OCA at 08:24, 16 August 2023

OCA — Wed, 16 Aug 2023 08:24:20 GMT

←Older revision		Revision as of 08:24, 16 August 2023
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 8h20 is ~~ON HOLD until Paper~~ Publication	+	==Serine Palmitoyltransferase from Sphingobacterium multivorum complexed with Glycine==
		+	<StructureSection load='8h20' size='340' side='right'caption='[[8h20]], [[Resolution\|resolution]] 1.45Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[8h20]] 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=8H20 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8H20 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]] 1.45Å</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=PLG:N-GLYCINE-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YL-METHANE]'>PLG</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=8h20 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8h20 OCA], [https://pdbe.org/8h20 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8h20 RCSB], [https://www.ebi.ac.uk/pdbsum/8h20 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8h20 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) is a key enzyme of sphingolipid biosynthesis, which catalyzes the pyridoxal-5'-phosphate-dependent decarboxylative condensation reaction of l-serine (l-Ser) and palmitoyl-CoA (PalCoA) to form 3-ketodihydrosphingosine called long chain base (LCB). SPT is also able to metabolize l-alanine (l-Ala) and glycine (Gly), albeit with much lower efficiency. Human SPT is a membrane-bound large protein complex containing SPTLC1/SPTLC2 heterodimer as the core subunits, and it is known that mutations of the SPTLC1/SPTLC2 genes increase the formation of deoxy-type of LCBs derived from l-Ala and Gly to cause some neurodegenerative diseases. In order to study the substrate recognition of SPT, we examined the reactivity of Sphingobacterium multivorum SPT on various amino acids in the presence of PalCoA. The S. multivorum SPT could convert not only l-Ala and Gly but also l-homoserine, in addition to l-Ser, into the corresponding LCBs. Furthermore, we obtained high-quality crystals of the ligand-free form and the binary complexes with a series of amino acids, including a nonproductive amino acid, l-threonine, and determined the structures at 1.40 to 1.55 A resolutions. The S. multivorum SPT accommodated various amino acid substrates through subtle rearrangements of the active-site amino acid residues and water molecules. It was also suggested that non-active-site residues mutated in the human SPT genes might indirectly influence the substrate specificity by affecting the hydrogen-bonding networks involving the bound substrate, water molecules, and amino acid residues in the active site of this enzyme. Collectively, our results highlight SPT structural features affecting substrate specificity for this stage of sphingolipid biosynthesis.

-	~~Authors: Murakami~~, T., Takahashi, A., Katayama, A., ~~Miyahara~~, I., ~~Kamiya~~, N., ~~Ikushiro~~, H., ~~Yano~~, T.	+	Structural insights into the substrate recognition of serine palmitoyltransferase from Sphingobacterium multivorum.,Ikushiro H, Murakami T, Takahashi A, Katayama A, Sawai T, Goto H, Koolath S, Murai Y, Monde K, Miyahara I, Kamiya N, Yano T J Biol Chem. 2023 May;299(5):104684. doi: 10.1016/j.jbc.2023.104684. Epub 2023 , Apr 7. PMID:37030501<ref>PMID:37030501</ref>

-	~~Description~~: ~~Serine Palmitoyltransferase from Sphingobacterium multivorum complexed with Glycine~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
-	[[Category: ~~Yano, T~~]]	+	<div class="pdbe-citations 8h20" style="background-color:#fffaf0;"></div>
-	[[Category: ~~Murakami, T~~]]	+	== References ==
-	[[Category: Kamiya, N]]	+	<references/>
-	[[Category: ~~Ikushiro, H~~]]	+	__TOC__
-	[[Category: ~~Takahashi, A~~]]	+	</StructureSection>
-	[[Category: ~~Katayama,~~ A]]	+	[[Category: Large Structures]]
-	[[Category: ~~Miyahara, I~~]]	+	[[Category: Sphingobacterium multivorum]]
		+	[[Category: Ikushiro H]]
		+	[[Category: Kamiya N]]
		+	[[Category: Katayama A]]
		+	[[Category: Miyahara I]]
		+	[[Category: Murakami T]]
		+	[[Category: Takahashi A]]
		+	[[Category: Yano T]]

OCA: Protected "8h20" [edit=sysop:move=sysop]

OCA — Wed, 19 Oct 2022 17:43:03 GMT

Protected "8h20" [edit=sysop:move=sysop]

←Older revision

Revision as of 17:43, 19 October 2022

OCA: New page: '''Unreleased structure''' The entry 8h20 is ON HOLD until Paper Publication Authors: Murakami, T., Takahashi, A., Katayama, A., Miyahara, I., Kamiya, N., Ikushiro, H., Yano, T. Descri...

OCA — Wed, 19 Oct 2022 17:43:02 GMT

New page: '''Unreleased structure''' The entry 8h20 is ON HOLD until Paper Publication Authors: Murakami, T., Takahashi, A., Katayama, A., Miyahara, I., Kamiya, N., Ikushiro, H., Yano, T. Descri...

New page

'''Unreleased structure'''

The entry 8h20 is ON HOLD until Paper Publication

Authors: Murakami, T., Takahashi, A., Katayama, A., Miyahara, I., Kamiya, N., Ikushiro, H., Yano, T.

Description: Serine Palmitoyltransferase from Sphingobacterium multivorum complexed with Glycine
[[Category: Unreleased Structures]]
[[Category: Yano, T]]
[[Category: Murakami, T]]
[[Category: Kamiya, N]]
[[Category: Ikushiro, H]]
[[Category: Takahashi, A]]
[[Category: Katayama, A]]
[[Category: Miyahara, I]]

8h20 - Revision history

OCA at 08:24, 16 August 2023

OCA: Protected "8h20" [edit=sysop:move=sysop]

OCA: New page: '''Unreleased structure''' The entry 8h20 is ON HOLD until Paper Publication Authors: Murakami, T., Takahashi, A., Katayama, A., Miyahara, I., Kamiya, N., Ikushiro, H., Yano, T. Descri...