Category:LBS: Difference between revisions

Line 115: Line 115:
NeuAc && ''N''-acetyl-neuraminic acid && ''N''-アセチルノイラミン酸
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
NeuGc && ''N''-glycolyl-neuraminic acid && ''N''-グリコリルノイラミン酸
KDN && 2-keto-3-deoxy-D-glycero-<br/>D-galacto-nononic acid && デアミノノイラミン酸
Kdn && 2-keto-3-deoxy-D-glycero-<br/>D-galacto-nononic acid && デアミノノイラミン酸
}}
}}
|-
|-

Revision as of 06:51, 28 February 2016

Sphingolipid


Upper classes: LB

Class Overview

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

Sphingolipid Overview

Phosphosphingolipid
(including GIPC)
LBSPP.png
スフィンゴリン脂質 (GIPC含む)

Cerebroside (monoglycosylceramide)
LBS01.png
セレブロシド (糖の数 n = 1)

Glycosphingolipid (glycosylceramide)
LBSnn.png
スフィンゴ糖脂質 (糖の数 n > 1)

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 for Sphinx, as well as sphincter muscle.) The basic structure is a long-chain base, usually sphingosine (2-amino-4-octadecene-1,3-diol abbreviated as d18:1), 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これに同じで、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d18:1と記載されるスフィンゴシン) 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 sphingoid are prevalent as membrane components of eukaryotic cells. Sphingomyelin is a ceramide with phosphocholine. Some ceramides are organ-specific.

スフィンゴ骨格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。セラミドにホスホコリンがついたものがスフィンゴミエリンです。臓器特異的なセラミドもあります。



Biosynthesis

Sphingosine is synthesized from decarboxylating condensation of palmitoyl CoA with serine on the ER membrane. It is a 18-carbon amino alcohol (16 carbons from palmitic acid and 2 from serine) with one unsaturated bond (trans-form) at the C-4 position (2-amino-4-octadecene-1,3-diol). (more details)

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)でトランス型の不飽和結合をC-4に1つ含みます。(詳細はこちら

Sphingolipid スフィンゴ脂質

Notation

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
Cerebroside For GalCer and GlcCer, visit this page.
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 Galα1-4/6Galβ1-Cer
Mainchain.*Galb1-4Glcb1-3Galb1-Cer|Spirometo Galβ1-4Glcβ1-3Galβ1-Cer
starting with
Glucose
LBSG2|G2
(LBSG2.....|7|8|9|9|Number_of_Sugars|Number_of_Sialic_acids|88 items)
GalNAcβ-Galβ-Glcβ-Cer
Mainchain.*GalNAcb1-4Galb1-4Glcb1-Cer|Ganglio GalNAcβ1-4Galβ1-4Glcβ1-Cer
Mainchain.*GalNAcb1-3Galb1-4Glcb1-Cer|Isoganglio[1] GalNAcβ1-3Galβ1-4Glcβ1-Cer
Structure.*GlcNAcb1-3\(.*GalNAcb1-4\)Galb1-4Glcb1-Cer|Lactoganglio GlcNAcβ1-3(GalNAcβ1-4)Galβ1-4Glcβ1-Cer
Structure.*\(?NeuAca2-3\)?Galb1-4Glcb1-Cer|a-series (NeuAcα2-3)Galβ1-4Glcβ1-Cer
Structure.*\(?NeuAca2-8NeuAca2-3\)?Galb1-4Glcb1-Cer|b-series (NeuAcα2-8NeuAcα2-3)Galβ1-4Glcβ1-Cer
Structure.*\(?NeuAca2-8NeuAca2-8NeuAca2-3\)?Galb1-4Glcb1-Cer|c-series (NeuAcα2-8NeuAcα2-8NeuAcα2-3)Galβ1-4Glcβ1-Cer
Structure.*\(?NeuAca2-6\)?GalNAcb1-4Galb1-4Glcb1-Cer|α-series (NeuAcα2-6)GalNAcβ1-4Galβ1-4Glcβ1-Cer
Structure.*\(?NeuAca2-8NeuAca2-6\)?GalNAcb1-4Galb1-4Glcb1-Cer|β-series (NeuAcα2-8NeuAcα2-6)GalNAcβ1-4Galβ1-4Glcβ1-Cer
LBSG3|G3
(LBSG3.....|7|8|9|9|Number_of_Sugars|Number_of_Sialic_acids|173 items)
GlcNAcβ-Galβ-Glcβ-Cer
Mainchain.*Galb1-3GlcNAcb1-3Galb1-4Glcb1-Cer|Lacto Galβ1-3GlcNAcβ1-3Galβ1-4Glcβ1-Cer
Mainchain.*Gal.1-4GlcNAcb1-3Galb1-4Glcb1-Cer|Neolacto[2] Galβ1-4GlcNAcβ1-3Galβ1-4Glcβ1-Cer
LBSG4|G4
(LBSG4.....|7|8|9|9|Number_of_Sugars|Number_of_Sialic_acids|55 items)
Galα-Galβ-Glcβ-Cer
Mainchain.*Gala1-4Galb1-4Glcb1-Cer|Globo Galα1-4Galβ1-4Glcβ1-Cer
Mainchain.*Gala1-3Galb1-4Glcb1-Cer|Isoglobo[1] Galα1-3Galβ1-4Glcβ1-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 Galβ1-4Galβ1-4Glcβ1-Cer
LBSG6|G6
(LBSG6.....|7|8|9|9|Number_of_Sugars|Number_of_Sialic_acids|68 items)
Man-Glcβ-Cer
Mainchain.*GlcNAcb1-3Manb1-4Glcb1-Cer|Arthro GlcNAcβ1-3Manβ1-4Glcβ1-Cer
Mainchain.*Mana1-3Manb1-4Glcb1-Cer|Mollu Manα1-3Manβ1-4Glcb1.Cer
LBSG7|G7
(LBSG7.....|7|8|9|9|Number_of_Sugars|Number_of_Sialic_acids|21 items)
NeuAc/NeuGc-Glcβ-Cer
Mainchain.*Neu(A~G)c.2-6Glcb1-Cer|Echino NeuGc or NeuAcα2-6Glcβ1-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 GalNAcβ1-4Glcβ1-Cer
starting with
Other Sugars
LBSG(A~B~C~D~E~F~G~H~J~K~M~N~O~P~Q~R)|G(AR) Symbols follow the Sugar-digit table.
First sugar Code Root sequence Major Series
No Sugar Attached P1 (LBSP) R-P-Cer Sphingomyelin and Phosphoetanolamine-ceramide
(Visit this page.)
starting with
Inositol
LBSP2|P2
(29 items)
GlcNα/β1−2/6Ins1-P-Cer
Mainchain.*GlcN.1-.Ins-P-Cer|Protozoa & Fungi-specific GlcNα/β1-2/6Ins1-P-Cer
LBSP3|P3
(10 items)
GlcAα/β1−2/6Ins1-P-Cer
Mainchain.*GlcA.1-.Ins-P-Cer|Plant-specific GlcAα/β1-2/6Ins1-P-Cer
LBSP4|P4
(52 items)
Manα/β1−2/6Ins1-P-Cer
Mainchain.*Man.1-.Ins-P-Cer|Fungi-specific Manα/β1-2/6Ins1-P-Cer
LBSP5|P5
(21 items)
Others Ins1-P-Cer
  1. 1.0 1.1 "iso" refers to a change from position 4 to position 3.
  2. "neo" refers to a change from position 3 to position 4.

Second (s2) Code for subsequent sugars

For abbreviations, see #Notation.

Code Structure
A Glc LBS-Monomer-Glc.png
B Gal LBS-Monomer-Gal.png
C GlcNAc LBS-Monomer-GlcNAc.png
D GalNAc LBS-Monomer-GalNAc.png
E GlcN LBS-Monomer-GlcN.png
F GalN LBS-Monomer-GalN.png
G GlcA LBS-Monomer-GlcA.png
H GalA LBS-Monomer-GalA.png
I not used
Code Structure
J Structure.*Man|Mannose LBS-Monomer-Man.png
K Structure.*Rha|Rhamnose LBS-Monomer-Rha.png
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 (%53%74%72%75%63%74%75%72%65%5B%5E%46%5D%2B%46%75%63%5B%5E%46%5D%2B%24| 1, %53%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, %53%74%72%75%63%74%75%72%65%28%5B%5E%46%5D%2B%46%75%63%29%7B%33}|>3) LBS-Monomer-Fuc.png
N Structure.*Ara|Arabinose LBS-Monomer-Ara.png
O Structure.*Xyl|Xylose LBS-Monomer-Xyl.png
P Structure.*(NeuAc~NeuNH)|NeuAc / NeuNH LBS-Monomer-NeuAc.png
Q Structure.*(NeuGc)|NeuGc LBS-Monomer-NeuGc.png
R Structure.*(KDN)|KDN LBS-Monomer-KDN.png
Code Structure
S Structure.*(Phospho)|Phosphate (except GIPC) LBS-Monomer-P.png
T Structure.*(AEPn)|(M)AEPn, Structure.*(EtnP)|EtnP, Structure.*(PC)|PC LBS-Monomer-AEPn.png
U Structure.*Sulfo|Sulfate LBS-Monomer-S.png
V acyl/alkyl/alkenyl chain LBS-Monomer-Alkyl.png


Subcategories

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