5FPX

The structure of KdgF from Yersinia enterocolitica.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.171 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Kdgf, the Missing Link in the Microbial Metabolism of Uronate Sugars from Pectin and Alginate.

Hobbs, J.K.Lee, S.M.Robb, M.Hof, F.Barr, C.Abe, K.T.Hehemann, J.Mclean, R.Abbott, D.W.Boraston, A.B.

(2016) Proc.Natl.Acad.Sci.USA 113: 6188

  • DOI: 10.1073/pnas.1524214113
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Uronates are charged sugars that form the basis of two abundant sources of biomass-pectin and alginate-found in the cell walls of terrestrial plants and marine algae, respectively. These polysaccharides represent an important source of carbon to thos ...

    Uronates are charged sugars that form the basis of two abundant sources of biomass-pectin and alginate-found in the cell walls of terrestrial plants and marine algae, respectively. These polysaccharides represent an important source of carbon to those organisms with the machinery to degrade them. The microbial pathways of pectin and alginate metabolism are well studied and essentially parallel; in both cases, unsaturated monouronates are produced and processed into the key metabolite 2-keto-3-deoxygluconate (KDG). The enzymes required to catalyze each step have been identified within pectinolytic and alginolytic microbes; yet the function of a small ORF, kdgF, which cooccurs with the genes for these enzymes, is unknown. Here we show that KdgF catalyzes the conversion of pectin- and alginate-derived 4,5-unsaturated monouronates to linear ketonized forms, a step in uronate metabolism that was previously thought to occur spontaneously. Using enzyme assays, NMR, mutagenesis, and deletion of kdgF, we show that KdgF proteins from both pectinolytic and alginolytic bacteria catalyze the ketonization of unsaturated monouronates and contribute to efficient production of KDG. We also report the X-ray crystal structures of two KdgF proteins and propose a mechanism for catalysis. The discovery of the function of KdgF fills a 50-y-old gap in the knowledge of uronate metabolism. Our findings have implications not only for the understanding of an important metabolic pathway, but also the role of pectinolysis in plant-pathogen virulence and the growing interest in the use of pectin and alginate as feedstocks for biofuel production.


    Organizational Affiliation

    Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, V8W 3P6, Canada; boraston@uvic.ca.,Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, V8W 3P6, Canada; MARUM MPG Bridge Group Marine Glycobiology, Center for Marine Environmental Sciences, University of Bremen, 28334 Bremen, Germany; Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany;,Lethbridge Research Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, T1J 4B1, Canada.,Department of Chemistry, University of Victoria, Victoria, BC, V8W 3P6, Canada;,Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, V8W 3P6, Canada;




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PECTIN DEGRADATION PROTEIN
A, B
113Yersinia enterocolitica serotype O:8 / biotype 1B (strain NCTC 13174 / 8081)Mutation(s): 0 
Gene Names: kdgF
Find proteins for A1JMF7 (Yersinia enterocolitica serotype O:8 / biotype 1B (strain NCTC 13174 / 8081))
Go to UniProtKB:  A1JMF7
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
PEPTIDE
E, F
8N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NI
Query on NI

Download SDF File 
Download CCD File 
A, B
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.171 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 39.920α = 90.00
b = 73.760β = 90.00
c = 83.680γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
XDSdata reduction
PHASERphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-05-04
    Type: Initial release
  • Version 1.1: 2016-06-01
    Type: Database references
  • Version 1.2: 2016-06-15
    Type: Database references