Sandbox Reserved 711: Difference between revisions
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The endo-polygalacturonase II (Polygalacturonase EC 3.2.1.15) of the fungus ''Aspergillus Niger'' is an enzyme which is involved in the rotting process. It specifically degrade polygalacturonate, a major carbohydrate constituent of plant cell wall pectin, by hydrolysis of the glycosidic bonds that link galacturonic acid residues. | The endo-polygalacturonase II (Polygalacturonase EC 3.2.1.15) of the fungus ''Aspergillus Niger'' is an enzyme which is involved in the rotting process. It specifically degrade polygalacturonate, a major carbohydrate constituent of plant cell wall pectin, by hydrolysis of the glycosidic bonds that link galacturonic acid residues. | ||
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. | 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.<ref>http://www.cazypedia.org/index.php/Inverting#Mechanistic_classification</ref> | ||
== Glycoside hydrolases and pectinases == | == 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. | 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. | ||
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== Description of the structure == | == Description of the structure == | ||
{{STRUCTURE_1czf| PDB=1czf | SCENE= }} | |||
The endopolygalacturonase II from Aspergillus niger has a beta-helix structure<ref>http://www.ncbi.nlm.nih.gov/pubmed/10521427</ref>: 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. | The endopolygalacturonase II from Aspergillus niger has a beta-helix structure<ref>http://www.ncbi.nlm.nih.gov/pubmed/10521427</ref>: 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 <scene name='Sandbox_Reserved_711/N_terminal_alpha_helix/1'>small alpha-helix</scene>. | ||
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 <scene name='Sandbox_Reserved_711/Chain_b_cleft/1'>loops separating PB1 and PB2a</scene> 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. | The <scene name='Sandbox_Reserved_711/Chain_b_cleft/1'>loops separating PB1 and PB2a</scene> 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. | ||
<scene name='Sandbox_Reserved_711/Active_site_residues/1'>8 particular amino-acids</scene> in this region are strictly conserved among polygalacturonases from other fungal and bacterial species: Asn178, Asp180, Asp201, Asp202, His223, Gly224, Arg256, and Lys258. | <scene name='Sandbox_Reserved_711/Active_site_residues/1'>8 particular amino-acids</scene> in this region are strictly conserved among polygalacturonases from other fungal and bacterial species: Asn178, Asp180, Asp201, Asp202, His223, Gly224, Arg256, and Lys258 (shown in red). | ||
The residues directly involved in the catalytic activity seem to be <scene name='Sandbox_Reserved_711/Active_site_residues/3'>Asp180, Asp201, Asp202, and His223</scene>, that form a plane above which space is available, while <scene name='Sandbox_Reserved_711/Active_site_residues/4'>Arg256 and Lys258 </scene> would bind the substrate.<scene name='Sandbox_Reserved_711/Active_site_residues/5'>Gly224</scene>, at the bottom of the cleft, doesn't point out of the helix. | The residues directly involved in the catalytic activity seem to be <scene name='Sandbox_Reserved_711/Active_site_residues/3'>Asp180, Asp201, Asp202, and His223</scene> (orange), that form a plane above which space is available, while <scene name='Sandbox_Reserved_711/Active_site_residues/4'>Arg256 and Lys258 </scene> (light pink) would bind the substrate.<scene name='Sandbox_Reserved_711/Active_site_residues/5'>Gly224</scene> (dark pink), at the bottom of the cleft, doesn't point out of the helix. | ||
== Endo-polygalacturonase II applications == | == Endo-polygalacturonase II applications == | ||
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== External links == | == External links == | ||
PDB entry: 1CZF[http://www.rcsb.org/pdb/explore.do?structureId=1czf] | |||
== Contributors == | == Contributors == | ||
Claire Baranger, Adeline Pauli | Claire Baranger, Adeline Pauli | ||