8guh: Difference between revisions
New page: '''Unreleased structure''' The entry 8guh is ON HOLD Authors: Murakami, T., Takahashi, A., Katayama, A., Miyahara, I., Kamiya, N., Ikushiro, H., Yano, T. Description: Serine Palmitoylt... |
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==Serine Palmitoyltransferase from Sphingobacterium multivorum complexed with Tris== | |||
<StructureSection load='8guh' size='340' side='right'caption='[[8guh]], [[Resolution|resolution]] 1.65Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[8guh]] 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=8GUH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8GUH 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]] 1.65Å</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=K9E:[4-[[[2-(hydroxymethyl)-1,3-bis(oxidanyl)propan-2-yl]amino]methyl]-6-methyl-5-oxidanyl-pyridin-3-yl]methyl+dihydrogen+phosphate'>K9E</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=8guh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8guh OCA], [https://pdbe.org/8guh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8guh RCSB], [https://www.ebi.ac.uk/pdbsum/8guh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8guh 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) catalyses the first reaction in sphingolipid biosynthesis: the decarboxylative condensation of L-serine (L-Ser) and palmitoyl-CoA to form 3-ketodihydrosphingosine. SPT from Sphingobacterium multivorum has been isolated and its crystal structure in complex with L-Ser has been determined at 2.3 A resolution (PDB entry 3a2b). However, the quality of the crystal was not good enough to judge the conformation of the cofactor molecule and the orientations of the side chains of the amino-acid residues in the enzyme active site. The crystal quality was improved by revision of the purification procedure and by optimization of both the crystallization procedure and the post-crystallization treatment conditions. Here, the crystal structure of SPT complexed with tris(hydroxymethyl)aminomethane (Tris), a buffer component, was determined at 1.65 A resolution. The protein crystallized at 20 degrees C and diffraction data were collected from the crystals to a resolution of 1.65 A. The crystal belonged to the tetragonal space group P4(1)2(1)2, with unit-cell parameters a = b = 61.32, c = 208.57 A. Analysis of the crystal structure revealed C4-C5-C5A-O4P (77 degrees ) and C5-C5A-O4P-P (-143 degrees ) torsion angles in the phosphate-group moiety of the cofactor pyridoxal 5'-phosphate (PLP) that are more reasonable than those observed in the previously reported crystal structure (14 degrees and 151 degrees , respectively). Furthermore, the clear electron density showing a Schiff-base linkage between PLP and the bulky artificial ligand Tris indicated exceptional flexibility of the active-site cavity of this enzyme. These findings open up the possibility for further study of the detailed mechanisms of substrate recognition and catalysis by this enzyme. | |||
Crystal structure of Sphingobacterium multivorum serine palmitoyltransferase complexed with tris(hydroxymethyl)aminomethane.,Ikushiro H, Takahashi A, Murakami T, Katayama A, Sawai T, Goto H, Miyahara I, Kamiya N, Yano T Acta Crystallogr F Struct Biol Commun. 2022 Dec 1;78(Pt 12):408-415. doi: , 10.1107/S2053230X22010937. Epub 2022 Nov 28. PMID:36458620<ref>PMID:36458620</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[Category: | </div> | ||
[[Category: | <div class="pdbe-citations 8guh" style="background-color:#fffaf0;"></div> | ||
[[Category: Ikushiro | |||
[[Category: | ==See Also== | ||
[[Category: | *[[Serine palmitoyltransferase 3D structures|Serine palmitoyltransferase 3D structures]] | ||
[[Category: | == References == | ||
[[Category: | <references/> | ||
[[Category: | __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]] | |||
Latest revision as of 21:14, 29 November 2023
Serine Palmitoyltransferase from Sphingobacterium multivorum complexed with TrisSerine Palmitoyltransferase from Sphingobacterium multivorum complexed with Tris
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) catalyses the first reaction in sphingolipid biosynthesis: the decarboxylative condensation of L-serine (L-Ser) and palmitoyl-CoA to form 3-ketodihydrosphingosine. SPT from Sphingobacterium multivorum has been isolated and its crystal structure in complex with L-Ser has been determined at 2.3 A resolution (PDB entry 3a2b). However, the quality of the crystal was not good enough to judge the conformation of the cofactor molecule and the orientations of the side chains of the amino-acid residues in the enzyme active site. The crystal quality was improved by revision of the purification procedure and by optimization of both the crystallization procedure and the post-crystallization treatment conditions. Here, the crystal structure of SPT complexed with tris(hydroxymethyl)aminomethane (Tris), a buffer component, was determined at 1.65 A resolution. The protein crystallized at 20 degrees C and diffraction data were collected from the crystals to a resolution of 1.65 A. The crystal belonged to the tetragonal space group P4(1)2(1)2, with unit-cell parameters a = b = 61.32, c = 208.57 A. Analysis of the crystal structure revealed C4-C5-C5A-O4P (77 degrees ) and C5-C5A-O4P-P (-143 degrees ) torsion angles in the phosphate-group moiety of the cofactor pyridoxal 5'-phosphate (PLP) that are more reasonable than those observed in the previously reported crystal structure (14 degrees and 151 degrees , respectively). Furthermore, the clear electron density showing a Schiff-base linkage between PLP and the bulky artificial ligand Tris indicated exceptional flexibility of the active-site cavity of this enzyme. These findings open up the possibility for further study of the detailed mechanisms of substrate recognition and catalysis by this enzyme. Crystal structure of Sphingobacterium multivorum serine palmitoyltransferase complexed with tris(hydroxymethyl)aminomethane.,Ikushiro H, Takahashi A, Murakami T, Katayama A, Sawai T, Goto H, Miyahara I, Kamiya N, Yano T Acta Crystallogr F Struct Biol Commun. 2022 Dec 1;78(Pt 12):408-415. doi: , 10.1107/S2053230X22010937. Epub 2022 Nov 28. PMID:36458620[2] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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