3a2b

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

spinqualitylabelsall models 3a2b, resolution 2.30Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 3a2b is a 1 chain structure with sequence from Sphingobacterium multivorum. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Ligands: PLP, SER Gene: spt (Sphingobacterium multivorum) Activity: Serine C-palmitoyltransferase, with EC number 2.3.1.50 Resources: FirstGlance, OCA, RCSB, PDBsum Evolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMed 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. Structural insights into the enzymatic mechanism of serine palmitoyltransferase from Sphingobacterium multivorum.,Ikushiro H, Islam MM, Okamoto A, Hoseki J, Murakawa T, Fujii S, Miyahara I, Hayashi H J Biochem. 2009 Oct;146(4):549-62. Epub 2009 Jun 29. PMID:19564159 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See Also Serine palmitoyltransferase

Proteopedia Page Contributors and Editors (what is this?)

OCA