Category:LBS: Difference between revisions

Revision as of 00:40, 13 January 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	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 108: / Line 108: @@
 ! Symbol || With <b>Gal</b><sub>&beta;</sub> || LipidBank ID
 {{#repeat:LBS/AbbrevTable/Row|1|
-$Galb1-Cer LBS.1
+$Galb1-Cer LBS1
-Galb1-6Galb1-Cer LBS.2
+Galb1-6Galb1-Cer LBS2
-Gal?-Galb1-Cer LBS.3
+Gal?-Galb1-Cer LBS3
-Glc?-Galb1-Cer LBS.4
+Glc?-Galb1-Cer LBS4
-GlcNAc?-Galb1-Cer LBS.5
+GlcNAc?-Galb1-Cer LBS5
-NeuAc?-Galb1-Cer LBS.6
+NeuAc?-Galb1-Cer LBS6
-Gal?1-Cer LBS.9
+Gal?1-Cer LBS9
 }}
 |}
@@ Line 122: / Line 122: @@
 ! Symbol || With <b>Glc</b><sub>&beta;</sub> || LipidBank ID
 {{#repeat:LBS/AbbrevTable/Row|1|
-A $Glcb1-Cer LBS.A
+A $Glcb1-Cer LBSA
-B Galb1-4Glcb1-Cer LBS.B
+B Galb1-4Glcb1-Cer LBSB
-C GalNAcb1-4Glcb1-Cer LBS.C
+C GalNAcb1-4Glcb1-Cer LBSC
-D Gal?-Glcb1-Cer LBS.D
+D Gal?-Glcb1-Cer LBSD
-E Glc?-Glcb1-Cer LBS.E
+E Glc?-Glcb1-Cer LBSE
-F Man?-Glcb1-Cer LBS.F
+F Man?-Glcb1-Cer LBSF
-G NeuAc?-Glcb1-Cer LBS.G
+G NeuAc?-Glcb1-Cer LBSG
-H Glc?1-Cer LBS.H
+H Glc?1-Cer LBSH
 }}
 |}
@@ Line 137: / Line 137: @@
 ! Symbol || With <b>InsP</b> and others || LipidBank ID
 {{#repeat:LBS/AbbrevTable/Row|1|
-J InsP-Cer LBS.J
+J InsP-Cer LBSJ
-K Fuc-Cer LBS.K
+K Fuc-Cer LBSK
-L GlcNAc/GalNAc?-Cer LBS.L
+L GlcNAc/GalNAc?-Cer LBSL
-N GlcN/GalN?-Cer LBS.N
+N GlcN/GalN?-Cer LBSN
-R Rha/Ara/Xyl?-Cer LBS.R
+R Rha/Ara/Xyl?-Cer LBSR
-M Man?-Cer LBS.M
+M Man?-Cer LBSM
 }}
 |}
@@ Line 209: / Line 209: @@
 |colspan="3" style="background:#efefef; text-align:center"| By GalCer Synthase (EC 2.4.1.62)
 {{#repeat:LBS/AbbrevTable/Row|1|
-Gala Gala1-4Galb1-Cer LBS.A2
+Gala Gala1-4Galb1-Cer LBSA2.
-Spirometo Galb1-4Glcb1-3Galb1-Cer LBS.AG5
+Spirometo Galb1-4Glcb1-3Galb1-Cer LBSAG5
 }}
 |-
 |colspan="3" style="background:#efefef; text-align:center"| By GlcCer Synthase (EC 2.4.1.80)
 {{#repeat:LBS/AbbrevTable/Row|1|
-Ganglio GalNAcb1-4Galb1-4Glcb1-Cer LBS.Z8
+Ganglio GalNAcb1-4Galb1-4Glcb1-Cer LBSZ8.
-Isoganglio GalNAcb1-3Galb1-4Glcb1-Cer LBS.Z7
+Isoganglio GalNAcb1-3Galb1-4Glcb1-Cer LBSZ7.
-Globo Gala1-4Galb1-4Glcb1-Cer LBS.Z2
+Globo Gala1-4Galb1-4Glcb1-Cer LBSZ2.
-Isoglobo Gala1-3Galb1-4Glcb1-Cer LBS.Z1
+Isoglobo Gala1-3Galb1-4Glcb1-Cer LBSZ1.
-Lacto Galb1-3GlcNAcb1-3Galb1-4Glcb1-Cer LBS.ZD4
+Lacto Galb1-3GlcNAcb1-3Galb1-4Glcb1-Cer LBSZD4
-NeoLacto Galb1-4GlcNAcb1-3Galb1-4Glcb1-Cer LBS.ZD5
+NeoLacto Galb1-4GlcNAcb1-3Galb1-4Glcb1-Cer LBSZD5
-Muco Galb1-4Galb1-4Glcb1-Cer LBS.Z5
+Muco Galb1-4Galb1-4Glcb1-Cer LBSZ5
 }}
 |-
 |colspan="3" style="background:#efefef; text-align:center"| With Mannose
 {{#repeat:LBS/AbbrevTable/Row|1|
-Arthro GlcNAcb1-3Manb1-4Glcb1-Cer LBS.Y
+Arthro GlcNAcb1-3Manb1-4Glcb1-Cer LBSY
-Mollu Mana1-3Manb1-4Glcb1-Cer LBS.GMM
+Mollu Mana1-3Manb1-4Glcb1-Cer LBSGMM
 }}
 |}
@@ Line 257: / Line 257: @@
 |+ Table 1. Classification by the Number of Sugars
 |- valign="top"
-|align="center" width=25%| {{MapLink|ListMol|LBS01|LBS....01: <br>1 sugar<br>糖の数1<br>}}
+|align="center" width=25%| {{MapLink|ListMol|LBS01|LBS...01: <br>1 sugar<br>糖の数1<br>}}
-|align="center" width=25%| {{MapLink|ListMol|LBS02|LBS....02: <br>2 sugars<br>糖の数2<br>}}
+|align="center" width=25%| {{MapLink|ListMol|LBS02|LBS...02: <br>2 sugars<br>糖の数2<br>}}
-|align="center" width=25%| {{MapLink|ListMol|LBS03|LBS....03: <br>3 sugars<br>糖の数3<br>}}
+|align="center" width=25%| {{MapLink|ListMol|LBS03|LBS...03: <br>3 sugars<br>糖の数3<br>}}
-|align="center" width=25%| {{MapLink|ListMol|LBS04|LBS....04: <br>4 sugars<br>糖の数4<br>}}
+|align="center" width=25%| {{MapLink|ListMol|LBS04|LBS...04: <br>4 sugars<br>糖の数4<br>}}
 |- valign="top"
-|align="center"| {{MapLink|ListMol|LBS05|LBS....05: <br>5 sugars<br>糖の数5<br>}}
+|align="center"| {{MapLink|ListMol|LBS05|LBS...05: <br>5 sugars<br>糖の数5<br>}}
-|align="center"| {{MapLink|ListMol|LBS06|LBS....06: <br>6 sugars<br>糖の数6<br>}}
+|align="center"| {{MapLink|ListMol|LBS06|LBS...06: <br>6 sugars<br>糖の数6<br>}}
-|align="center"| {{MapLink|ListMol|LBS07|LBS....07: <br>7 sugars<br>糖の数7<br>}}
+|align="center"| {{MapLink|ListMol|LBS07|LBS...07: <br>7 sugars<br>糖の数7<br>}}
-|align="center"| {{MapLink|ListMol|LBS08|LBS....08: <br>8 sugars<br>糖の数8<br>}}
+|align="center"| {{MapLink|ListMol|LBS08|LBS...08: <br>8 sugars<br>糖の数8<br>}}
 |- valign="top"
-|align="center"| {{MapLink|ListMol|LBS09|LBS....09: <br>9 sugars<br>糖の数9<br>}}
+|align="center"| {{MapLink|ListMol|LBS09|LBS...09: <br>9 sugars<br>糖の数9<br>}}
-|align="center"| {{MapLink|ListMol|LBS10|LBS....10: <br>10 sugars<br>糖の数10<br>}}
+|align="center"| {{MapLink|ListMol|LBS10|LBS...10: <br>10 sugars<br>糖の数10<br>}}
-|align="center"| {{MapLink|ListMol|LBS11|LBS....11: <br>11 sugars<br>糖の数11<br>}}
+|align="center"| {{MapLink|ListMol|LBS11|LBS...11: <br>11 sugars<br>糖の数11<br>}}
-|align="center"| {{MapLink|ListMol|LBS12|LBS....12: <br>12 sugars<br>糖の数12<br>}}
+|align="center"| {{MapLink|ListMol|LBS12|LBS...12: <br>12 sugars<br>糖の数12<br>}}
 |- valign="top"
-|align="center"| {{MapLink|ListMol|LBS13|LBS....13: <br>13 sugars<br>糖の数13<br>}}
+|align="center"| {{MapLink|ListMol|LBS13|LBS...13: <br>13 sugars<br>糖の数13<br>}}
-|align="center"| {{MapLink|ListMol|LBS14|LBS....14: <br>14 sugars<br>糖の数14<br>}}
+|align="center"| {{MapLink|ListMol|LBS14|LBS...14: <br>14 sugars<br>糖の数14<br>}}
-|align="center"| {{MapLink|ListMol|LBS15|LBS....15: <br>15 sugars<br>糖の数15<br>}}
+|align="center"| {{MapLink|ListMol|LBS15|LBS...15: <br>15 sugars<br>糖の数15<br>}}
-|align="center"| {{MapLink|ListMol|LBS16|LBS....16: <br>16 sugars<br>糖の数16<br>}}
+|align="center"| {{MapLink|ListMol|LBS16|LBS...16: <br>16 sugars<br>糖の数16<br>}}
 |- valign="top"
-|align="center"| {{MapLink|ListMol|LBS17|LBS....17: <br>17 sugars<br>糖の数17<br>}}
+|align="center"| {{MapLink|ListMol|LBS17|LBS...17: <br>17 sugars<br>糖の数17<br>}}
-|align="center"| {{MapLink|ListMol|LBS18|LBS....18: <br>18 sugars<br>糖の数18<br>}}
+|align="center"| {{MapLink|ListMol|LBS18|LBS...18: <br>18 sugars<br>糖の数18<br>}}
-|align="center"| {{MapLink|ListMol|LBS19|LBS....19: <br>19 sugars<br>糖の数19<br>}}
+|align="center"| {{MapLink|ListMol|LBS19|LBS...19: <br>19 sugars<br>糖の数19<br>}}
-|align="center"| {{MapLink|ListMol|LBS20|LBS....20: <br>20 sugars<br>糖の数20<br>}}
+|align="center"| {{MapLink|ListMol|LBS20|LBS...20: <br>20 sugars<br>糖の数20<br>}}
 |- valign="top"
-|align="center"| {{MapLink|ListMol|LBS21|LBS....21: <br>21 sugars<br>糖の数21<br>}}
+|align="center"| {{MapLink|ListMol|LBS21|LBS...21: <br>21 sugars<br>糖の数21<br>}}
-|align="center"| {{MapLink|ListMol|LBS22|LBS....22: <br>22 sugars<br>糖の数22<br>}}
+|align="center"| {{MapLink|ListMol|LBS22|LBS...22: <br>22 sugars<br>糖の数22<br>}}
-|align="center"| {{MapLink|ListMol|LBS00|LBS....00: <br>0 sugar<br>糖の数0<br>}}
+|align="center"| {{MapLink|ListMol|LBS00|LBS...00: <br>0 sugar<br>糖の数0<br>}}
-|align="center"| {{MapLink|ListMol|LBSPP|LBS....PP: <br>Sphingophospholipid<br>スフィンゴリン脂質<br>}}
+|align="center"| {{MapLink|ListMol|LBSPP|LBS...PP: <br>Sphingophospholipid<br>スフィンゴリン脂質<br>}}
 |}
 </center>