KpsC D160C ternary complex

Experimental Data Snapshot

  • Resolution: 1.20 Å
  • R-Value Free: 0.157 
  • R-Value Work: 0.124 
  • R-Value Observed: 0.125 

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Mechanism and linkage specificities of the dual retaining beta-Kdo glycosyltransferase modules of KpsC from bacterial capsule biosynthesis.

Doyle, L.Ovchinnikova, O.G.Huang, B.S.Forrester, T.J.B.Lowary, T.L.Kimber, M.S.Whitfield, C.

(2023) J Biol Chem 299: 104609-104609

  • DOI: https://doi.org/10.1016/j.jbc.2023.104609
  • Primary Citation of Related Structures:  
    8FUW, 8FUX

  • PubMed Abstract: 

    KpsC is a dual-module glycosyltransferase (GT) essential for "group 2" capsular polysaccharide biosynthesis in Escherichia coli and other Gram-negative pathogens. Capsules are vital virulence determinants in high-profile pathogens, making KpsC a viable target for intervention with small-molecule therapeutic inhibitors. Inhibitor development can be facilitated by understanding the mechanism of the target enzyme. Two separate GT modules in KpsC transfer 3-deoxy-β-d-manno-oct-2-ulosonic acid (β-Kdo) from cytidine-5'-monophospho-β-Kdo donor to a glycolipid acceptor. The N-terminal and C-terminal modules add alternating Kdo residues with β-(2→4) and β-(2→7) linkages, respectively, generating a conserved oligosaccharide core that is further glycosylated to produce diverse capsule structures. KpsC is a retaining GT, which retains the donor anomeric carbon stereochemistry. Retaining GTs typically use an S N i (substitution nucleophilic internal return) mechanism, but recent studies with WbbB, a retaining β-Kdo GT distantly related to KpsC, strongly suggest that this enzyme uses an alternative double-displacement mechanism. Based on the formation of covalent adducts with Kdo identified here by mass spectrometry and X-ray crystallography, we determined that catalytically important active site residues are conserved in WbbB and KpsC, suggesting a shared double-displacement mechanism. Additional crystal structures and biochemical experiments revealed the acceptor binding mode of the β-(2→4)-Kdo transferase module and demonstrated that acceptor recognition (and therefore linkage specificity) is conferred solely by the N-terminal α/β domain of each GT module. Finally, an Alphafold model provided insight into organization of the modules and a C-terminal membrane-anchoring region. Altogether, we identified key structural and mechanistic elements providing a foundation for targeting KpsC.

  • Organizational Affiliation

    Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Capsule polysaccharide export protein KpsC
A, B
329Escherichia coliMutation(s): 1 
Gene Names: kpsC
Find proteins for A0A0H2Z2W8 (Escherichia coli O1:K1 / APEC)
Explore A0A0H2Z2W8 
Go to UniProtKB:  A0A0H2Z2W8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0H2Z2W8
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
C5P (Subject of Investigation/LOI)
Query on C5P

Download Ideal Coordinates CCD File 
C9 H14 N3 O8 P
PXV (Subject of Investigation/LOI)
Query on PXV

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F [auth A],
K [auth B]
C16 H25 N O3
Query on KDO

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G [auth A],
L [auth B]
3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid
C8 H14 O8
KD3 (Subject of Investigation/LOI)
Query on KD3

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
I [auth B],
J [auth B]
3-deoxy-beta-D-manno-oct-2-ulopyranosonic acid
C8 H14 O8
Query on PO4

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O4 P
Query on CL

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H [auth A],
M [auth B]
Experimental Data & Validation

Experimental Data

  • Resolution: 1.20 Å
  • R-Value Free: 0.157 
  • R-Value Work: 0.124 
  • R-Value Observed: 0.125 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.54α = 90
b = 80.3β = 103.039
c = 65.98γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Natural Sciences and Engineering Research Council (NSERC, Canada)Canada400427

Revision History  (Full details and data files)

  • Version 1.0: 2023-03-08
    Type: Initial release
  • Version 1.1: 2023-04-05
    Changes: Database references
  • Version 1.2: 2023-05-03
    Changes: Database references