Category:LBS: Difference between revisions

Revision as of 08:57, 3 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

Template:BilingualID番号 (ページタイトル) の設計

L

B

S

s1

s2

s3

n1

n2

x1

y1

c1

s1 ∼ s3 ... Structure code

The first letter s1 is:

Z for Gal_β1-4Glc_β1-1Cer root, prevalent in higher animals

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

0 to Q for the 1st sugar as explained below.

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

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

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

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

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. R = Galβ1-4Glcβ1-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 17: / Line 17: @@
 ==={{Bilingual|利用する略称|Abbreviations}}===
-{|
+{| class="collapsible collapsed"
+!colspan="3" align="center" style="background:lightgray"| Sugar Abbreviations (Ex. Glc &rarr; glucose)
 {{#repeatnum:LBS/AbbrevRow|1|
 Cer && ceramides && セラミド
@@ Line 37: / Line 38: @@
 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)
+NeuNH && (deacetyl) neuraminic acid<br/>(pyruvate + mannosamine) && ノイラミン酸<br/>(ピルビン酸＋マンノサミン)
-KDN && 2-keto-3-deoxy-D-glycero-D-galacto-nononic acid && KDN
+KDN && 2-keto-3-deoxy-D-glycero-<br/>D-galacto-nononic acid && KDN
+}}
+|-
+!colspan="3" align="center" style="background:lightgray"| Modifiers
+{{#repeatnum:LBS/AbbrevRow|1|
+AEPn && (2-Aminoethyl-)hydroxyphosphoryl &&
+MAEPn && (''N''-Methyl-2-aminoethyl-)hydroxyphosphoryl &&
+EtnP && 2-Aminoethanolphospho &&
+MAEPr && (''N''-Methyl-2-aminoethyl-)phosphoryl &&
+HPO3 && Phosphono &&
+HSO3 && Sulfono &&
+C=CH && Ethyl &&
+PC && Phosphocholine &&
 }}
 |}
+=={{BilingualID番号 (ページタイトル) の設計 |Design of Sphingolipid Page Titles}}==
+<center>
-==Design of Sphingolipid Identifiers <small>ID番号の設計</small>==
-<center>
--DIGIT(5+9+9+2)
 <table border=1>
 <tr>
@@ Line 51: / 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:Blue; color:white" width=15px align="center"><big>''a''</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>''a''</big>
+<td style="background-color:Blue; color:white" width=15px align="center"><big>''s2''</big>
-<td style="background-color:gray;" width=15px align="center"><big>:</big>
+<td style="background-color:Blue; color:white" width=15px align="center"><big>''s3''</big>
-<td style="background-color:tomato; color:white" width=15px align="center"><big>''x1''</big>
+<td style="background-color:tomato; color:white" width=15px align="center"><big>''n1''</big>
-<td style="background-color:tomato; color:white" width=15px align="center"><big>''x1''</big>
+<td style="background-color:tomato; color:white" width=15px align="center"><big>''n2''</big>
-<td style="background-color:purple; color:white" width=15px align="center"><big>''y1''</big>
+<td style="background-color:firebrick; color:white" width=15px align="center"><big>''x1''</big>
-<td style="background-color:firebrick; color:white" width=15px align="center"><big>''z1''</big>
+<td style="background-color:firebrick; color:white" width=15px align="center"><big>''y1''</big>
-<td style="background-color:firebrick; color:white" width=15px align="center"><big>''z1''</big>
-<td style="background-color:green; color:white" width=15px align="center"><big>''w1''</big>
-<td style="background-color:green; color:white" width=15px align="center"><big>''w1''</big>
 <td style="background-color:white;" width=15px align="center"><big>''c1''</big>
 <td style="background-color:white;" width=15px align="center"><big>''c1''</big>
-<td style="background-color:gray;" width=15px align="center"><big>:</big>
-<td style="background-color:tomato; color:white" width=15px align="center"><big>''x2''</big>
-<td style="background-color:tomato; color:white" width=15px align="center"><big>''x2''</big>
-<td style="background-color:purple; color:white" width=15px align="center"><big>''y2''</big>
-<td style="background-color:firebrick; color:white" width=15px align="center"><big>''z2''</big>
-<td style="background-color:firebrick; color:white" width=15px align="center"><big>''z2''</big>
-<td style="background-color:green; color:white" width=15px align="center"><big>''w2''</big>
-<td style="background-color:green; color:white" width=15px align="center"><big>''w2''</big>
-<td style="background-color:white;" width=15px align="center"><big>''c2''</big>
-<td style="background-color:white;" width=15px align="center"><big>''c2''</big>
 </tr>
 </table>
 </center>
 {{Twocolumn|
-* ''a'' ... the number of attached sugars　(glycosphingolipid) or the code of phosphorylation (PP: phosphosphingolipid)
+'''s1 &sim; s3''' ... Structure code
+: The first letter '''s1''' is:
-* ''x1'' ... carbon chain length (sphingoid base)
+:: '''Z''' for Gal<sub>&beta;1-4</sub>Glc<sub>&beta;1-1</sub>Cer root, prevalent in higher animals
-* ''y1'' ... degree of unsaturation (sphingoid base)
+:: '''Y''' for GlcNAc<sub>&beta;1-3</sub>Man<sub>&beta;1-4</sub>Glc<sub>&beta;1-1</sub>Cer root (''Arthro'' type)
-* ''z1'' ... position of n－''z'' (n minus z; also ω－z or omega-z) nomenclature (sphingoid base)
+:: '''0''' to '''Q''' for the 1st sugar as explained below.
-* ''w1'' ... structure type (sphingoid base)
+: The 2<sup>nd</sup> and 3<sup>rd</sup>  letters '''s2''' and '''s3''' are:
-* ''c1'' ... serial number (sphingoid base)
+:: '''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>rd</sup> and 5<sup>th</sup> sugars for '''Y''' class
-* ''x2'' ... carbon chain length (acyl chain)
+:: '''0''' to '''Q''' for the 2<sup>rd</sup> and 3<sup>th</sup> sugars for others
-* ''y2'' ... degree of unsaturation (acyl chain)
-* ''z2'' ... position of n－''z'' (n minus z; also ω－z or omega-z) nomenclature (acyl chain)
-* ''w2'' ... structure type (acyl chain)
-* ''c2'' ... serial number (acyl chain)
 |
-* ''a'' ... 修飾する糖の個数 (glycosphingolipid) もしくはリン酸化修飾を示す記号 (PP: phosphosphingolipid)
-* ''x1'' ... 炭素鎖長 (スフィンゴイド塩基)
-* ''y1'' ... 不飽和度 (スフィンゴイド塩基)
-* ''z1'' ... n－''z'' (またはω－zやomega-z)　における数 (スフィンゴイド塩基)
-* ''w1'' ... 骨格のタイプ (スフィンゴイド塩基)
-* ''c1'' ... 通し番号 (スフィンゴイド塩基)
-* ''x2'' ... 炭素鎖長 (アシル基)
-* ''y2'' ... 不飽和度 (アシル基)
-* ''z2'' ... n－''z'' (またはω－zやomega-z)　における数(脂肪酸)
-* ''w2'' ... 骨格のタイプ (アシル基)
-* ''c2'' ... 通し番号 (アシル基)
 }}