8iyp | pdb_00008iyp
Crystal structure of serine palmitoyltransferase soaked in 190 mM D-serine solution
Structural highlights
FunctionSPT_SPHMU Catalyzes the condensation of L-serine with palmitoyl-CoA (hexadecanoyl-CoA) to produce 3-oxosphinganine (PubMed:17557831). Exhibits a broad substrate specificity concerning the chain length and the degree of unsaturation of acyl-CoA (PubMed:17557831).[1] Publication Abstract from PubMedSerine palmitoyltransferase (SPT) catalyzes the pyridoxal-5'-phosphate (PLP)-dependent decarboxylative condensation of l-serine and palmitoyl-CoA to form 3-ketodihydrosphingosine (KDS). Although SPT was shown to synthesize corresponding products from amino acids other than l-serine, it is still arguable whether SPT catalyzes the reaction with d-serine, which is a question of biological importance. Using high substrate and enzyme concentrations, KDS was detected after the incubation of SPT from Sphingobacterium multivorum with d-serine and palmitoyl-CoA. Furthermore, the KDS comprised equal amounts of 2S and 2R isomers. (1)H-NMR study showed a slow hydrogen-deuterium exchange at Calpha of serine mediated by SPT. We further confirmed that SPT catalyzed the racemization of serine. The rate of the KDS formation from d-serine was comparable to those for the alpha-hydrogen exchange and the racemization reaction. The structure of the d-serine-soaked crystal (1.65 A resolution) showed a distinct electron density of the PLP-l-serine aldimine, interpreted as the racemized product trapped in the active site. The structure of the alpha-methyl-d-serine-soaked crystal (1.70 A resolution) showed the PLP-alpha-methyl-d-serine aldimine, mimicking the d-serine-SPT complex prior to racemization. Based on these enzymological and structural analyses, the synthesis of KDS from d-serine was explained as the result of the slow racemization to l-serine, followed by the reaction with palmitoyl-CoA, and SPT would not catalyze the direct condensation between d-serine and palmitoyl-CoA. It was also shown that the S. multivorum SPT catalyzed the racemization of the product KDS, which would explain the presence of (2R)-KDS in the reaction products. Racemization of the substrate and product by serine palmitoyltransferase from Sphingobacterium multivorum yields two enantiomers of the product from d-serine.,Ikushiro H, Honda T, Murai Y, Murakami T, Takahashi A, Sawai T, Goto H, Ikushiro SI, Miyahara I, Hirabayashi Y, Kamiya N, Monde K, Yano T J Biol Chem. 2024 Mar;300(3):105728. doi: 10.1016/j.jbc.2024.105728. Epub 2024 , Feb 5. PMID:38325740[2] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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