of our knowledge, this is the first report describing acyl-ACP in the role of a cofactor necessary for the production and stability of a protein partner.


    Organizational Affiliation

    Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, Basel, Switzerland.,Infectious Diseases, Novartis Institutes for Biomedical Research, Emeryville, CA, USA. tsuyoshi.uehara@gmail.com.,Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, Cambridge, MA, USA.,Infectious Diseases, Novartis Institutes for Biomedical Research, Emeryville, CA, USA.,Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, Cambridge, MA, USA. rajiv.chopra@novartis.com.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Lipopolysaccharide core heptose(I) kinase RfaP
A
259Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)Mutation(s): 0 
Gene Names: rfaP (waaP)
EC: 2.7.1.-, 2.7.10.2
Find proteins for Q9HUF7 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Go to UniProtKB:  Q9HUF7
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Acyl carrier protein
B
72Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: acpP
Find proteins for P0A6A8 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A6A8
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
G9S
Query on G9S

Download SDF File 
Download CCD File 
B
S-[2-({N-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] hexadecanethioate
C27 H53 N2 O8 P S
JSWBEHRITPIXLC-RUZDIDTESA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.396 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.233 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 92.023α = 90.00
b = 92.023β = 90.00
c = 99.172γ = 120.00
Software Package:
Software NamePurpose
XDSdata reduction
PDB_EXTRACTdata extraction
Aimlessdata scaling
SHELXphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2018-05-15 
  • Released Date: 2019-04-03 
  • Deposition Author(s): Chopra, R., Vash, B.

Revision History 

  • Version 1.0: 2019-04-03
    Type: Initial release
  • Version 1.1: 2019-10-16
    Type: Data collection, Database references