Category:LBS: Difference between revisions

Revision as of 14:21, 3 February 2012

Sphingolipid

Class Overview

Sphingosine & Ceramide

Sphingosine is synthesized from decarboxylating condensation of palmitoyl CoA with serine. It is a 18-carbon amino alcohol (16 carbons from palmitic acid and 2 from serine) with one unsaturated bond (2-amino-4-octadecene-1,3-diol). Sphingosine is further acylated to form ceramide, an important component of cell membranes.
The Sphingolipid category (LBS) in this database includes glycosphingolipid, phosphosphingolipid, and ceramide.

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)で不飽和結合を1つ含んでいます (2-amino-4-octadecene-1,3-diol)。スフィンゴシンがアシル化したものが、細胞膜の重要な成分であるセラミドです。
このデータベースにおけるスフィンゴ脂質カテゴリー (LBS) には、スフィンゴ糖脂質 (glycosphingolipid)、スフィンゴリン脂質 (phosphosphingolipid) 、セラミド (ceramide) が含まれています。

Abbreviations

Sugar Abbreviations (Ex. Glc → glucose)
Cer	ceramides	セラミド
Sph	sphingosine	スフィンゴシン
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
GalN	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
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
NeuNH	(deacetyl) neuraminic acid (pyruvate + mannosamine)	ノイラミン酸 (ピルビン酸＋マンノサミン)
KDN	2-keto-3-deoxy-D-glycero- D-galacto-nononic acid	KDN
Modifiers
AEPn	(2-Aminoethyl-)hydroxyphosphoryl
MAEPn	(N-Methyl-2-aminoethyl-)hydroxyphosphoryl
EtnP	2-Aminoethanolphospho
MAEPr	(N-Methyl-2-aminoethyl-)phosphoryl
HPO3	Phosphono
HSO3	Sulfono
2C=CH	Ethyl
PC	Phosphocholine

Page/ID Design for Sphingolipid

L

B

S

s1

s2

s3

n1

n2

y

c

c1

c2

s1 ∼ s3 ... Structure code (3 digits)

Explained below

n1, n2 ... the number of sugars (2 digits)
y ... the number of sialic acids ( 1 digit)
c ... ceramide identification (1 digit)
c1, c2 ... serial numbers

s1 ∼ s3 ... 構造コード (3桁）

下に詳述

n1, n2 ... 糖の数 (2桁)
y ... シアル酸の数 (1桁)
c ... セラミドの同定 (1桁)
c1, c2 ... 通し番号

Structure Code

NOTE

Most common patterns

GalNAc_β1-4Gal_β1-4-Glc_β1-Cer:Ganglio series ... over 110 molecules
GlcNAc_β1-3Gal_β1-4-Glc_β1-Cer:Lacto or Neolacto series ... over 170 molecules
Neuraminic acid + Gal_β1-4-Glc_β1-Cer:??... over 50 molecules
GlcNAc_β1-3Man_β1-4Glc_β1-1Cer:Arthro series ... over 50 molecules

Digits

"I" and "O" are not used to avoid confusion with "1" or "0".

code	sugar	code	sugar	code	sugar
0	no sugar	A	GlcNAc_β1-3	L	Pentose sugars (Ara, Xyl)
1	Gal_α1-3	B	GlcNAc_β1-4	M	Mannose and Rhamnose (= 6-deoxymannose) (Man, Rha)
2	Gal_α1-4	C	GlcNAc_β1-6	N	Neuraminic acids (NeuAc, NeuNH, NeuGc, KDN)
3	Gal_α1-6	D	GalNAc, GalN	P	Phosphocholine (PC), Phosphate (HPO3), Sulphate (HSO3)
4	Gal_β1-3	E	GlcNAc, GlcN	Q	Aminoethylphosphates (AEPn, MAEPr, EtnP)
5	Gal_β1-4	F	Other Galactose (Gal)	R	O-Alkyl and O-acyl groups including ethylene (OAc, CH3, 2C=CH)
6	Gal_β1-6	G	Other Glucose (Glc)
7	GalNAc_β1-3
8	GalNAc_β1-4	J	Inositol	Y	GlcNAc_β1-3Man_β1-4Glc_β1-1Cer
9	GalNAc_β1-6	K	Fucose (Fuc)	Z	Gal_β1-4Glc_β1-1bCer

Polysaccharide Chain

Table 1. Common Categories
Common Name	Sequence	LipidBank ID
By GalCer Synthase (EC 2.4.1.62)
Gala	0	Gal_α1-4Gal_β1-Cer
Spirometo	0	Gal_β1-4Glc_β1-3Gal_β1-Cer
By GlcCer Synthase (EC 2.4.1.80)
Ganglio	0	GalNAc_β1-4Gal_β1-4Glc_β1-Cer
Isoganglio	0	GalNAc_β1-3Gal_β1-4Glc_β1-Cer
Globo	0	Gal_α1-4Gal_β1-4Glc_β1-Cer
Isoglobo	0	Gal_α1-3Gal_β1-4Glc_β1-Cer
Lacto	0	Gal_β1-3GlcNAc_β1-3Gal_β1-4Glc_β1-Cer
NeoLacto	0	Gal_β1-4GlcNAc_β1-3Gal_β1-4Glc_β1-Cer
Muco	0	Gal_β1-4Gal_β1-4Glc_β1-Cer
With Mannose
Arthro	0	GlcNAc_β1-3Man_β1-4Glc_β1-Cer
Mollu	0	Man_α1-3Man_β1-4Glc_β1-Cer

Classification

By the Number of Sugars 糖の個数

For glycosphingolipid, 2 digits following LBS stand for the number of attached sugars. For phosphosphingolipid, the code of phosphorylation, PP.

スフィンゴ糖脂質は結合している糖の総数をLBSに続く2桁の数字で、スフィンゴリン脂質は数字の代わりにリン酸化修飾を示す記号PPで分類しています。

Sphingolipid Overview
Glycosphingolipid スフィンゴ糖脂質: LBSnn	Phosphosphingolipid スフィンゴリン脂質: LBSPP

Table 1. Classification by the Number of Sugars
(41 pages)	(49 pages)	(95 pages)	(111 pages)
(124 pages)	(102 pages)	(84 pages)	(57 pages)
(35 pages)	(18 pages)	(10 pages)	(10 pages)
(0 pages)	(5 pages)	(4 pages)	(1 pages)
(0 pages)	(1 pages)	(0 pages)	(3 pages)
(0 pages)	(1 pages)	(1 pages)	(0 pages)

Subcategories

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

@@ Line 160: / Line 160: @@
 |-
 | '''0''' || no sugar
-| '''A''' || other Galactose (<span style="color:gold"><b>Gal</b></span>)<br/> including methylation
+| '''A''' || {{LBS/FormatSugar|GlcNAcb1-3}}
-| '''L''' || Rhamnose (<b>Rha</b>) or pentose sugars (<b>Ara, Xyl</b>)
+| '''L''' || Pentose sugars (<span style="color:DarkOrange"><b>Ara, Xyl</b></span>)
 |-
 | '''1''' || {{LBS/FormatSugar|Gala1-3}}
-| '''B''' || Other ''N''-acetyl galactosamine (<span style="color:gold"><b>GalNAc</b></span>) or <br/> glucosamine (<span style="color:blue"><b>GlcNAc</b></span>)
+| '''B''' || {{LBS/FormatSugar|GlcNAcb1-4}}
-| '''M''' || <span style="color:green">Mannose (<b>Man</b>)</span>
+| '''M''' || Mannose and Rhamnose (= 6-deoxymannose) (<span style="color:green"><b>Man, Rha</b></span>)
 |-
 | '''2''' || {{LBS/FormatSugar|Gala1-4}}
-| '''C''' || Galactosamine (<span style="color:gold"><b>GalN</b></span>) or<br/> Glucosamine (<span style="color:blue"><b>GlcN</b></span>)
+| '''C''' || {{LBS/FormatSugar|GlcNAcb1-6}}
-| '''N''' || <span style="color:pink">Neuraminic acids (<b>NeuAc, NeuGc, NeuNH, KDN</b>)</span>
+| '''N''' || Neuraminic acids (<b><span style="color:Purple">NeuAc, NeuNH</span>, <span style="color:gray">NeuGc</span>, <span style="color:Green">KDN</span></b>)
 |-
 | '''3''' || {{LBS/FormatSugar|Gala1-6}}
-| '''D''' || {{LBS/FormatSugar|GlcNAcb1-3}}
+| '''D''' || {{LBS/FormatSugar|GalNAc, GalN}}
-| '''P''' || phosphocholine (<b>PC</b>), phosphate (<b>HPO3</b>), sulphate (<b>HSO3</b>), and ethylene (<b>2C=CH</b>)
+| '''P''' || Phosphocholine (<b>PC</b>), Phosphate (<b>HPO3</b>), Sulphate (<b>HSO3</b>)
 |-
 | '''4''' || {{LBS/FormatSugar|Galb1-3}}
-| '''E''' || {{LBS/FormatSugar|GlcNAcb1-4}}
+| '''E''' || {{LBS/FormatSugar|GlcNAc, GlcN}}
-| '''Q''' || Aminoethylphosphate (<b>AEPn, MAEPr, EtnP</b>)
+| '''Q''' || Aminoethylphosphates (<b>AEPn, MAEPr, EtnP</b>)
 |-
 | '''5''' || {{LBS/FormatSugar|Galb1-4}}
-| '''F''' || {{LBS/FormatSugar|GlcNAcb1-6}}
+| '''F''' || Other Galactose (<span style="color:gold"><b>Gal</b></span>)
-| ||
+| '''R''' || O-Alkyl and O-acyl groups including ethylene (<b>OAc, CH3, 2C=CH</b>)
 |-
 | '''6''' || {{LBS/FormatSugar|Galb1-6}}
@@ Line 188: / Line 188: @@
 |-
 | '''7''' || {{LBS/FormatSugar|GalNAcb1-3}}
-| '''H''' || Glucuronic acid (<span style="color:blue"><b>GlcA</b></span>)
+| ||
 | ||
 |-
 | '''8''' || {{LBS/FormatSugar|GalNAcb1-4}}
-| '''J''' || <span style="color:purple">Inositol (<b>Ins</b>)</span>
+| '''J''' || Inositol
 | '''Y''' || {{LBS/FormatSugar|GlcNAcb1-3Manb1-4Glcb1-1Cer}}
 |-
 | '''9''' || {{LBS/FormatSugar|GalNAcb1-6}}
-| '''K''' || <span style="color:red">Fucose (<b>Fuc</b>)</span>
+| '''K''' || Fucose (<span style="color:red"><b>Fuc</b></span>)
 | '''Z''' || {{LBS/FormatSugar|Galb1-4Glcb1-1bCer}}
 |}