Category:LBS: Difference between revisions

Revision as of 07:57, 15 March 2016

Sphingolipid

Upper classes: LB

Class Overview

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

Sphingolipid Overview
Phosphosphingolipid (including GIPC) スフィンゴリン脂質 (GIPC含む)	Glycosphingolipid スフィンゴ糖脂質 Cerebroside セレブロシド (n = 1) Glycosylceramide (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 basic structure is a long-chain base (long-chain amino-alcohol) whose amino-group is acylated with a long-chain fatty acid. This hydrophobic structure is called ceramides. Sphingolipids consist of phospho-sphingolipids and glyco-sphingolipids, whose ceramide structure is bonded with phosphate and (poly)saccharides, respectively. Phosphosphingolipids include sphingomyelin and glycosphingolipids include cerebrosides and gangliosides. They are abundant in neural tissues.

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。基本骨格は長鎖塩基 (長鎖アミノアルコール) 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。スフィンゴ脂質はセラミドにリン酸が結合したスフィンゴリン脂質と糖が結合したスフィンゴ糖脂質に分けられます。スフィンゴリン脂質にはスフィンゴミエリンが、スフィンゴ糖脂質にはセレブロシドやガングリオシドなどが含まれ、いずれも神経系に多く存在します。

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

Major series in this database are determined by phosphate-bound molecules or sugars for phosphosphingolipids, and by polysaccharide chains bound to ceramides for glycosphingolipids. The IUPAC series for glycosphingolipids (1977) are based on the order and bonding patterns of four sugars, but our series are based on three sugars for a wider coverage. Two original series, Echino and Plathy, are also included.

スフィンゴリン脂質はリン酸に結合する分子や糖の種類、スフィンゴ糖脂質はセラミドに結合する糖鎖により系列を作成しています。1977年にIUPACにより提唱されたスフィンゴ糖脂質の系列は長鎖塩基に結合する四糖の並びと結合を基準にしていますが、ここではより広い糖鎖の系列を検索できるよう、三糖を基準に分類しています。またIUPACには無いEchinoとPlathyの系列を加えています。

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^[1]	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^[2]	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^[1]	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~J~K~M~N~O~P~Q~R)|G(A∼R)

Symbols follow the Sugar-digit table.

First sugar

Code

Root sequence

Major Series

No Sugar Attached

P1 (LBSP)

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

↑ ^1.0 ^1.1 "iso" refers to a change from position 4 to position 3.
↑ "neo" refers to a change from position 3 to position 4.

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

[iso-1] 1.0 ^1.1 "iso" refers to a change from position 4 to position 3.

[neo-2] "neo" refers to a change from position 3 to position 4.

[1]

[2]

@@ Line 124: / Line 124: @@
 ==={{Bilingual|分類体系 |Page/ID-Code Design}}===
+{{Twocolumn|
+Major series in this database are determined by phosphate-bound molecules or sugars for phosphosphingolipids, and by polysaccharide chains bound to ceramides for glycosphingolipids. The IUPAC series for glycosphingolipids (1977) are based on the order and bonding patterns of four sugars, but our series are based on three sugars for a wider coverage. Two original series, Echino and Plathy, are also included.
+|スフィンゴリン脂質はリン酸に結合する分子や糖の種類、スフィンゴ糖脂質はセラミドに結合する糖鎖により系列を作成しています。1977年にIUPACにより提唱されたスフィンゴ糖脂質の系列は長鎖塩基に結合する四糖の並びと結合を基準にしていますが、ここではより広い糖鎖の系列を検索できるよう、三糖を基準に分類しています。またIUPACには無いEchinoとPlathyの系列を加えています。
+}}
 {|