4MZU

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

Summary for 4MZU

• Entry DOI: 10.2210/pdb4mzu/pdb
• Descriptor: WxcM-like protein, COENZYME A, THYMIDINE-5'-DIPHOSPHATE, ... (6 entities in total)
• Functional Keywords: beta-helix, cupin, ketoisomerase, n-acetyltransferase, acetyl-coenzyme a, dtdp-fuc3n, dtdp-4-keto-6-deoxyglucose, isomerase, transferase
• Biological source: Shewanella denitrificans
• Total number of polymer chains: 12
• Total formula weight: 433464.71

Authors

Chantigian, D.P.,Thoden, J.B.,Holden, H.M. (deposition date: 2013-09-30, release date: 2013-10-09, Last modification date: 2024-04-03)

Primary citation

Chantigian, D.P.,Thoden, J.B.,Holden, H.M.
Structural and Biochemical Characterization of a Bifunctional Ketoisomerase/N-Acetyltransferase from Shewanella denitrificans.
Biochemistry, 52:8374-8385, 2013

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 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.

PubMed: 24128043
DOI: 10.1021/bi401170t

Experimental method

X-RAY DIFFRACTION (2.2 Å)