Category:LBS: Difference between revisions

Revision as of 17:35, 23 October 2011

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

1st Digit

Symbol	With Gal_β	LipidBank ID
1	79	$Gal_β1-Cer
2	117	Gal_β1-6Gal_β1-Cer
3	183	Gal_?-Gal_β1-Cer
4	107	Glc_?-Gal_β1-Cer
5	134	GlcNAc_?-Gal_β1-Cer
6	68	NeuAc_?-Gal_β1-Cer
9	21	Other_?-Gal_β1-Cer

Symbol	With Glc_β	LipidBank ID
A	15	$Glc_β1-Cer
B	0	Gal_β1-4Glc_β1-Cer
C	3	GalNAc_β1-4Glc_β1-Cer
D	0	Gal_?-Glc_β1-Cer
E	2	Glc_?-Glc_β1-Cer
F	0	Man_?-Glc_β1-Cer
G	4	NeuAc_?-Glc_β1-Cer
H	0	Other_?-Glc_β1-Cer

Symbol	With InsP and others	LipidBank ID
K	0	InsP-Cer
L	0	Fuc-Cer
M	1	Rha/Ara/Xyl_?-Cer
P	1	Man_?-Cer
Q	1	-Cer
R	0	-Cer

2nd & 3rd Digits

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

code	sugar	code	sugar	code	sugar
0	no sugar	A	other Galactose (Gal) including methylation	L	Rhamnose (Rha) or pentose sugars (Ara, Xyl)
1	Gal_α1-3	B	Other N-acetyl galactosamine (GalNAc) or glucosamine (GlcNAc)	M	Mannose (Man)
2	Gal_α1-4	C	Galactosamine (GalN) or Glucosamine (GlcN)	N	Neuraminic acids (NeuAc, NeuGc, NeuNH, KDN)
3	Gal_α1-6	D	GlcNAc_β1-3	P	phosphocholine (PC), phosphate (HPO3), sulphate (HSO3), and ethylene (2C=CH)
4	Gal_β1-3	E	GlcNAc_β1-4	Q	Aminoethylphosphate (AEPn, MAEPr, EtnP)
5	Gal_β1-4	F	GlcNAc_β1-6
6	Gal_β1-6	G	Other Glucose (Glc)
7	GalNAc_β1-3	H	Glucuronic acid (GlcA)
8	GalNAc_β1-4	J	Inositol (Ins)	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
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Subcategories

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

@@ Line 93: / Line 93: @@
 ===Structure Code===
 ;{{Bilingual|一桁目|1st Digit}}
-{{Twocolumn|
+{|
+|valign="top"|
+{| class="wikitable"
+|-
+! Symbol || With <b>Gal</b><sub>&beta;</sub> || LipidBank ID
+{{#repeat:LBS/AbbrevTable/Row|1|
+$Galb1-Cer LBS.1
+Galb1-6Galb1-Cer LBS.2
+Gal?-Galb1-Cer LBS.3
+Glc?-Galb1-Cer LBS.4
+GlcNAc?-Galb1-Cer LBS.5
+NeuAc?-Galb1-Cer LBS.6
+Other?-Galb1-Cer LBS.7
 }}
+|}
+|valign="top"|
+{| class="wikitable"
+|-
+! Symbol || With <b>Glc</b><sub>&beta;</sub> || LipidBank ID
+{{#repeat:LBS/AbbrevTable/Row|1|
+A $Glcb1-Cer LBS.A
+B Galb1-4Glcb1-Cer LBS.B
+C GalNAcb1-4Glcb1-Cer LBS.C
+D Gal?-Glcb1-Cer LBS.D
+E Glc?-Glcb1-Cer LBS.E
+F Man?-Glcb1-Cer LBS.F
+G NeuAc?-Glcb1-Cer LBS.G
+H Other?-Glcb1-Cer LBS.H
+}}
+|}
+|valign="top"|
+{| class="wikitable"
+|-
+! Symbol || With <b>InsP</b> and others || LipidBank ID
+{{#repeat:LBS/AbbrevTable/Row|1|
+K InsP-Cer LBS.K
+L Fuc-Cer LBS.L
+M Rha/Ara/Xyl?-Cer LBS.M
+P Man?-Cer LBS.P
+Q -Cer LBS.Q
+R -Cer LBS.R
+}}
+|}
+|}
+;{{Bilingual|二、三桁目|2nd & 3rd Digits}}
-: The 1<sup>st</sup> letter '''s1''':
-:: '''Z''' for {{LBS/FormatSugar|Galb1-4Glcb1-1bCer}}
-:: '''Y''' (''Arthro'') for {{LBS/FormatSugar|GlcNAcb1-3Manb1-4Glcb1-1Cer}}
-:: For others, '''0''' &sim; '''Q''' of the 1<sup>st</sup> sugar
-: The 2<sup>nd</sup> and 3<sup>rd</sup> letters '''s2''' and '''s3''':
-:: '''0''' to '''Q''' for the 3<sup>rd</sup> and 4<sup>th</sup> sugars for '''Z''' class
-:: '''0''' to '''Q''' for the 4<sup>th</sup> and 5<sup>th</sup> sugars for '''Y''' class
-:: '''0''' to '''Q''' for the 2<sup>nd</sup> and 3<sup>rd</sup> sugars for others
-===Sugar Code===
 <small>"I" and "O" are not used to avoid confusion with "1" or "0".</small>
 {| class="wikitable" style="text-align:center"