1GA8

CRYSTAL STRUCTURE OF GALACOSYLTRANSFERASE LGTC IN COMPLEX WITH DONOR AND ACCEPTOR SUGAR ANALOGS.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.189 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of the retaining galactosyltransferase LgtC from Neisseria meningitidis in complex with donor and acceptor sugar analogs.

Persson, K.Ly, H.D.Dieckelmann, M.Wakarchuk, W.W.Withers, S.G.Strynadka, N.C.

(2001) Nat.Struct.Mol.Biol. 8: 166-175

  • DOI: 10.1038/84168
  • Primary Citation of Related Structures:  1G9R

  • PubMed Abstract: 
  • Many bacterial pathogens express lipooligosaccharides that mimic human cell surface glycoconjugates, enabling them to attach to host receptors and to evade the immune response. In Neisseria meningitidis, the galactosyltransferase LgtC catalyzes a key ...

    Many bacterial pathogens express lipooligosaccharides that mimic human cell surface glycoconjugates, enabling them to attach to host receptors and to evade the immune response. In Neisseria meningitidis, the galactosyltransferase LgtC catalyzes a key step in the biosynthesis of lipooligosaccharide structure by transferring alpha-d-galactose from UDP-galactose to a terminal lactose. The product retains the configuration of the donor sugar glycosidic bond; LgtC is thus a retaining glycosyltranferase. We report the 2 A crystal structures of the complex of LgtC with manganese and UDP 2-deoxy-2-fluoro-galactose (a donor sugar analog) in the presence and absence of the acceptor sugar analog 4'-deoxylactose. The structures, together with results from site-directed mutagenesis and kinetic analysis, give valuable insights into the unique catalytic mechanism and, as the first structure of a glycosyltransferase in complex with both the donor and acceptor sugars, provide a starting point for inhibitor design.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, University of British Columbia, 2146 Health Sciences Mall, Vancouver, British Columbia, Canada V6T 1Z3.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GALACTOSYL TRANSFERASE LGTC
A
311Neisseria meningitidisGene Names: lgtC
Find proteins for Q93EK7 (Neisseria meningitidis)
Go to UniProtKB:  Q93EK7
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
A
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
UPF
Query on UPF

Download SDF File 
Download CCD File 
A
URIDINE-5'-DIPHOSPHATE-2-DEOXY-2-FLUOROGALACTOSE
URIDINE-5'-MONOPHOSPHATE 2-DEOXY-2-FLUORO-GALACTOPYRANOSYL-MONOPHOSPHATE ESTER
C15 H23 F N2 O16 P2
NGTCPFGWXMBZEP-KBQKSTHMSA-N
 Ligand Interaction
DEL
Query on DEL

Download SDF File 
Download CCD File 
A
4-DEOXYLACTOSE
C12 H22 O10
DSYGIMVFFQCOQZ-KYYLAPRMSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
DELKi: 16000000 nM BINDINGMOAD
UPFKi: 2000 nM BINDINGMOAD
DELKi: 16000000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.189 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 39.975α = 90.00
b = 76.158β = 90.00
c = 87.228γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
SCALEPACKdata scaling
CNSphasing
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-02-14
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance