Category:LBS: Difference between revisions

Revision as of 04:11, 6 June 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。

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

Glycosphingolipid スフィンゴ糖脂質

Common Abbreviations

Sugar Abbreviations (e.g. Glc = glucose)
Cer	ceramide	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
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	(2-Aminoethyl)hydroxyphosphoryl
EtnP	2-Aminoethanolphospho
MAEPn	(N-Methyl-2-aminoethyl)hydroxyphosphoryl
MAEPr	(N-Methyl-2-aminoethyl)phosphoryl
HPO3	Phosphono
HSO3	Sulfono
PC	Phosphocholine
CH3CH2CH=CH	Butenyl
Me	Methyl
Et	Ethyl

Page/ID Design for Sphingolipid

L

B

S

s1

s2

s3

n1

n2

d

y

c1

c2

s1 ∼ s3 ... Structure code (3 digits)

Explained below

n1, n2 ... the number of sugars (2 digits)
d ... distribution (Vertebrate; Invertebrate; N both; Plant; Chemical synthesis) (1 digit)
y ... the number of sialic acids ( 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)
d ... 分布 (V 脊椎; I 無脊椎; N 両方; P 植物; C 合成品) (1桁)
y ... シアル酸の数 (1桁)
c1, c2 ... 通し番号

Structure Code

code	Galactose
0	no sugar
1	Galactose (α form)	Gal_α1-3 ...
2		Gal_α1-4 ...
3		Gal_α1-6 ...
4	Galactose (β form)	Gal_β1-3 ...
5		Gal_β1-4 ...
6		Gal_β1-6 ...

code	N-Acetylated Sugars
7	N-Acetyl Galactosamine (β form)	GalNAc_β1-3 ...
8		GalNAc_β1-4 ...
9		GalNAc_β1-6 ...
A	N-Acetyl Glucosamine (β form)	GlcNAc_β1-3 ...
B		GlcNAc_β1-4 ...
C		GlcNAc_β1-6 ...

code	Galactose & Glucose
D	Aminated Sugars (Except for Code 7∼C)	GalNAc, GalN
E	Aminated Sugars (Except for Code 7∼C)	GlcNAc, GlcN
F	Galactose (Except Code 1∼6)	Gal
G	Glucose	Glc

code	Other Sugars
J	Inositol (Ins)
K	Fucose (Fuc)
L	Pentose sugars (Ara, Xyl)
M	Mannose and Rhamnose (= 6-deoxymannose) (Man, Rha)
N	Neuraminic acids (NeuAc, NeuNH, NeuGc, KDN)

code	Modifiers
P	Phosphate (HPO4), Sulphate (HSO4), and Phosphocholine (PC)
Q	Aminoethylphosphates AEPn, MAEPr, EtnP
R	Alkyl and acyl groups OAc, Methyl, Butenyl

code	Abbreviations
Y	GlcNAc_β1-3Man_β1-4Glc_β1-1Cer
Z	Gal_β1-4Glc_β1-1bCer

Common Patterns

Table 1. Common Categories
Common Name	Sequence
By GalCer Synthase (EC 2.4.1.62)
Gala_(Ga)	0	Gal_α1-4/6Gal_β1-Cer
Spirometo_(Sp)	0	Gal_β1-4Glc_β1-3Gal_β1-Cer
By GlcCer Synthase (EC 2.4.1.80)
Ganglio_(Gg)	0	GalNAc_β1-4Gal_β1-4Glc_β1-Cer
Isoganglio_(iGg)	0	GalNAc_β1-3Gal_β1-4Glc_β1-Cer
Globo_(Gb)	0	Gal_α1-4Gal_β1-4Glc_β1-Cer
Isoglobo_(iGb)	0	Gal_α1-3Gal_β1-4Glc_β1-Cer
Lacto_(Lc)	0	Gal_β1-3GlcNAc_β1-3Gal_β1-4Glc_β1-Cer
NeoLacto_(nLc)	0	Gal_β1-4GlcNAc_β1-3Gal_β1-4Glc_β1-Cer
Muco_(Mc)	0	Gal_β1-4Gal_β1-4Glc_β1-Cer
With Mannose
Arthro_(At)	0	GlcNAc_β1-3Man_β1-4Glc_β1-Cer
Mollu_(Mu)	0	Man_α1-3Man_β1-4Glc_β1-Cer

Classification

By the Number of Sugars

Table 1. Classification by the Number of Sugars
# of sugars	Verbebrates (0 items)	Invertebrate (0 items)
1	(0 pages)	(0 pages)
2	(0 pages)	(0 pages)
3	(0 pages)	(0 pages)
4	(0 pages)	(0 pages)
5	(0 pages)	(0 pages)
6	(0 pages)	(0 pages)
7	(0 pages)	(0 pages)
8	(0 pages)	(0 pages)
9	(0 pages)	(0 pages)
10-19	(0 pages)	(0 pages)
20-29	(0 pages)	(0 pages)

By the Number of Sialic acids

Table 2. Classification by the Number of Sialic acids
# of sialic acids	Verbebrates (0 items)	Invertebrate (0 items)
1	(0 pages)	(0 pages)
2	(0 pages)	(0 pages)
3	(0 pages)	(0 pages)
4	(0 pages)	(0 pages)
5	(0 pages)	(0 pages)
6	(0 pages)	(0 pages)
7	(0 pages)	(0 pages)
8	(0 pages)	(0 pages)

Subcategories

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

@@ Line 230: / Line 230: @@
 |+ Table 1. Common Categories
 |-
-! Common Name || Sequence || LipidBank ID
+! Common Name || Sequence
 |-
-|colspan="3" style="background:#efefef; text-align:center"| By GalCer Synthase (EC 2.4.1.62)
+|colspan="2" style="background:#efefef; text-align:center"| By GalCer Synthase (EC 2.4.1.62)
 {{#repeat:LBS/AbbrevTable/Row|1|
-Gala Gala1-4Galb1-Cer LBSF2.
+Gala_(Ga) Gala1-4/6Galb1-Cer LBSF2.
-Spirometo Galb1-4Glcb1-3Galb1-Cer LBSFG5
+Spirometo_(Sp) Galb1-4Glcb1-3Galb1-Cer LBSFG5
 }}
 |-
-|colspan="3" style="background:#efefef; text-align:center"| By GlcCer Synthase (EC 2.4.1.80)
+|colspan="2" style="background:#efefef; text-align:center"| By GlcCer Synthase (EC 2.4.1.80)
 {{#repeat:LBS/AbbrevTable/Row|1|
-Ganglio GalNAcb1-4Galb1-4Glcb1-Cer LBSZ8.
+Ganglio_(Gg) GalNAcb1-4Galb1-4Glcb1-Cer LBSZ8.
-Isoganglio GalNAcb1-3Galb1-4Glcb1-Cer LBSZ7.
+Isoganglio_(iGg) GalNAcb1-3Galb1-4Glcb1-Cer LBSZ7.
-Globo Gala1-4Galb1-4Glcb1-Cer LBSZ2.
+Globo_(Gb) Gala1-4Galb1-4Glcb1-Cer LBSZ2.
-Isoglobo Gala1-3Galb1-4Glcb1-Cer LBSZ1.
+Isoglobo_(iGb) Gala1-3Galb1-4Glcb1-Cer LBSZ1.
-Lacto Galb1-3GlcNAcb1-3Galb1-4Glcb1-Cer LBSZD4
+Lacto_(Lc) Galb1-3GlcNAcb1-3Galb1-4Glcb1-Cer LBSZD4
-NeoLacto Galb1-4GlcNAcb1-3Galb1-4Glcb1-Cer LBSZA5
+NeoLacto_(nLc) Galb1-4GlcNAcb1-3Galb1-4Glcb1-Cer LBSZA5
-Muco Galb1-4Galb1-4Glcb1-Cer LBSZ5.
+Muco_(Mc) Galb1-4Galb1-4Glcb1-Cer LBSZ5.
 }}
 |-
-|colspan="3" style="background:#efefef; text-align:center"| With Mannose
+|colspan="2" style="background:#efefef; text-align:center"| With Mannose
 {{#repeat:LBS/AbbrevTable/Row|1|
-Arthro GlcNAcb1-3Manb1-4Glcb1-Cer LBSY
+Arthro_(At) GlcNAcb1-3Manb1-4Glcb1-Cer LBSY
-Mollu Mana1-3Manb1-4Glcb1-Cer LBSGMM
+Mollu_(Mu) Mana1-3Manb1-4Glcb1-Cer LBSGMM
 }}
 |}