1rmg
From Proteopedia
(New page: 200px<br /><applet load="1rmg" size="450" color="white" frame="true" align="right" spinBox="true" caption="1rmg, resolution 2.0Å" /> '''RHAMNOGALACTURONASE A...) |
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| - | [[Image:1rmg.gif|left|200px]]<br /><applet load="1rmg" size=" | + | [[Image:1rmg.gif|left|200px]]<br /><applet load="1rmg" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="1rmg, resolution 2.0Å" /> | caption="1rmg, resolution 2.0Å" /> | ||
'''RHAMNOGALACTURONASE A FROM ASPERGILLUS ACULEATUS'''<br /> | '''RHAMNOGALACTURONASE A FROM ASPERGILLUS ACULEATUS'''<br /> | ||
==Overview== | ==Overview== | ||
| - | BACKGROUND: Pectic substances are the major polysaccharide components of | + | BACKGROUND: Pectic substances are the major polysaccharide components of the middle lamella and primary cell wall of dicotyledonous plants. They consist of homogalacturonan 'smooth' regions and highly rhamnified 'hairy' regions of rhamnogalacturonan. The backbone in rhamnogalacturonan-l (RG-l), which is composed of alternating galacturonic acid and rhamnose residues, is the substrate for a new class of enzymes known as rhamnogalacturnoases (RGases). RGase A is a novel enzyme implicated in the enzymatic degradation of RG-l. RESULTS: The structure of RGase A from Aspergillus aculeatus has been solved by the single isomorphous replacement method including anomalous scattering (SIRAS method) to 2.0 A resolution. The enzyme folds into a large right-handed parallel beta helix, with a core composed of 13 turns of beta strands. Four parallel beta sheets (PB1, PB1a, PB2 and PB3), formed by the consecutive turns, are typically separated by a residue in the conformation of a left-handed alpha helix. As a consequence of the consecutive turns, 32% of all residues have their sidechains aligned at the surface or in the interior of the parallel beta helix. The aligned residues at the surface are dominated by threonine, aspartic acid and asparagine, whereas valine, leucine and isoleucine are most frequently found in the interior. A very large hydrophobic cavity is found in the interior of the parallel beta helix. The potential active site is a groove, oriented almost perpendicular to the helical axis, containing a cluster of three aspartic acid residues and one glutamic acid residue. The enzyme is highly glycosylated; two N-linked and eighteen O-linked glycosylation sites have been found in the structure. CONCLUSIONS: Rhamnogalacturonase A from A. aculeatus is the first three-dimensional structure of an enzyme hydrolyzing glycoside bonds within the backbone of RG-l. The large groove, which is the potential active site of RGase A, is also seen in the structures of pectate lyases. Two catalytic aspartic acid residues, which have been proposed to have a catalytic role, reside in this area of RGase A. The distance between the aspartic acid residues is consistent with the inverting mechanism of catalysis. The glycan groups bound to RGase A are important to the stability of the crystal, as the carbohydrate moiety is involved in most of the intermolecular hydrogen bonds. |
==About this Structure== | ==About this Structure== | ||
| - | 1RMG is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Aspergillus_aculeatus Aspergillus aculeatus] with MAN, BMA and GLC as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http:// | + | 1RMG is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Aspergillus_aculeatus Aspergillus aculeatus] with <scene name='pdbligand=MAN:'>MAN</scene>, <scene name='pdbligand=BMA:'>BMA</scene> and <scene name='pdbligand=GLC:'>GLC</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RMG OCA]. |
==Reference== | ==Reference== | ||
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[[Category: Kauppinen, S.]] | [[Category: Kauppinen, S.]] | ||
[[Category: Larsen, S.]] | [[Category: Larsen, S.]] | ||
| - | [[Category: Petersen, T | + | [[Category: Petersen, T N.]] |
[[Category: BMA]] | [[Category: BMA]] | ||
[[Category: GLC]] | [[Category: GLC]] | ||
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[[Category: parallel beta-helix]] | [[Category: parallel beta-helix]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 14:52:25 2008'' |
Revision as of 12:52, 21 February 2008
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RHAMNOGALACTURONASE A FROM ASPERGILLUS ACULEATUS
Overview
BACKGROUND: Pectic substances are the major polysaccharide components of the middle lamella and primary cell wall of dicotyledonous plants. They consist of homogalacturonan 'smooth' regions and highly rhamnified 'hairy' regions of rhamnogalacturonan. The backbone in rhamnogalacturonan-l (RG-l), which is composed of alternating galacturonic acid and rhamnose residues, is the substrate for a new class of enzymes known as rhamnogalacturnoases (RGases). RGase A is a novel enzyme implicated in the enzymatic degradation of RG-l. RESULTS: The structure of RGase A from Aspergillus aculeatus has been solved by the single isomorphous replacement method including anomalous scattering (SIRAS method) to 2.0 A resolution. The enzyme folds into a large right-handed parallel beta helix, with a core composed of 13 turns of beta strands. Four parallel beta sheets (PB1, PB1a, PB2 and PB3), formed by the consecutive turns, are typically separated by a residue in the conformation of a left-handed alpha helix. As a consequence of the consecutive turns, 32% of all residues have their sidechains aligned at the surface or in the interior of the parallel beta helix. The aligned residues at the surface are dominated by threonine, aspartic acid and asparagine, whereas valine, leucine and isoleucine are most frequently found in the interior. A very large hydrophobic cavity is found in the interior of the parallel beta helix. The potential active site is a groove, oriented almost perpendicular to the helical axis, containing a cluster of three aspartic acid residues and one glutamic acid residue. The enzyme is highly glycosylated; two N-linked and eighteen O-linked glycosylation sites have been found in the structure. CONCLUSIONS: Rhamnogalacturonase A from A. aculeatus is the first three-dimensional structure of an enzyme hydrolyzing glycoside bonds within the backbone of RG-l. The large groove, which is the potential active site of RGase A, is also seen in the structures of pectate lyases. Two catalytic aspartic acid residues, which have been proposed to have a catalytic role, reside in this area of RGase A. The distance between the aspartic acid residues is consistent with the inverting mechanism of catalysis. The glycan groups bound to RGase A are important to the stability of the crystal, as the carbohydrate moiety is involved in most of the intermolecular hydrogen bonds.
About this Structure
1RMG is a Single protein structure of sequence from Aspergillus aculeatus with , and as ligands. Full crystallographic information is available from OCA.
Reference
The crystal structure of rhamnogalacturonase A from Aspergillus aculeatus: a right-handed parallel beta helix., Petersen TN, Kauppinen S, Larsen S, Structure. 1997 Apr 15;5(4):533-44. PMID:9115442
Page seeded by OCA on Thu Feb 21 14:52:25 2008
Categories: Aspergillus aculeatus | Single protein | Kauppinen, S. | Larsen, S. | Petersen, T N. | BMA | GLC | MAN | Glycosidase | Hydrolase | Inverting | Parallel beta-helix
