Category:LBS: Difference between revisions

Revision as of 03:46, 2 December 2015

Sphingolipid

Upper classes: LB

Class Overview

The Sphingolipid category (LBS) in the database includes phosphosphingolipid and glycosphingolipid.

Sphingolipid Overview
Phosphosphingolipid (including glycosyl phosphoinositolceramide or GIPC) スフィンゴリン脂質 (GIPC含む)	Cerebroside (monoglycosylceramide) セレブロシド (糖の数 n = 1)	Glycosphingolipid (glycosylceramide) スフィンゴ糖脂質 (糖の数 n > 1)

Sphingosine & Ceramide

Sphingolipids were first isolated from brain by J.L.W. Thudichum (1829-1901) as lipids of unknown function and structure. The name "sphingo" comes from the Greek word sphingein for holding tight. (The Sphinx also comes from this word root. See the Wikipedia article for Sphinx, as well as sphincter muscle.) The basic structure is a long-chain base, usually sphingosine (2-amino-4-octadecene-1,3-diol abbreviated as d18:1), whose amino-group is acylated with a long-chain fatty acid. This hydrophobic structure is called ceramides.

スフィンゴ脂質は J.L.W. Thudichum (1829-1901) により機能や構造未知の脂質として脳から見いだされました。スフィンゴという名前はギリシャ語の sphingein に由来しており、「固く縛る」という意味です。（スフィンクスの語源もこれに同じで、括約筋のことを英語で sphincter muscle といいます。）基本骨格は長鎖塩基 (長鎖アミノアルコール、通常はd18:1と記載されるスフィンゴシン) のアミノ基が長鎖脂肪酸とアミド結合したもので、セラミドと呼ばれます。

Ceramides with the sphingoid are prevalent as membrane components of eukaryotic cells. Sphingomyelin is a ceramide with phosphocholine. Some ceramides are organ-specific.

スフィンゴ骨格をもつセラミドは細胞組織の膜成分として普遍的に存在します。セラミドにホスホコリンがついたものが有名なスフィンゴミエリンです。臓器特異的なセラミドもあります。

Biosynthesis

Sphingosine is synthesized from decarboxylating condensation of palmitoyl CoA with serine on the ER membrane. It is a 18-carbon amino alcohol (16 carbons from palmitic acid and 2 from serine) with one unsaturated bond (trans-form) at the C-4 position (2-amino-4-octadecene-1,3-diol). (more details)

スフィンゴシンはパルミトイルCoAがアミノ酸セリンと脱炭酸縮合して生成します。炭素を18個含むアミノアルコール(16個がパルミチン酸、2個がセリン由来)でトランス型の不飽和結合をC-4に1つ含みます。（詳細はこちら）

Sphingolipid スフィンゴ脂質

Notation

Symbol Abbreviations (e.g. Glc = glucose)
Backbones
Cer	ceramide	セラミド
Sph	sphingosine	スフィンゴシン
Sugars
Glc	glucose	グルコース
Gal	galactose	ガラクトース
GlcNAc	N-acetyl-glucosamine	N-アセチルグルコサミン
GalNAc	N-acetyl-galactosamine	N-アセチルガラクトサミン
GlcN	glucosamine	グルコサミン
GalN	galactosamine	ガラクトサミン
GlcA	glucuronic acid	グルクロン酸
GalA	galacturonic acid	ガラクツロン酸
Man	mannose	マンノース
Rha	rhamnose (= 6-deoxy-mannose)	ラムノース (6-デオキシマンノース)
Ins	inositol	イノシトール
Fuc	fucose (= 6-deoxy-galactose)	フコース (6-デオキシガラクトース)
Ara	arabinose	アラビノース
Xyl	xylose	キシロース
NeuNH	(deacetyl) neuraminic acid (pyruvate + mannosamine)	ノイラミン酸 (ピルビン酸＋マンノサミン)
NeuAc	N-acetyl-neuraminic acid	N-アセチルノイラミン酸
NeuGc	N-glycolyl-neuraminic acid	N-グリコリルノイラミン酸
KDN	2-keto-3-deoxy-D-glycero- D-galacto-nononic acid	デアミノノイラミン酸
Modifiers
AEPn	aminoethylphosphonic acid, or (2-aminoethyl)hydroxyphosphoryl-	アミノエチルホスホン酸（C-P結合）
MAEPn	N-methyl aminoethylphosphonic acid, or (N-methyl-2-aminoethyl) hydroxyphosphoryl-	AEPnのN-メチル体（C-P結合）
EtnP	phosphoethanolamine (PEA), or 2-aminoethanolphospho-	ホスホエタノールアミン
PC	Phosphocholine	ホスホコリン
Butenyl	Butenyl	ブテニル基
Me	Methyl	メチル基
Et	Ethyl	エチル基

Page/ID-Code Design

L

B

S

G/P

s1

s2

n1

n2

y

c1

c2

G/P	G (glyco)	P (phospho)
s1, s2	structure code as explained below
n1, n2	number of sugars (2 digits)
y	number of sialic acids (1 digit)
c1, c2	serial numbers

First (s1) Code for Glycosphingolipid

First sugar

Code

Root sequence

Major Series

Cerebroside

For GalCer and GlcCer, visit this page.

starting with
Galactose

LBSG1|G1
(LBSG1.....|7|8|9|9|Number_of_Sugars|Number_of_Sialic_acids|79 items)

Gal-Cer

Mainchain.*Gala1-4?6?Galb1-Cer\|Gala	Gal_α1-4/6Gal_β1-Cer
Mainchain.*Galb1-4Glcb1-3Galb1-Cer\|Spirometo	Gal_β1-4Glc_β1-3Gal_β1-Cer

starting with
Glucose

LBSG2|G2
(LBSG2.....|7|8|9|9|Number_of_Sugars|Number_of_Sialic_acids|88 items)

GalNAc_β-Gal_β-Glc_β-Cer

Mainchain.*GalNAcb1-4Galb1-4Glcb1-Cer\|Ganglio	GalNAc_β1-4Gal_β1-4Glc_β1-Cer
Mainchain.*GalNAcb1-3Galb1-4Glcb1-Cer\|Isoganglio	GalNAc_β1-3Gal_β1-4Glc_β1-Cer
Structure.GlcNAcb1-3\(.GalNAcb1-4\)Galb1-4Glcb1-Cer\|Lactoganglio	GlcNAc_β1-3(GalNAc_β1-4)Gal_β1-4Glc_β1-Cer
Structure.*\(?NeuAca2-3\)?Galb1-4Glcb1-Cer\|a-series	(NeuAc_α2-3)Gal_β1-4Glc_β1-Cer
Structure.*\(?NeuAca2-8NeuAca2-3\)?Galb1-4Glcb1-Cer\|b-series	(NeuAc_α2-8NeuAc_α2-3)Gal_β1-4Glc_β1-Cer
Structure.*\(?NeuAca2-8NeuAca2-8NeuAca2-3\)?Galb1-4Glcb1-Cer\|c-series	(NeuAc_α2-8NeuAc_α2-8NeuAc_α2-3)Gal_β1-4Glc_β1-Cer
Structure.*\(?NeuAca2-6\)?GalNAcb1-4Galb1-4Glcb1-Cer\|α-series	(NeuAc_α2-6)GalNAc_β1-4Gal_β1-4Glc_β1-Cer
Structure.*\(?NeuAca2-8NeuAca2-6\)?GalNAcb1-4Galb1-4Glcb1-Cer\|β-series	(NeuAc_α2-8NeuAc_α2-6)GalNAc_β1-4Gal_β1-4Glc_β1-Cer

LBSG3|G3
(LBSG3.....|7|8|9|9|Number_of_Sugars|Number_of_Sialic_acids|173 items)

GlcNAc_β-Gal_β-Glc_β-Cer

Mainchain.*Galb1-3GlcNAcb1-3Galb1-4Glcb1-Cer\|Lacto	Gal_β1-3GlcNAc_β1-3Gal_β1-4Glc_β1-Cer
Mainchain.*Gal.1-4GlcNAcb1-3Galb1-4Glcb1-Cer\|Neolacto	Gal_β1-4GlcNAc_β1-3Gal_β1-4Glc_β1-Cer

LBSG4|G4
(LBSG4.....|7|8|9|9|Number_of_Sugars|Number_of_Sialic_acids|55 items)

Gal_α-Gal_β-Glc_β-Cer

Mainchain.*Gala1-4Galb1-4Glcb1-Cer\|Globo	Gal_α1-4Gal_β1-4Glc_β1-Cer
Mainchain.*Gala1-3Galb1-4Glcb1-Cer\|Isoglobo	Gal_α1-3Gal_β1-4Glc_β1-Cer

LBSG5|G5
(LBSG5.....|7|8|9|9|Number_of_Sugars|Number_of_Sialic_acids|113 items)

Gal-Glc-Cer
(Other than G2∼G4)

Mainchain.*Galb1-4Galb1-4Glcb1-Cer|Muco

Gal_β1-4Gal_β1-4Glc_β1-Cer

LBSG6|G6
(LBSG6.....|7|8|9|9|Number_of_Sugars|Number_of_Sialic_acids|68 items)

Man-Glc_β-Cer

Mainchain.*GlcNAcb1-3Manb1-4Glcb1-Cer\|Arthro	GlcNAc_β1-3Man_β1-4Glc_β1-Cer
Mainchain.*Mana1-3Manb1-4Glcb1-Cer\|Mollu	Man_α1-3Man_β1-4Glcb1.Cer

LBSG7|G7
(LBSG7.....|7|8|9|9|Number_of_Sugars|Number_of_Sialic_acids|21 items)

NeuAc/NeuGc-Glc_β-Cer

Mainchain.*Neu(A~G)c.2-6Glcb1-Cer|Echino

NeuGc or NeuAc_α2-6Glc_β1-Cer

LBSG8|G8
(LBSG8.....|7|8|9|9|Number_of_Sugars|Number_of_Sialic_acids|12 items)

GalNAc-Glc-Cer

Mainchain.*GalNAc.1-4Glc.1-Cer|Plathy

GalNAc_β1-4Glc_β1-Cer

starting with
Other Sugars

LBSG(A~B~C~D~E~F~G~H~I~J~K~L~M~N~O~P~Q~R~S~T~U)|G(A∼Z)

Symbols follow the Sugar-digit table.

First sugar

Code

Root sequence

Major Series

No Sugar Attached

LBSP1|P1

R-P-Cer

Sphingomyelin and Phosphoetanolamine-ceramide
(Visit this page.)

starting with
Inositol

LBSP2|P2
(29 items)

GlcN_α/β1−2/6Ins₁-P-Cer

Mainchain.*GlcN.1-.Ins-P-Cer|Protozoa & Fungi-specific

GlcN_α/β1-2/6Ins1-P-Cer

LBSP3|P3
(10 items)

GlcA_α/β1−2/6Ins₁-P-Cer

Mainchain.*GlcA.1-.Ins-P-Cer|Plant-specific

GlcA_α/β1-2/6Ins1-P-Cer

LBSP4|P4
(52 items)

Man_α/β1−2/6Ins₁-P-Cer

Mainchain.*Man.1-.Ins-P-Cer|Fungi-specific

Man_α/β1-2/6Ins1-P-Cer

LBSP5|P5
(21 items)

Others

Ins1-P-Cer

Second (s2) Code for subsequent sugars

For abbreviations, see #Notation.

Code	Structure
A	Glc
B	Gal
C	GlcNAc
D	GalNAc
E	GlcN
F	GalN
G	GlcA
H	GalA
I	not used

Code	Structure
J	Structure.*Man\|Mannose
K	Structure.*Rha\|Rhamnose
L	%53%74%72%75%63%74%75%72%65%2e%2A%49%6e%73%28%4d%65%29%3F%2d%50%2d%5B%5E%43%65%72%5D\|Inositol
M	Fucose (%53%74%72%75%63%74%75%72%65%5B%5E%46%5D%2B%46%75%63%5B%5E%46%5D%2B%24\| 1, %53%74%72%75%63%74%75%72%65%28%5B%5E%46%5D%2B%46%75%63%29%7B%32%7D%5B%5E%46%5D%2B%24\|2, %53%74%72%75%63%74%75%72%65%28%5B%5E%46%5D%2B%46%75%63%29%7B%33}\|>3)
N	Structure.*Ara\|Arabinose
O	Structure.*Xyl\|Xylose
P	Structure.*(NeuAc~NeuNH)\|NeuAc / NeuNH
Q	Structure.*(NeuGc)\|NeuGc
R	Structure.*(KDN)\|KDN

Code	Structure
S	Structure.*(Phospho)\|Phosphate (except GIPC)
T	Structure.(AEPn)\|(M)AEPn, Structure.(EtnP)\|EtnP, Structure.*(PC)\|PC
U	Structure.*Sulfo\|Sulfate
V	acyl/alkyl/alkenyl chain

Subcategories

This category has the following 4 subcategories, out of 4 total.

L

@@ Line 19: / Line 19: @@
 | align="center" style="vertical-align:top" width=33%|
 [[:Category:LBSC|'''Cerebroside''' (monoglycosylceramide)]]
-<br>[[Image:LBSnn.png|120px]]<br/><small>セレブロシド (糖の数 n = 1)</small>
+<br>[[Image:LBS01.png|120px]]<br/><small>セレブロシド (糖の数 n = 1)</small>
 | align="center" style="vertical-align:top" width=33%|
 '''Glyco'''sphingolipid (glycosylceramide)