8iyp: Difference between revisions
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New page: '''Unreleased structure''' The entry 8iyp is ON HOLD Authors: Description: Category: Unreleased Structures |
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==Crystal structure of serine palmitoyltransferase soaked in 190 mM D-serine solution== | |||
<StructureSection load='8iyp' size='340' side='right'caption='[[8iyp]], [[Resolution|resolution]] 1.65Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[8iyp]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Sphingobacterium_multivorum Sphingobacterium multivorum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8IYP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8IYP FirstGlance]. <br> | |||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.651Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=PLS:[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL]-SERINE'>PLS</scene></td></tr> | |||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=8iyp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8iyp OCA], [https://pdbe.org/8iyp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8iyp RCSB], [https://www.ebi.ac.uk/pdbsum/8iyp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8iyp ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/SPT_SPHMU SPT_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).<ref>PMID:17557831</ref> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Serine 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<ref>PMID:38325740</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[Category: | </div> | ||
<div class="pdbe-citations 8iyp" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Large Structures]] | |||
[[Category: Sphingobacterium multivorum]] | |||
[[Category: Ikushiro H]] | |||
[[Category: Kamiya N]] | |||
[[Category: Katayama A]] | |||
[[Category: Miyahara I]] | |||
[[Category: Murakami T]] | |||
[[Category: Takahashi A]] | |||
[[Category: Yano T]] | |||
