3A2B

Crystal Structure of Serine Palmitoyltransferase from Sphingobacterium multivorum with substrate L-serine

Summary for 3A2B

• Entry DOI: 10.2210/pdb3a2b/pdb
• Descriptor: Serine palmitoyltransferase, SERINE, PYRIDOXAL-5'-PHOSPHATE, ... (4 entities in total)
• Functional Keywords: vitamin b6-dependent enzyme fold type i, acyltransferase, pyridoxal phosphate, transferase
• Biological source: Sphingobacterium multivorum
• Total number of polymer chains: 1
• Total formula weight: 44043.92

Authors

Okamoto, A.,Hoseki, J. (deposition date: 2009-05-09, release date: 2009-07-14, Last modification date: 2023-11-01)

Primary citation

Ikushiro, H.,Islam, M.M.,Okamoto, A.,Hoseki, J.,Murakawa, T.,Fujii, S.,Miyahara, I.,Hayashi, H.
Structural Insights into the Enzymatic Mechanism of Serine Palmitoyltransferase from Sphingobacterium multivorum
J.Biochem., 146:549-562, 2009

PubMed Abstract: Serine palmitoyltransferase (SPT) is a key enzyme of sphingolipid biosynthesis and catalyses the pyridoxal 5'-phosphate (PLP)-dependent decarboxylative condensation reaction of l-serine with palmitoyl-CoA to generate 3-ketodihydrosphingosine. The crystal structure of SPT from Sphingobacterium multivorum GTC97 complexed with l-serine was determined at 2.3 A resolution. The electron density map showed the Schiff base formation between l-serine and PLP in the crystal. Because of the hydrogen bond formation with His138, the orientation of the Calpha-H bond of the PLP-l-serine aldimine was not perpendicular to the PLP-Schiff base plane. This conformation is unfavourable for the alpha-proton abstraction by Lys244 and the reaction is expected to stop at the PLP-l-serine aldimine. Structural modelling of the following intermediates indicated that His138 changes its hydrogen bond partner from the carboxyl group of l-serine to the carbonyl group of palmitoyl-CoA upon the binding of palmitoyl-CoA, making the l-serine Calpha-H bond perpendicular to the PLP-Schiff base plane. These crystal and model structures well explained the observations on bacterial SPTs that the alpha-deprotonation of l-serine occurs only in the presence of palmitoyl-CoA. This study provides the structural evidence that directly supports our proposed mechanism of the substrate synergism in the SPT reaction.

PubMed: 19564159
DOI: 10.1093/jb/mvp100

Experimental method

X-RAY DIFFRACTION (2.3 Å)