4MZU

Crystal structure of FdtD, a bifunctional ketoisomerase/N-acetyltransferase from Shewanella denitrificans


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.204 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural and Biochemical Characterization of a Bifunctional Ketoisomerase/N-Acetyltransferase from Shewanella denitrificans.

Chantigian, D.P.Thoden, J.B.Holden, H.M.

(2013) Biochemistry 52: 8374-8385

  • DOI: 10.1021/bi401170t

  • PubMed Abstract: 
  • Unusual N-acetylated sugars have been observed on the O-antigens of some Gram-negative bacteria and on the S-layers of both Gram-positive and Gram-negative bacteria. One such sugar is 3-acetamido-3,6-dideoxy-α-d-galactose or Fuc3NAc. The pathway for ...

    Unusual N-acetylated sugars have been observed on the O-antigens of some Gram-negative bacteria and on the S-layers of both Gram-positive and Gram-negative bacteria. One such sugar is 3-acetamido-3,6-dideoxy-α-d-galactose or Fuc3NAc. The pathway for its production requires five enzymes with the first step involving the attachment of dTMP to glucose-1-phosphate. Here, we report a structural and biochemical characterization of a bifunctional enzyme from Shewanella denitificans thought to be involved in the biosynthesis of dTDP-Fuc3NAc. On the basis of a bioinformatics analysis, the enzyme, hereafter referred to as FdtD, has been postulated to catalyze the third and fifth steps in the pathway, namely, a 3,4-keto isomerization and an N-acetyltransferase reaction. For the X-ray analysis reported here, the enzyme was crystallized in the presence of dTDP and CoA. The crystal structure shows that FdtD adopts a hexameric quaternary structure with 322 symmetry. Each subunit of the hexamer folds into two distinct domains connected by a flexible loop. The N-terminal domain adopts a left-handed β-helix motif and is responsible for the N-acetylation reaction. The C-terminal domain folds into an antiparallel flattened β-barrel that harbors the active site responsible for the isomerization reaction. Biochemical assays verify the two proposed catalytic activities of the enzyme and reveal that the 3,4-keto isomerization event leads to the inversion of configuration about the hexose C-4' carbon.


    Organizational Affiliation

    Department of Biochemistry, University of Wisconsin , Madison, Wisconsin 53706, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
WxcM-like protein
A, B, C, D, E, F, G, H, I, J, K, L
312Shewanella denitrificans (strain OS217 / ATCC BAA-1090 / DSM 15013)Mutation(s): 0 
Find proteins for Q12KT8 (Shewanella denitrificans (strain OS217 / ATCC BAA-1090 / DSM 15013))
Go to UniProtKB:  Q12KT8
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TDR
Query on TDR

Download SDF File 
Download CCD File 
A, B, C, D, E, F, J, K, L
THYMINE
C5 H6 N2 O2
RWQNBRDOKXIBIV-UHFFFAOYSA-N
 Ligand Interaction
COA
Query on COA

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, I, J, K, L
COENZYME A
C21 H36 N7 O16 P3 S
RGJOEKWQDUBAIZ-IBOSZNHHSA-N
 Ligand Interaction
TYD
Query on TYD

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H, I, J, K, L
THYMIDINE-5'-DIPHOSPHATE
C10 H16 N2 O11 P2
UJLXYODCHAELLY-XLPZGREQSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
B, C, D, G, J
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.204 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 85.314α = 79.23
b = 109.443β = 79.98
c = 127.847γ = 84.89
Software Package:
Software NamePurpose
HKL-3000data scaling
HKL-3000data reduction
HKL-3000data collection
REFMACrefinement
SOLVEphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-10-09
    Type: Initial release
  • Version 1.1: 2013-12-18
    Type: Database references