5OON

Structure of Undecaprenyl-Pyrophosphate Phosphatase, BacA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.206 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of undecaprenyl-pyrophosphate phosphatase and its role in peptidoglycan biosynthesis.

El Ghachi, M.Howe, N.Huang, C.Y.Olieric, V.Warshamanage, R.Touze, T.Weichert, D.Stansfeld, P.J.Wang, M.Kerff, F.Caffrey, M.

(2018) Nat Commun 9: 1078-1078

  • DOI: 10.1038/s41467-018-03477-5

  • PubMed Abstract: 
  • As a protective envelope surrounding the bacterial cell, the peptidoglycan sacculus is a site of vulnerability and an antibiotic target. Peptidoglycan components, assembled in the cytoplasm, are shuttled across the membrane in a cycle that uses undec ...

    As a protective envelope surrounding the bacterial cell, the peptidoglycan sacculus is a site of vulnerability and an antibiotic target. Peptidoglycan components, assembled in the cytoplasm, are shuttled across the membrane in a cycle that uses undecaprenyl-phosphate. A product of peptidoglycan synthesis, undecaprenyl-pyrophosphate, is converted to undecaprenyl-phosphate for reuse in the cycle by the membrane integral pyrophosphatase, BacA. To understand how BacA functions, we determine its crystal structure at 2.6 Å resolution. The enzyme is open to the periplasm and to the periplasmic leaflet via a pocket that extends into the membrane. Conserved residues map to the pocket where pyrophosphorolysis occurs. BacA incorporates an interdigitated inverted topology repeat, a topology type thus far only reported in transporters and channels. This unique topology raises issues regarding the ancestry of BacA, the possibility that BacA has alternate active sites on either side of the membrane and its possible function as a flippase.


    Organizational Affiliation

    Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91190, Gif-sur-Yvette, Cedex, France.,Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK.,Membrane Structural and Functional Biology (MS&FB) Group, School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin, Dublin 2, D02 R590, Ireland. martin.caffrey@tcd.ie.,Centre d'Ingénierie des Protéines, InBioS, Université de Liège, allée du 6 Août 19, Bât B5a, 4000, Liège, Belgium.,Swiss Light Source, Paul Scherrer Institute, CH-5232, Villigen, Switzerland.,Membrane Structural and Functional Biology (MS&FB) Group, School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin, Dublin 2, D02 R590, Ireland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Undecaprenyl-diphosphatase
A
282Escherichia coli O157:H7Mutation(s): 0 
Gene Names: uppP (bacA, upk)
EC: 3.6.1.27
Membrane protein
mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Phosphatidic Acid Phosphatases
Protein: 
BacA (UppP) undecaprenyl-pyrophosphate phosphatase
Find proteins for P60933 (Escherichia coli O157:H7)
Go to UniProtKB:  P60933
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
OLC
Query on OLC

Download SDF File 
Download CCD File 
A
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
1-Oleoyl-R-glycerol
C21 H40 O4
RZRNAYUHWVFMIP-GDCKJWNLSA-N
 Ligand Interaction
TRS
Query on TRS

Download SDF File 
Download CCD File 
A
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
TRIS BUFFER
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
 Ligand Interaction
HG
Query on HG

Download SDF File 
Download CCD File 
A
MERCURY (II) ION
Hg
BQPIGGFYSBELGY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.206 
  • Space Group: C 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 113.260α = 90.00
b = 145.000β = 90.00
c = 40.490γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
XDSdata reduction
PHENIXrefinement
SHELXCDphasing
PHENIXmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Science Foundation IrelandIreland12/IA/1255
German Research FoundationGermany--
Biotechnology and Biological Sciences Research CouncilFranceBB/I019855/1

Revision History 

  • Version 1.0: 2018-03-21
    Type: Initial release
  • Version 1.1: 2018-03-28
    Type: Database references
  • Version 1.2: 2018-06-06
    Type: Data collection, Database references, Source and taxonomy