Category:LBS: Difference between revisions

Revision as of 01:12, 27 April 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

Notation

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	aminoethylphosphonic acid, or (2-aminoethyl)hydroxyphosphoryl-	アミノエチルホスホン酸（C-P結合）
MAEPn	N-methyl aminoethylphosphonic acid, or (N-methyl-2-aminoethyl) hydroxyphosphoryl-	AEPnのN-メチル体（C-P結合）
EtnP	phosphoethanolamine (PEA), or 2-aminoethanolphospho-	ホスホエタノールアミン
PC	Phosphocholine	ホスホコリン
Butenyl	Butenyl	ブテニル基
Me	Methyl	メチル基
Et	Ethyl	エチル基

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	number of sialic acids (1 digit)
c1, c2	serial numbers

First (s1) Code for Glycosphingolipid

First sugar

Code

Root sequence

Major Series

starting with
Galactose

LBSG1|G1
(LBSG1.....|7|8|9|9|Number_of_Sugars|Number_of_Sialic_acids|79 items)

Gal-Cer

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

starting with
Glucose

LBSG2|G2
(LBSG2.....|7|8|9|9|Number_of_Sugars|Number_of_Sialic_acids|88 items)

GalNAc_β-Gal_β-Glc_β-Cer

Mainchain.*GalNAcb1-4Galb1-4Glcb1-Cer\|Ganglio	GalNAc_β1-4Gal_β1-4Glc_β1-Cer
Mainchain.*GalNAcb1-3Galb1-4Glcb1-Cer\|Isoganglio	GalNAc_β1-3Gal_β1-4Glc_β1-Cer
Structure.GlcNAcb1-3\(.GalNAcb1-4\)Galb1-4Glcb1-Cer\|Lactoganglio	GlcNAc_β1-3(GalNAc_β1-4)Gal_β1-4Glc_β1-Cer
Structure.*\(?NeuAca2-3\)?Galb1-4Glcb1-Cer\|a-series	(NeuAc_α2-3)Gal_β1-4Glc_β1-Cer
Structure.*\(?NeuAca2-8NeuAca2-3\)?Galb1-4Glcb1-Cer\|b-series	(NeuAc_α2-8NeuAc_α2-3)Gal_β1-4Glc_β1-Cer
Structure.*\(?NeuAca2-8NeuAca2-8NeuAca2-3\)?Galb1-4Glcb1-Cer\|c-series	(NeuAc_α2-8NeuAc_α2-8NeuAc_α2-3)Gal_β1-4Glc_β1-Cer
Structure.*\(?NeuAca2-6\)?GalNAcb1-4Galb1-4Glcb1-Cer\|α-series	(NeuAc_α2-6)GalNAc_β1-4Gal_β1-4Glc_β1-Cer
Structure.*\(?NeuAca2-8NeuAca2-6\)?GalNAcb1-4Galb1-4Glcb1-Cer\|β-series	(NeuAc_α2-8NeuAc_α2-6)GalNAc_β1-4Gal_β1-4Glc_β1-Cer

LBSG3|G3
(LBSG3.....|7|8|9|9|Number_of_Sugars|Number_of_Sialic_acids|173 items)

GlcNAc_β-Gal_β-Glc_β-Cer

Mainchain.*Galb1-3GlcNAcb1-3Galb1-4Glcb1-Cer\|Lacto	Gal_β1-3GlcNAc_β1-3Gal_β1-4Glc_β1-Cer
Mainchain.*Gal.1-4GlcNAcb1-3Galb1-4Glcb1-Cer\|Neolacto	Gal_α/β1-4GlcNAc_β1-3Gal_β1-4Glc_β1-Cer

LBSG4|G4
(LBSG4.....|7|8|9|9|Number_of_Sugars|Number_of_Sialic_acids|55 items)

Gal_α-Gal_β-Glc_β-Cer

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

LBSG5|G5
(LBSG5.....|7|8|9|9|Number_of_Sugars|Number_of_Sialic_acids|113 items)

Gal-Glc-Cer
(Other than G2∼G4)

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

Gal_β1-4Gal_β1-4Glc_β1-Cer

LBSG6|G6
(LBSG6.....|7|8|9|9|Number_of_Sugars|Number_of_Sialic_acids|68 items)

Man-Glc_β-Cer

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

LBSG7|G7
(LBSG7.....|7|8|9|9|Number_of_Sugars|Number_of_Sialic_acids|21 items)

NeuAc/NeuGc-Glc_β-Cer

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

NeuGc or NeuAc_α/β2-6Glc_β1-Cer

LBSG8|G8
(LBSG8.....|7|8|9|9|Number_of_Sugars|Number_of_Sialic_acids|12 items)

GalNAc-Glc-Cer

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

GalNAc_α/β1-4Glc_α/β1-Cer

starting with
Other Sugars

G(A∼Z)

Symbols follow the Sugar-digit table.

First sugar

Code

Root sequence

Major Series

No Sugar Attached

LBSP1|P1
(0 items)

R-P-Cer

Sphingomyelins

starting with
Inositol

LBSP2|P2
(29 items)

GlcN_α/β1−2/6Ins₁-P-Cer

GlcN_α/β1-2/6Ins1-P-Cer

LBSP3|P3
(10 items)

GlcA_α/β1−2/6Ins₁-P-Cer

GlcA_α/β1-2/6Ins1-P-Cer

LBSP4|P4
(52 items)

Man_α/β1−2/6Ins₁-P-Cer

Man_α/β1-2/6Ins1-P-Cer

LBSP5|P5
(21 items)

Others

Ins1-P-Cer

Second (s2) Code for subsequent sugars

For abbreviations, see #Notation.

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	%53%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 (except GIPC)
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 376: / Line 376: @@
 |-
 ! '''S'''
-| [[Volatile:ListMol/LBS|Structure.*(Phospho)|Phosphate (except GIPC)]] <big>[P]</big>
+| [[Volatile:ListMol/LBS|Structure.*(Phospho)|Phosphate (except GIPC)]] [[File:LBS-Monomer-P.png]]
 |-
 ! '''T'''
-| [[Volatile:ListMol/LBS|Structure.*(AEPn)|(M)AEPn]], [[Volatile:ListMol/LBS|Structure.*(EtnP)|EtnP]], [[Volatile:ListMol/LBS|Structure.*(PC)|PC]] <big>[E/C]</big>
+| [[Volatile:ListMol/LBS|Structure.*(AEPn)|(M)AEPn]], [[Volatile:ListMol/LBS|Structure.*(EtnP)|EtnP]], [[Volatile:ListMol/LBS|Structure.*(PC)|PC]] [[File:LBS-Monomer-AEPn.png]]
 |-
 ! '''U'''
-| [[Volatile:ListMol/LBS|Structure.*Sulfo|Sulfate]] <big>[S]</big>
+| [[Volatile:ListMol/LBS|Structure.*Sulfo|Sulfate]] [[File:LBS-Monomer-S.png]]
 |-
 ! '''V'''
-| acyl/alkyl/alkenyl chain
+| acyl/alkyl/alkenyl chain [[File:LBS-Monomer-Alkyl.png]]
 |}