Sandbox Reserved 711: Difference between revisions

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Polygalacturonase belongs to the Glycoside hydrolysases 28 (GH28) according to the sequence-based classification of glycoside hydrolysases. The enzyme of the GH28 family achieves the hydrolysis with an inverting molecular mechanism.

~~== Glycoside hydrolases and pectinases ==~~

The endopolygalacturonase II belongs to the family of glycoside hydrolases, enzymes that hydrolyse glycosidic bonds in polysaccharidic chains and release smaller sugars, classified in the EC 3.2.1.x group. Within this family, endopolygalacturonases are pectinases, enzymes involved in the degradation of pectin, a polymer of galacturonic acid and rhamnose that is the jelly-like component of plant cell walls.

Endopolygalacturonase II is part of the family 28 of glycoside hydrolases. It is not the only endopolygalacturonase from A. niger - a family of seven genes encode such enzymes, and six different proteins have been identified: endopolygalacturonases I, II, A, B, C and E.

== The catalysed reaction ==

The endopolygalacturonase II is an endo-acting enzyme that hydrolyses alpha(1,4)-glycosidic bonds between the D-galacturonic acid monomeres of pectin chains. One of its particularities is the inversion of configuration that occurs during the reaction. Its functionning is optimal at a pH of 4.2 and with a non-methylated substrate.

[[Image:mechanisme.png |center]]

'''ICI'''

The putative mechanism is the following:

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The endopolygalacturonase II from Aspergillus niger has a beta-helix structure: the chain folds into 10 turns, shaping the faces of a right-handed helix consisting in 4 parallel beta-sheets - PB1, PB2a, PB2b and PB3 - separated by loops. The helix is closed at its N-terminal end by a small alpha-helix.

4 disulfide bridges, conserved in all endopolygalacturonases of ''A. ~~niger~~'', hold together different parts of the chain, and particularily one of these attaches the N-terminal helix to the PB2b sheet.

4 disulfide bridges, conserved in all endopolygalacturonases of ''A. Niger'', hold together different parts of the chain, and particularily one of these attaches the N-terminal helix to the PB2b sheet.

The loops separating PB1 and PB2a are longer on the C-terminal end, and those between PB3 and PB1 on the N-terminal end, what forms a cleft between two extensions outside of the the beta-helix. Its shape, open at both ends of the protein, allows the fixation of a linear glucidic chain, and is suited to the endohydrolytic mode of action. This cleft is a higly conserved region.

Sandbox Reserved 711: Difference between revisions

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@@ Line 13: / Line 13: @@
 Polygalacturonase belongs to the Glycoside hydrolysases 28 (GH28) according to the sequence-based classification of glycoside hydrolysases. The enzyme of the GH28 family achieves the hydrolysis with an inverting molecular mechanism.
-== Glycoside hydrolases and pectinases ==
-The endopolygalacturonase II belongs to the family of glycoside hydrolases, enzymes that hydrolyse glycosidic bonds in polysaccharidic chains and release smaller sugars, classified in the EC 3.2.1.x group. Within this family, endopolygalacturonases are pectinases, enzymes involved in the degradation of pectin, a polymer of galacturonic acid and rhamnose that is the jelly-like component of plant cell walls.
-Endopolygalacturonase II  is part of the family 28 of glycoside hydrolases. It is not the only endopolygalacturonase from A. niger - a family of seven genes encode such enzymes, and six different proteins have been identified: endopolygalacturonases I, II, A, B, C and E.
 == The catalysed reaction ==
 The endopolygalacturonase II is an endo-acting enzyme that hydrolyses alpha(1,4)-glycosidic bonds between the D-galacturonic acid monomeres  of pectin chains. One of its particularities is the inversion of configuration that occurs during the reaction. Its functionning is optimal at a pH of 4.2 and with a non-methylated substrate.
+[[Image:mechanisme.png |center]]
 '''ICI'''
 The putative mechanism is the following:
@@ Line 30: / Line 25: @@
 The endopolygalacturonase II from Aspergillus niger has a beta-helix structure: the chain folds into 10 turns, shaping the faces of a right-handed helix consisting in 4 parallel beta-sheets - PB1, PB2a, PB2b and PB3 - separated by loops. The helix is closed at its N-terminal end by a small alpha-helix.
-disulfide bridges, conserved in all endopolygalacturonases of ''A. niger'', hold together different parts of the chain, and particularily one of these attaches the N-terminal helix to the PB2b sheet.
+disulfide bridges, conserved in all endopolygalacturonases of ''A. Niger'', hold together different parts of the chain, and particularily one of these attaches the N-terminal helix to the PB2b sheet.
 The loops separating PB1 and PB2a are longer on the C-terminal end, and those between PB3 and PB1 on the N-terminal end, what forms a cleft between two extensions outside of the the beta-helix. Its shape, open at both ends of the protein, allows the fixation of a linear glucidic chain, and is suited to the endohydrolytic mode of action. This cleft is a higly conserved region.