1ib4
From Proteopedia
(New page: 200px<br /><applet load="1ib4" size="450" color="white" frame="true" align="right" spinBox="true" caption="1ib4, resolution 2.00Å" /> '''CRYSTAL STRUCTURE OF...) |
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| - | [[Image:1ib4.jpg|left|200px]]<br /><applet load="1ib4" size=" | + | [[Image:1ib4.jpg|left|200px]]<br /><applet load="1ib4" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="1ib4, resolution 2.00Å" /> | caption="1ib4, resolution 2.00Å" /> | ||
'''CRYSTAL STRUCTURE OF POLYGALACTURONASE FROM ASPERGILLUS ACULEATUS AT PH4.5'''<br /> | '''CRYSTAL STRUCTURE OF POLYGALACTURONASE FROM ASPERGILLUS ACULEATUS AT PH4.5'''<br /> | ||
==Overview== | ==Overview== | ||
| - | Polygalacturonases hydrolyze the alpha-(1-4) glycosidic bonds of | + | Polygalacturonases hydrolyze the alpha-(1-4) glycosidic bonds of de-esterified pectate in the smooth region of the plant cell wall. Crystal structures of polygalacturonase from Aspergillus aculeatus were determined at pH 4.5 and 8.5 both to 2.0 A resolution. A. aculeatus polygalacturonase is a glycoprotein with one N and ten O-glycosylation sites and folds into a right-handed parallel beta-helix. The structures of the three independent molecules are essentially the same, showing no dependency on pH or crystal packing, and are very similar to that of Aspergillus niger polygalacturonase. However, the structures of the long T1 loop containing a catalytic tyrosine residue are significantly different in the two proteins. A three-dimensional model showing the substrate binding mode for a family 28 hydrolase was obtained by a combined approach of flexible docking, molecular dynamics simulations, and energy minimization. The octagalacturonate substrate was modeled as an unbent irregular helix with the -1 ring in a half-chair ((4)H(3)) form that approaches the transition state conformation. A comparative modeling of the three polygalacturonases with known structure shows that six subsites ranging from -4 to +2 are clearly defined but subsites -5 and +3 may or may not be shaped depending on the nearby amino acid residues. Both distal subsites are mostly exposed to the solvent region and have weak binding affinity even if they exist. The complex model provides a clear explanation for the functions, either in catalysis or in substrate binding, of all conserved amino acid residues in the polygalacturonase family of proteins. Modeling suggests that the role of the conserved Asn157 and Tyr270, which had previously been unidentified, may be in transition state stabilization. In A. niger polygalacturonase, the long T1 loop may have to undergo conformational change upon binding of the substrate to bring the tyrosine residue close to subsite -1. |
==About this Structure== | ==About this Structure== | ||
| - | 1IB4 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 and CD as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Polygalacturonase Polygalacturonase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.15 3.2.1.15] Full crystallographic information is available from [http:// | + | 1IB4 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> and <scene name='pdbligand=CD:'>CD</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Polygalacturonase Polygalacturonase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.15 3.2.1.15] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IB4 OCA]. |
==Reference== | ==Reference== | ||
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[[Category: Polygalacturonase]] | [[Category: Polygalacturonase]] | ||
[[Category: Single protein]] | [[Category: Single protein]] | ||
| - | [[Category: Cho, S | + | [[Category: Cho, S W.]] |
[[Category: Shin, W.]] | [[Category: Shin, W.]] | ||
[[Category: CD]] | [[Category: CD]] | ||
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[[Category: polygalacturonase]] | [[Category: polygalacturonase]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 13:09:55 2008'' |
Revision as of 11:09, 21 February 2008
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CRYSTAL STRUCTURE OF POLYGALACTURONASE FROM ASPERGILLUS ACULEATUS AT PH4.5
Overview
Polygalacturonases hydrolyze the alpha-(1-4) glycosidic bonds of de-esterified pectate in the smooth region of the plant cell wall. Crystal structures of polygalacturonase from Aspergillus aculeatus were determined at pH 4.5 and 8.5 both to 2.0 A resolution. A. aculeatus polygalacturonase is a glycoprotein with one N and ten O-glycosylation sites and folds into a right-handed parallel beta-helix. The structures of the three independent molecules are essentially the same, showing no dependency on pH or crystal packing, and are very similar to that of Aspergillus niger polygalacturonase. However, the structures of the long T1 loop containing a catalytic tyrosine residue are significantly different in the two proteins. A three-dimensional model showing the substrate binding mode for a family 28 hydrolase was obtained by a combined approach of flexible docking, molecular dynamics simulations, and energy minimization. The octagalacturonate substrate was modeled as an unbent irregular helix with the -1 ring in a half-chair ((4)H(3)) form that approaches the transition state conformation. A comparative modeling of the three polygalacturonases with known structure shows that six subsites ranging from -4 to +2 are clearly defined but subsites -5 and +3 may or may not be shaped depending on the nearby amino acid residues. Both distal subsites are mostly exposed to the solvent region and have weak binding affinity even if they exist. The complex model provides a clear explanation for the functions, either in catalysis or in substrate binding, of all conserved amino acid residues in the polygalacturonase family of proteins. Modeling suggests that the role of the conserved Asn157 and Tyr270, which had previously been unidentified, may be in transition state stabilization. In A. niger polygalacturonase, the long T1 loop may have to undergo conformational change upon binding of the substrate to bring the tyrosine residue close to subsite -1.
About this Structure
1IB4 is a Single protein structure of sequence from Aspergillus aculeatus with and as ligands. Active as Polygalacturonase, with EC number 3.2.1.15 Full crystallographic information is available from OCA.
Reference
The X-ray structure of Aspergillus aculeatus polygalacturonase and a modeled structure of the polygalacturonase-octagalacturonate complex., Cho SW, Lee S, Shin W, J Mol Biol. 2001 Aug 24;311(4):863-78. PMID:11518536
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