Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction | Predict Membrane 

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 32.12 kDa 
• Atom Count: 2124 
• Modelled Residue Count: 270 
• Deposited Residue Count: 282 
• Unique protein chains: 1

5OON

Structure of Undecaprenyl-Pyrophosphate Phosphatase, BacA

• PDB DOI: 10.2210/pdb5OON/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Escherichia coli
• Expression System: Escherichia coli DH1
• Mutation(s): No 
• Membrane Protein: Yes  PDBTMMemProtMD


• Deposited: 2017-08-08 Released: 2018-03-21 
• Deposition Author(s): Huang, C.-Y., Olieric, V., Warshamanage, R., Wang, M., Howe, N., Ghachi, M.E.I., Weichert, D., Kerff, F., Stansfeld, P., Touze, T., Caffrey, M.
• Funding Organization(s): Science Foundation Ireland, German Research Foundation, Biotechnology and Biological Sciences Research Council

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.244 
• R-Value Work: 0.206 
• R-Value Observed: 0.208 

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

• PubMed: 29540682 
• DOI: 10.1038/s41467-018-03477-5
• Primary Citation of Related Structures:  
  5OON


• 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 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.

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Organizational Affiliation: 

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. [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Undecaprenyl-diphosphatase	A	282	Escherichia coli	Mutation(s): 0  Gene Names: bacA, uppP EC: 3.6.1.27 Membrane Entity: Yes
UniProt
Find proteins for P60933 (Escherichia coli O157:H7) Explore P60933  Go to UniProtKB:  P60933

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
OLC	E [auth A], F [auth A]	(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate C21 H40 O4 RZRNAYUHWVFMIP-GDCKJWNLSA-N
HG	B [auth A], C [auth A]	MERCURY (II) ION Hg BQPIGGFYSBELGY-UHFFFAOYSA-N
TRS	D [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.244 
• R-Value Work: 0.206 
• R-Value Observed: 0.208 
• Space Group: C 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 113.26	α = 90
b = 145	β = 90
c = 40.49	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
SHELXCD	phasing
PHENIX	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2017-08-08 
• Released Date: 2018-03-21 
Deposition Author(s): Huang, C.-Y., Olieric, V., Warshamanage, R., Wang, M., Howe, N., Ghachi, M.E.I., Weichert, D., Kerff, F., Stansfeld, P., Touze, T., Caffrey, M.

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Funding Organization	Location	Grant Number
Science Foundation Ireland	Ireland	12/IA/1255
German Research Foundation	Germany	--
Biotechnology and Biological Sciences Research Council	France	BB/I019855/1

Revision History  

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