6MGB

Thermosulfurimonas dismutans KpsC, beta Kdo 2,4 transferase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.183 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Biosynthesis of a conserved glycolipid anchor for Gram-negative bacterial capsules.

Doyle, L.Ovchinnikova, O.G.Myler, K.Mallette, E.Huang, B.S.Lowary, T.L.Kimber, M.S.Whitfield, C.

(2019) Nat.Chem.Biol. --: --

  • DOI: 10.1038/s41589-019-0276-8
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Several important Gram-negative bacterial pathogens possess surface capsular layers composed of hypervariable long-chain polysaccharides linked via a conserved 3-deoxy-β-D-manno-oct-2-ulosonic acid (β-Kdo) oligosaccharide to a phosphatidylglycerol re ...

    Several important Gram-negative bacterial pathogens possess surface capsular layers composed of hypervariable long-chain polysaccharides linked via a conserved 3-deoxy-β-D-manno-oct-2-ulosonic acid (β-Kdo) oligosaccharide to a phosphatidylglycerol residue. The pathway for synthesis of the terminal glycolipid was elucidated by determining the structures of reaction intermediates. In Escherichia coli, KpsS transfers a single Kdo residue to phosphatidylglycerol; this primer is extended using a single enzyme (KpsC), possessing two cytidine 5'-monophosphate (CMP)-Kdo-dependent glycosyltransferase catalytic centers with different linkage specificities. The structure of the N-terminal β-(2→4) Kdo transferase from KpsC reveals two α/β domains, supplemented by several helices. The N-terminal Rossmann-like domain, typically responsible for acceptor binding, is severely reduced in size compared with canonical GT-B folds in glycosyltransferases. The similar structure of the C-terminal β-(2→7) Kdo transferase indicates a past gene duplication event. Both Kdo transferases have a narrow active site tunnel, lined with key residues shared with GT99 β-Kdo transferases. This enzyme provides the prototype for the GT107 family.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Capsular polysaccharide export system protein KpsC
A
326Thermosulfurimonas dismutansMutation(s): 0 
Find proteins for A0A179D1D1 (Thermosulfurimonas dismutans)
Go to UniProtKB:  A0A179D1D1
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
C5P
Query on C5P

Download SDF File 
Download CCD File 
A
CYTIDINE-5'-MONOPHOSPHATE
C9 H14 N3 O8 P
IERHLVCPSMICTF-XVFCMESISA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.183 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 50.020α = 90.00
b = 65.540β = 90.00
c = 121.080γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
PHENIXphasing
XSCALEdata scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Natural Sciences and Engineering Research Council (Canada)Canada04045-2015

Revision History 

  • Version 1.0: 2019-03-27
    Type: Initial release
  • Version 1.1: 2019-05-01
    Type: Data collection, Database references
  • Version 1.2: 2019-05-08
    Type: Data collection, Database references
  • Version 1.3: 2019-05-15
    Type: Data collection, Database references