Category:LBS: Difference between revisions

Revision as of 00:59, 19 March 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

Design of Page Titles for Sphingolipid

L

B

S

V/I

s1

s2

s3

n1

n2

y

c1

c2

V for vertebrates and I for invertebrates
s1 ∼ s3 ... Structure code

The 1^st letter s1:

Z for Gal_β1-4Glc_β1-1bCer

Y (Arthro) for GlcNAc_β1-3Man_β1-4Glc_β1-1Cer

For others, 0 ∼ Q of the 1^st sugar

The 2^nd and 3^rd letters s2 and s3:

0 to Q for the 3^rd and 4^th sugars for Z class

0 to Q for the 4^th and 5^th sugars for Y class

0 to Q for the 2^nd and 3^rd sugars for others

n1, n2 ... the number of sugars
y ... the number of sialic acids
c1, c2 ... serial numbers

x ... 脊椎動物は V 無脊椎動物は I
s1 ∼ s3 ... 構造コード

最初の文字 s1:

Z は Gal_β1-4Glc_β1-1bCer

Y (Arthro型) は GlcNAc_β1-3Man_β1-4Glc_β1-1Cer

それ以外は最初の糖タイプにより 0 ∼ Q

２番目、３番目の文字 s2 and s3:

Zクラスの場合、３,４番目の糖タイプにより 0 to Q

Yクラスの場合、４,５番目の糖タイプにより 0 to Q

それ以外の場合、２,３番目の糖タイプにより 0 to Q

n1, n2 ... 糖の数
y ... シアル酸の数
c1, c2 ... 通し番号

Sugar Code

"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

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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Polysaccharide Chain

Table 1. Glycosphingolipids and Phosphosphingolipids

Glycosphingolipids (Abbr. Z = Gal_β1-4Glc_β1-Cer)

Ganglio [Gg] (??)
GalNAcβ1-4R

Lacto [Lc] (??)
GlcNAcβ1-3R

Globo [Gb] (??)
Galα1-4R

Root [R] (??)
derivatives of R

3rd saccharide

3rd saccharide
Lacto? GlcNAcβ1-3 R
Lacto Galβ1-3GlcNAcβ1-3 R
Neolacto Galβ1-4GlcNAcβ1-3 R

3rd saccharide
[Galα1-3]_n Galα1-4 R
Galβ1-3GalNAcβ1-3 Galα1-4 R
GlcNAcβ1-6GalNAcβ1-3 Galα1-4 R
GalNAcβ1-3 Galα1-4 R

structure
hemato SAs (GM3,GD3,GT3)

Isoganglio [IG] (??)
GalNAcβ1-3R

Lacto with β1-6 [L6] (??)
GlcNAcβ1-6R

Isoglobo [IB] (??)
Galα1-3R

Lactoganglio [LG]

GalNAcβ1-4
GlcNAcβ1-3

R

Isogloboganglio [BG]

GalNAcβ1-4
Galα1-3

R

Table 1. Glycosphingolipids and Phosphosphingolipids

Glycosphingolipids without ROOT

Glc-Cer (??)
Glcβ1-Cer

Gal-Cer (??)
Galβ1-Cer

2nd saccharide
Glc-Cer Glcβ1-Cer
Arthro GlcNAcβ1-3Manβ1-4Glcβ1-Cer
Mollu Manα1-3Manβ1-4Glcβ1-Cer
Muco Galβ1-4Galβ1-4Glcβ1-Cer

2nd saccharide
Gala Galα1-4(6)Galβ1-Cer
??? Galβ1-4(6)Galβ1-Cer
Spirometo Galβ1-4Glcβ1-3Galβ1-Cer
NeuAcα2-3Galβ1-Cer

Phospho (??)
Ino-P-Cer

Others (??)

2nd saccharide

2nd saccharide

Subcategories

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

@@ Line 63: / Line 63: @@
 <td style="background-color:yellowgreen;" width=15px align="center"><big>B</big>
 <td style="background-color:darkseagreen;" width=15px align="center"><big>S</big>
-<td style="background-color:firebrick;" width=15px align="center"><big>''H/L''</big>
+<td style="background-color:firebrick;" width=15px align="center"><big>''V/I''</big>
 <td style="background-color:Blue; color:white" width=15px align="center"><big>''s1''</big>
 <td style="background-color:Blue; color:white" width=15px align="center"><big>''s2''</big>
@@ Line 76: / Line 76: @@
 </center>
 {{Twocolumn|
-* '''H''' for vertebrates and '''L''' for invertebrates
+* '''V''' for vertebrates and '''I''' for invertebrates
 * '''s1 &sim; s3''' ... Structure code
 : The 1<sup>st</sup> letter '''s1''':
@@ Line 90: / Line 90: @@
 * '''c1, c2''' ... serial numbers
 |
-* '''x''' ... 脊椎動物は '''H''' 無脊椎動物は '''L'''
+* '''x''' ... 脊椎動物は '''V''' 無脊椎動物は '''I'''
 * '''s1 &sim; s3''' ... 構造コード
 : 最初の文字 '''s1''':
@@ Line 114: / Line 114: @@
 |-
 | '''0''' || no sugar
-| '''A''' || other <span style="color:gold">Galactose (<b>Gal</b>)</span><br/> including methylation
+| '''A''' || other Galactose (<span style="color:gold"><b>Gal</b></span>)<br/> including methylation
 | '''L''' || Rhamnose (<b>Rha</b>) or pentose sugars (<b>Ara, Xyl</b>)
 |-
 | '''1''' || {{LBS/FormatSugar|Gala1-3}}
-| '''B''' || Other ''N''-acetyl <span style="color:gold">galactosamine (<b>GalNAc</b>)</span> or <br/> <span style="color:blue">glucosamine (<b>GlcNAc</b>)</span>
+| '''B''' || Other ''N''-acetyl galactosamine (<span style="color:gold"><b>GalNAc</b></span>) or <br/> glucosamine (<span style="color:blue"><b>GlcNAc</b></span>)
 | '''M''' || <span style="color:green">Mannose (<b>Man</b>)</span>
 |-
 | '''2''' || {{LBS/FormatSugar|Gala1-4}}
-| '''C''' || <span style="color:gold">Galactosamine (<b>GalN</b>)</span> or<br/> <span style="color:blue">Glucosamine (<b>GlcN</b>)</span>
+| '''C''' || Galactosamine (<span style="color:gold"><b>GalN</b></span>) or<br/> Glucosamine (<span style="color:blue"><b>GlcN</b></span>)
 | '''N''' || <span style="color:pink">Neuraminic acids (<b>NeuAc, NeuGc, NeuNH, KDN</b>)</span>
 |-
@@ Line 138: / Line 138: @@
 |-
 | '''6''' || {{LBS/FormatSugar|Galb1-6}}
-| '''G''' || Other <span style="color:blue">Glucose (<b>Glc</b>)</span>
+| '''G''' || Other Glucose (<span style="color:blue"><b>Glc</b></span>)
 | ||
 |-
 | '''7''' || {{LBS/FormatSugar|GalNAcb1-3}}
-| '''H''' || <span style="color:blue">Glucuronic acid (<b>GlcA</b>)</span>
+| '''H''' || Glucuronic acid (<span style="color:blue"><b>GlcA</b></span>)
 | ||
 |-
@@ Line 180: / Line 180: @@
 |+ Table 1. Classification by the Number of Sugars
 |- valign="top"
-|align="center" width=25%| {{MapLink|ListMol|LBS01|LBS01: <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|LBS02: <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|LBS03: <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|LBS04: <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|LBS05: <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|LBS06: <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|LBS07: <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|LBS08: <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|LBS09: <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|LBS10: <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|LBS11: <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|LBS12: <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|LBS13: <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|LBS14: <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|LBS15: <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|LBS16: <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|LBS17: <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|LBS18: <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|LBS19: <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|LBS20: <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|LBS21: <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|LBS22: <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|LBS00: <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|LBSPP: <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>
@@ Line 224: / Line 224: @@
 |-
 ! style="background:#efefef; text-align:center;" colspan="4"|
-Glycosphingolipids (Abbr. R = Gal&beta;1-4Glc&beta;1-Cer)
+Glycosphingolipids (Abbr. Z = {{LBS/FormatSugar|Galb1-4Glcb1-Cer}})
 |- valign="top"
 | <big>'''Ganglio''' [Gg] (??)</big><br/> GalNAc&beta;1-4R