6WJ9 | pdb_00006wj9

UDP-GlcNAc C4-epimerase mutant S121A/Y146F from Pseudomonas protegens in complex with UDP-GlcNAc

• PDB DOI: https://doi.org/10.2210/pdb6WJ9/pdb

• Classification: ISOMERASE
• Organism(s): Pseudomonas protegens Pf-5
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2020-04-13 Released: 2020-07-08 
• Deposition Author(s): Marmont, L.S., Willams, R.J., Whitney, J.C., Whitfield, G.B., Robinson, H., Parsek, M.R., Nitz, M., Harrison, J.J., Howell, P.L.
• Funding Organization(s): Canadian Institutes of Health Research

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.11 Å
• R-Value Free: 
  0.195 (Depositor), 0.191 (DCC) 
• R-Value Work: 
  0.156 (Depositor) 
• R-Value Observed: 
  0.158 (Depositor) 

Starting Model: experimental

Literature

PelX is a UDP-N-acetylglucosamine C4-epimerase involved in Pel polysaccharide-dependent biofilm formation.

Marmont, L.S., Whitfield, G.B., Pfoh, R., Williams, R.J., Randall, T.E., Ostaszewski, A., Razvi, E., Groves, R.A., Robinson, H., Nitz, M., Parsek, M.R., Lewis, I.A., Whitney, J.C., Harrison, J.J., Howell, P.L.

(2020) J Biological Chem 295: 11949-11962

• PubMed: 32601062 
• DOI: https://doi.org/10.1074/jbc.RA120.014555
• Primary Citation Related Structures: 
  6WJ9, 6WJA, 6WJB


• PubMed Abstract: 
  

  Pel is a GalNAc-rich bacterial polysaccharide that contributes to the structure and function of Pseudomonas aeruginosa biofilms. The pelABCDEFG operon is highly conserved among diverse bacterial species, and Pel may therefore be a widespread biofilm determinant. Previous annotation of pel gene clusters has helped us identify an additional gene, pelX , that is present adjacent to pelABCDEFG in >100 different bacterial species. The pelX gene is predicted to encode a member of the short-chain dehydrogenase/reductase (SDR) superfamily, but its potential role in Pel-dependent biofilm formation is unknown. Herein, we have used Pseudomonas protegens Pf-5 as a model to elucidate PelX function as Pseudomonas aeruginosa lacks a pelX homologue in its pel gene cluster. We found that P. protegens forms Pel-dependent biofilms; however, despite expression of pelX under these conditions, biofilm formation was unaffected in a Δ pelX strain. This observation led us to identify a pelX paralogue, PFL_5533, which we designate here PgnE, that appears to be functionally redundant to pelX In line with this, a Δ pelX Δ pgnE double mutant was substantially impaired in its ability to form Pel-dependent biofilms. To understand the molecular basis for this observation, we determined the structure of PelX to 2.1 Å resolution. The structure revealed that PelX resembles UDP-GlcNAc C4-epimerases. Using ¹ H NMR analysis, we show that PelX catalyzes the epimerization between UDP-GlcNAc and UDP-GalNAc. Our results indicate that Pel-dependent biofilm formation requires a UDP-GlcNAc C4-epimerase that generates the UDP-GalNAc precursors required by the Pel synthase machinery for polymer production.

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Organizational Affiliation: 
• Program in Molecular Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada; Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada.
Program in Molecular Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada.
Department of Chemistry, University of Toronto, Toronto, Ontario, Canada.
Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada.
Photon Science Division, Brookhaven National Laboratory, Upton, New York, USA.
Department of Microbiology, University of Washington, Seattle, Washington, USA.
Program in Molecular Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada; Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 67.82 kDa 
• Atom Count: 5,132 
• Modeled Residue Count: 615 
• Deposited Residue Count: 620 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NAD-dependent epimerase/dehydratase family protein	A, B	310	Pseudomonas protegens Pf-5	Mutation(s): 3  Gene Names: PFL_2971
UniProt
Find proteins for Q4KCF6 (Pseudomonas fluorescens (strain ATCC BAA-477 / NRRL B-23932 / Pf-5)) Explore Q4KCF6  Go to UniProtKB:  Q4KCF6

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD (Subject of Investigation/LOI)	C [auth A], E [auth B]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
UD1 (Subject of Investigation/LOI)	D [auth A], F [auth B]	URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE C17 H27 N3 O17 P2 LFTYTUAZOPRMMI-CFRASDGPSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.11 Å
• R-Value Free:  0.195 (Depositor), 0.191 (DCC) 
• R-Value Work:  0.156 (Depositor) 
• R-Value Observed: 0.158 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 124.195	α = 90
b = 75.487	β = 90
c = 79.271	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
DENZO	data reduction
SCALEPACK	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-07-08 
Deposition Author(s): Marmont, L.S., Willams, R.J., Whitney, J.C., Whitfield, G.B., Robinson, H., Parsek, M.R., Nitz, M., Harrison, J.J., Howell, P.L.

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Funding Organization	Location	Grant Number
Canadian Institutes of Health Research	Canada	--

Revision History  

• Version 1.0: 2020-07-08
  Type: Initial release
  
• Version 1.1: 2020-07-15
  Changes: Database references
• Version 1.2: 2020-09-02
  Changes: Database references
• Version 1.3: 2023-10-18
  Changes: Data collection, Database references, Refinement description