Category:LBS: Difference between revisions

Revision as of 07:16, 22 January 2015

Sphingolipid

Upper classes: LB

Class Overview

The Sphingolipid category (LBS) in the database includes glycosphingolipid and phosphosphingolipid.

Sphingolipid Overview
Glyco-sphingolipid (including its lyso form) スフィンゴ糖脂質 (リゾ体を含む)	Phospho-sphingolipid (including glycosyl phosphoinositolceramide or GIPC) スフィンゴリン脂質 (GIPC含む)

Sphingosine & Ceramide

Sphingolipids were first isolated from brain by J.L.W. Thudichum (1829-1901) as lipids of unknown function and structure. The name "sphingo" comes from the Greek word sphingein for holding tight. (The Sphinx also comes from this word root. See the Wikipedia article in English., as well as sphincter muscle.) The basic structure is a long-chain base, usually sphingosine (2-amino-4-octadecene-1,3-diol), whose amino-group is acylated with a long-chain fatty acid. This hydrophobic structure is called ceramides.

スフィンゴ脂質は J.L.W. Thudichum (1829-1901) により機能や構造未知の脂質として脳から見いだされました。スフィンゴという名前はギリシャ語の sphingein に由来しており、「固く縛る」という意味です。（スフィンクスの語源も之に同じで、括約筋のことを英語で sphincter muscle といいます。）基本骨格は長鎖塩基 (長鎖アミノアルコール、通常はスフィンゴシン) のアミノ基が長鎖脂肪酸とアミド結合したもので、セラミドと呼ばれます。

Ceramides with the sphingosine base are prevalent as membrane components of eukaryotic cells. Those with the phytosphingosine base localize in particular organs such as small intestines. Sphingomyelin is a ceramide with phosphocholine.

スフィンゴシンをもつセラミドは細胞組織の膜成分として普遍的に存在します。その他にも臓器特異的にフィトスフィンゴシンを含むセラミドが知られています。セラミドにホスフォコリンがついたものが有名なスフィンゴミエリンです。

Biosynthesis

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.

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)。

Sph 骨格へのリンク

Sphingolipid スフィンゴ脂質

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)hydroxyphosphonic acid
MAEPn	(N-Methyl-2-aminoethyl)hydroxyphosphonic acid
EtnP	2-aminoethanolphospho-
PC	Phosphocholine
CH3CH2CH=CH	Butenyl
Me	Methyl
Et	Ethyl

Page/ID-Code Design

L

B

S

G/P

s1

s2

n1

n2

y

c1

c2

G/P	G (glyco)	P (phospho)
s1, s2	structure code as explained below
n1, n2	number of sugars (2 digits)
y	~~N (neutral), A (acidic), B (basic), or M (amphoteric)~~
c1, c2	serial numbers

First (s1) Code for Glycosphingolipid

First sugar

Code

Root sequence

Major Series

starting with Galactose

G1

Gal-Cer

mainchain.*Gala1-4?6?Galb1-Cer\|Gala	Gal_α1−4/6Gal_β1−1Cer
mainchain.*Galb1-4Glcb1-3Galb1-Cer\|Spirometo	Gal_β1−4Glc_β1−3Gal_β1−1Cer

starting with Glucose

G2

GalNAc_β-Gal_β-Glc_β-Cer

mainchain.*GalNAcb1-4Galb1-4Glcb1-Cer|Ganglio

GalNAc_β1−4Gal_β1−4Glc_β1−1Cer

mainchain.*GalNAcb1-3Galb1-4Glcb1-Cer|Isoganglio

GalNAc_β1−3Gal_β1−4Glc_β1−1Cer

structure.*GlcNAcb1-3\(.*GalNAcb1-4\)Galb1-4Glcb1-Cer|Lactoganglio

GalNAc_β1-4

GlcNAc_β1/³

Gal_β1−4Glc_β1−1Cer

G3

GlcNAc_β-Gal_β-Glc_β-Cer

mainchain.*Galb1-3GlcNAcb1-3Galb1-4Glcb1-Cer\|Lacto	Gal_β1−3GlcNAc_β1−3Gal_β1−4Glc_β1−1Cer
mainchain.*Galb1-4GlcNAcb1-3Galb1-4Glcb1-Cer\|Neolacto	Gal_β1−4GlcNAc_β1−3Gal_β1−4Glc_β1−1Cer
mainchain.*Gala1-3GlcNAcb1-3Galb1-4Glcb1-Cer\|Isoneolacto	Gal_α1−3GlcNAc_β1−3Gal_β1−4Glc_β1−1Cer

G4

Gal_α-Gal_β-Glc_β-Cer

mainchain.*Gala1-4Galb1-4Glcb1-Cer\|Globo	Gal_α1−4Gal_β1−4Glc_β1−1Cer
mainchain.*Gala1-3Galb1-4Glcb1-Cer\|Isoglobo	Gal_α1−3Gal_β1−4Glc_β1−1Cer

G5

Gal-Glc-Cer
(Except G2∼G4)

mainchain.*Galb1-4Galb1-4Glcb1-Cer|Muco

Gal_β1−4Gal_β1−4Glc_β1−1Cer

G6

Man-Glc_β-Cer

mainchain.*GlcNAcb1-3Manb1-4Glcb1-Cer\|Arthro	GlcNAc_β1−3Man_β1−4Glc_β1−1Cer
mainchain.*Mana1.3Manb1.4Glcb1.Cer\|Mollu	Man_α1−3Man_β1−4Glc_β1−1Cer

G7

NeuAc/NeuGc-Glc_β-Cer

mainchain.*Neu(A~G)c.2-6Glcb1-Cer|Echino

NeuAc or NeuGc₁₋₆Glc_β1−1Cer

G8

GalNAc-Glc-Cer

mainchain.*GalNAc.1-4Glc.1-Cer|Plathy

GalNAc_α/β1−4Glc_α/β1−1Cer

Others

G(A∼Z)

Symbols follow the Sugar-digit table.

First sugar

Code

Root sequence

Major Series

No Sugar

P1

LBSP1|R-P-Cer

Sphingomyelins

Inositol

P2

LBSP2|GlcN_α/β1−2/6Ins₁-P-Cer

GIPC

P3

LBSP3|GlcA_α/β1−2/6Ins₁-P-Cer

GIPC

P4

LBSP4|Man_α/β1−2/6Ins₁-P-Cer

GIPC

P5

LBSP5|Ins₁-P-Cer

Others

Second (s2) Code for subsequent sugars

Code	Structure
A	Glc
B	Gal
C	GlcNAc
D	GalNAc
E	GlcN
F	GalN
G	GlcA
H	GalA
I	not used

Code	Structure
J	structure.*Man\|Mannose
K	structure.*Rha\|Rhamnose
L	%73%74%72%75%63%74%75%72%65%2e%2A%49%6e%73%28%4d%65%29%3F%2d%50%2d%5B%5E%43%65%72%5D\|Inositol
M	Fucose (%73%74%72%75%63%74%75%72%65%5B%5E%46%5D%2B%46%75%63%5B%5E%46%5D%2B%24\| 1, %73%74%72%75%63%74%75%72%65%28%5B%5E%46%5D%2B%46%75%63%29%7B%32%7D%5B%5E%46%5D%2B%24\|2, %73%74%72%75%63%74%75%72%65%28%5B%5E%46%5D%2B%46%75%63%29%7B%33}\|>3)
N	structure.*Ara\|Arabinose
O	structure.*Xyl\|Xylose
P	structure.*(NeuAc~NeuNH)\|NeuAc / NeuNH
Q	structure.*(NeuGc)\|NeuGc
R	structure.*(KDN)\|KDN

Code	Structure
S	structure.*Phospho\|Phosphate
T	structure.(AEPn)\|(M)AEPn, structure.(EtnP)\|EtnP, structure.*(PC)\|PC
U	structure.*Sulfo\|Sulfate
V	acyl/alkyl/alkenyl chain

Subcategories

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

L

@@ Line 169: / Line 169: @@
 ===First (s1) Code for Glycosphingolipid===
-{| class="wikitable"
+{| class="wikitable" style="text-align:right; background-color:white"
 ! First sugar || Code || Root sequence
 ! colspan=2 | Major Series
@@ Line 177: / Line 177: @@
 |style="text-align:right"| '''Gal'''-Cer
 |
-{| class="wikitable"
+{|
-|-
 |[[Volatile:ListMol/LBS|mainchain.*Gala1-4?6?Galb1-Cer|Gala]]
 |style="text-align:right"| '''Gal'''<sub>&alpha;1&minus;4/6</sub>Gal<sub>&beta;1&minus;1</sub>Cer
@@ Line 191: / Line 190: @@
 |style="text-align:right"| '''GalNAc<sub>&beta;</sub>'''-Gal<sub>&beta;</sub>-Glc<sub>&beta;</sub>-Cer
 |
-{| class="wikitable"
+{|
 |-
 |[[Volatile:ListMol/LBS|mainchain.*GalNAcb1-4Galb1-4Glcb1-Cer|Ganglio]]
@@ Line 201: / Line 200: @@
 |[[Volatile:ListMol/LBS|structure.*GlcNAcb1-3\(.*GalNAcb1-4\)Galb1-4Glcb1-Cer|Lactoganglio]]
 |
-{| style="background:#f9f9f9" cellspacing=0 cellpadding=0 align="right"
+{|cellspacing=0 cellpadding=0 align="right"
 |
-{| style="background:#f9f9f9" cellspacing=0 cellpadding=0
+{|cellspacing=0 cellpadding=0
 |GalNAc<sub>&beta;'''1-4'''</sub>
 |-
@@ Line 215: / Line 214: @@
 |style="text-align:right"| '''GlcNAc<sub>&beta;</sub>'''-Gal<sub>&beta;</sub>-Glc<sub>&beta;</sub>-Cer
 |
-{| class="wikitable"
+{|
 |-
 |[[Volatile:ListMol/LBS|mainchain.*Galb1-3GlcNAcb1-3Galb1-4Glcb1-Cer|Lacto]]
@@ Line 230: / Line 229: @@
 |style="text-align:right"| '''Gal<sub>&alpha;</sub>'''-Gal<sub>&beta;</sub>-Glc<sub>&beta;</sub>-Cer
 |
-{| class="wikitable"
+{|
 |-
 |[[Volatile:ListMol/LBS|mainchain.*Gala1-4Galb1-4Glcb1-Cer|Globo]]
@@ Line 242: / Line 241: @@
 |style="text-align:right"| Gal-Glc-Cer<br/>(Except G2&sim;G4)
 |
-{| class="wikitable"
+{|
 |[[Volatile:ListMol/LBS|mainchain.*Galb1-4Galb1-4Glcb1-Cer|Muco]]
 |Gal<sub>'''&beta;1&minus;4'''</sub>Gal<sub>&beta;1&minus;4</sub>Glc<sub>&beta;1&minus;1</sub>Cer
@@ Line 250: / Line 249: @@
 |style="text-align:right"| '''Man'''-Glc<sub>&beta;</sub>-Cer
 |
-{| class="wikitable"
+{|
 |[[Volatile:ListMol/LBS|mainchain.*GlcNAcb1-3Manb1-4Glcb1-Cer|Arthro]]
 |style="text-align:right"| '''GlcNAc'''<sub>&beta;1&minus;3</sub>Man<sub>&beta;1&minus;4</sub>Glc<sub>&beta;1&minus;1</sub>Cer
@@ Line 261: / Line 260: @@
 |style="text-align:right"| '''NeuAc'''/'''NeuGc'''-Glc<sub>&beta;</sub>-Cer
 |
-{| class="wikitable"
+{|
 |[[Volatile:ListMol/LBS|mainchain.*Neu(A~G)c.2-6Glcb1-Cer|Echino]]
 |NeuAc or NeuGc<sub>1&minus;6</sub>Glc<sub>&beta;1&minus;1</sub>Cer
@@ Line 269: / Line 268: @@
 |style="text-align:right"| '''GalNAc'''-Glc-Cer
 |
-{| class="wikitable"
+{|
 |[[Volatile:ListMol/LBS|mainchain.*GalNAc.1-4Glc.1-Cer|Plathy]]
 |GalNAc<sub>&alpha;/&beta;1&minus;4</sub>Glc<sub>&alpha;/&beta;1&minus;1</sub>Cer
@@ Line 303: / Line 302: @@
 | Others
 |}
 ===Second (s2) Code for subsequent sugars===

Category:LBS: Difference between revisions

Revision as of 07:16, 22 January 2015

Contents

Class Overview

Sphingosine & Ceramide

Biosynthesis

Sphingolipid スフィンゴ脂質

Common Abbreviations

Page/ID-Code Design

First (s1) Code for Glycosphingolipid

Second (s2) Code for subsequent sugars

Subcategories

L

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