2vgd: Difference between revisions

Revision as of 19:55, 21 February 2008

CRYSTAL STRUCTURE OF ENVIRONMENTAL ISOLATED GH11 IN COMPLEX WITH XYLOBIOSE AND FERULOYL-ARABINO-XYLOTRIOSE

OverviewOverview

Endo-beta1,4-xylanases (xylanases) hydrolyse the beta1,4 glycosidic bonds in the backbone of xylan. Although xylanases from glycoside hydrolase family 11 (GH11) have been extensively studied, several issues remain unresolved. Thus, the mechanism by which these enzymes hydrolyse decorated xylans is unclear and the structural basis for the variation in catalytic activity within this family is unknown. Furthermore, the mechanism for the differences in the inhibition of fungal GH11 enzymes by the wheat protein XIP-I remains opaque. To address these issues we report the crystal structure and biochemical properties of the Neocallimastix patriciarum xylanase NpXyn11A, which displays unusually high catalytic activity and is one of the few fungal GH11 proteins not inhibited by XIP-I. Although the structure of NpXyn11A could not be determined in complex with substrates, we have been able to investigate how GH11 enzymes hydrolyse decorated substrates by solving the crystal structure of a second GH11 xylanase, EnXyn11A (encoded by an environmental DNA sample), bound to ferulic acid-1,5-arabinofuranose-alpha1,3-xylotriose (FAX(3)). The crystal structure of the EnXyn11A-FAX(3) complex shows that solvent exposure of the backbone xylose O2 and O3 groups at subsites -3 and +2 allow accommodation of alpha1,2-linked 4-methyl-D-glucuronic acid and L-arabinofuranose side chains. Furthermore, the ferulated arabinofuranose side chain makes hydrogen bonds and hydrophobic interactions at the +2 subsite, indicating that the decoration may represent a specificity determinant at this aglycone subsite. The structure of NpXyn11A reveals potential -3 and +3 subsites that are kinetically significant. The extended substrate-binding cleft of NpXyn11A, compared to other GH11 xylanases, may explain why the Neocallimastix enzyme displays unusually high catalytic activity. Finally, the crystal structure of NpXyn11A shows that the resistance of the enzyme to XIP-I is not due solely to insertions in the loop connecting beta strands 11 and 12, as suggested previously, but is highly complex.

About this StructureAbout this Structure

2VGD is a Single protein structure of sequence from Escherichia coli with , and as ligands. Active as Endo-1,4-beta-xylanase, with EC number 3.2.1.8 Known structural/functional Sites: , , , , , , , , , and . Full crystallographic information is available from OCA.

ReferenceReference

Understanding the structural basis for substrate and inhibitor recognition in eukaryotic GH11 xylanases., Vardakou M, Dumon C, Murray JW, Christakopoulos P, Weiner DP, Juge N, Lewis RJ, Gilbert HJ, Flint JE, J Mol Biol. 2008 Feb 1;375(5):1293-305. Epub 2007 Nov 12. PMID:18078955

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 ==Overview==
-Endo-beta1,4-xylanases (xylanases) hydrolyse the beta1,4 glycosidic bonds, in the backbone of xylan. Although xylanases from glycoside hydrolase, family 11 (GH11) have been extensively studied, several issues remain, unresolved. Thus, the mechanism by which these enzymes hydrolyse decorated, xylans is unclear and the structural basis for the variation in catalytic, activity within this family is unknown. Furthermore, the mechanism for the, differences in the inhibition of fungal GH11 enzymes by the wheat protein, XIP-I remains opaque. To address these issues we report the crystal, structure and biochemical properties of the Neocallimastix patriciarum, xylanase NpXyn11A, which displays unusually high catalytic activity and is, one of the few fungal GH11 proteins not inhibited by XIP-I. Although the, structure of NpXyn11A could not be determined in complex with substrates, we have been able to investigate how GH11 enzymes hydrolyse decorated, substrates by solving the crystal structure of a second GH11 xylanase, EnXyn11A (encoded by an environmental DNA sample), bound to ferulic, acid-1,5-arabinofuranose-alpha1,3-xylotriose (FAX(3)). The crystal, structure of the EnXyn11A-FAX(3) complex shows that solvent exposure of, the backbone xylose O2 and O3 groups at subsites -3 and +2 allow, accommodation of alpha1,2-linked 4-methyl-D-glucuronic acid and, L-arabinofuranose side chains. Furthermore, the ferulated arabinofuranose, side chain makes hydrogen bonds and hydrophobic interactions at the +2, subsite, indicating that the decoration may represent a specificity, determinant at this aglycone subsite. The structure of NpXyn11A reveals, potential -3 and +3 subsites that are kinetically significant. The, extended substrate-binding cleft of NpXyn11A, compared to other GH11, xylanases, may explain why the Neocallimastix enzyme displays unusually, high catalytic activity. Finally, the crystal structure of NpXyn11A shows, that the resistance of the enzyme to XIP-I is not due solely to insertions, in the loop connecting beta strands 11 and 12, as suggested previously, but is highly complex.
+Endo-beta1,4-xylanases (xylanases) hydrolyse the beta1,4 glycosidic bonds in the backbone of xylan. Although xylanases from glycoside hydrolase family 11 (GH11) have been extensively studied, several issues remain unresolved. Thus, the mechanism by which these enzymes hydrolyse decorated xylans is unclear and the structural basis for the variation in catalytic activity within this family is unknown. Furthermore, the mechanism for the differences in the inhibition of fungal GH11 enzymes by the wheat protein XIP-I remains opaque. To address these issues we report the crystal structure and biochemical properties of the Neocallimastix patriciarum xylanase NpXyn11A, which displays unusually high catalytic activity and is one of the few fungal GH11 proteins not inhibited by XIP-I. Although the structure of NpXyn11A could not be determined in complex with substrates, we have been able to investigate how GH11 enzymes hydrolyse decorated substrates by solving the crystal structure of a second GH11 xylanase, EnXyn11A (encoded by an environmental DNA sample), bound to ferulic acid-1,5-arabinofuranose-alpha1,3-xylotriose (FAX(3)). The crystal structure of the EnXyn11A-FAX(3) complex shows that solvent exposure of the backbone xylose O2 and O3 groups at subsites -3 and +2 allow accommodation of alpha1,2-linked 4-methyl-D-glucuronic acid and L-arabinofuranose side chains. Furthermore, the ferulated arabinofuranose side chain makes hydrogen bonds and hydrophobic interactions at the +2 subsite, indicating that the decoration may represent a specificity determinant at this aglycone subsite. The structure of NpXyn11A reveals potential -3 and +3 subsites that are kinetically significant. The extended substrate-binding cleft of NpXyn11A, compared to other GH11 xylanases, may explain why the Neocallimastix enzyme displays unusually high catalytic activity. Finally, the crystal structure of NpXyn11A shows that the resistance of the enzyme to XIP-I is not due solely to insertions in the loop connecting beta strands 11 and 12, as suggested previously, but is highly complex.
 ==About this Structure==
-VGD is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] with <scene name='pdbligand=NA:'>NA</scene>, <scene name='pdbligand=FX3:'>FX3</scene> and <scene name='pdbligand=GOL:'>GOL</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Endo-1,4-beta-xylanase Endo-1,4-beta-xylanase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.8 3.2.1.8] Known structural/functional Sites: <scene name='pdbsite=AC1:Na Binding Site For Chain A'>AC1</scene>, <scene name='pdbsite=AC2:Xyp Binding Site For Chain A'>AC2</scene>, <scene name='pdbsite=AC3:Xyp Binding Site For Chain A'>AC3</scene>, <scene name='pdbsite=AC4:Xyp Binding Site For Chain A'>AC4</scene>, <scene name='pdbsite=AC5:Fx3 Binding Site For Chain A'>AC5</scene>, <scene name='pdbsite=AC6:Gol Binding Site For Chain A'>AC6</scene>, <scene name='pdbsite=AC7:Gol Binding Site For Chain A'>AC7</scene>, <scene name='pdbsite=AC8:Gol Binding Site For Chain A'>AC8</scene>, <scene name='pdbsite=AC9:Gol Binding Site For Chain A'>AC9</scene>, <scene name='pdbsite=BC1:Xyp Binding Site For Chain A'>BC1</scene> and <scene name='pdbsite=BC2:Xyp Binding Site For Chain A'>BC2</scene>. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VGD OCA].
+VGD is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] with <scene name='pdbligand=NA:'>NA</scene>, <scene name='pdbligand=FX3:'>FX3</scene> and <scene name='pdbligand=GOL:'>GOL</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Endo-1,4-beta-xylanase Endo-1,4-beta-xylanase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.8 3.2.1.8] Known structural/functional Sites: <scene name='pdbsite=AC1:Na+Binding+Site+For+Chain+A'>AC1</scene>, <scene name='pdbsite=AC2:Xyp+Binding+Site+For+Chain+A'>AC2</scene>, <scene name='pdbsite=AC3:Xyp+Binding+Site+For+Chain+A'>AC3</scene>, <scene name='pdbsite=AC4:Xyp+Binding+Site+For+Chain+A'>AC4</scene>, <scene name='pdbsite=AC5:Fx3+Binding+Site+For+Chain+A'>AC5</scene>, <scene name='pdbsite=AC6:Gol+Binding+Site+For+Chain+A'>AC6</scene>, <scene name='pdbsite=AC7:Gol+Binding+Site+For+Chain+A'>AC7</scene>, <scene name='pdbsite=AC8:Gol+Binding+Site+For+Chain+A'>AC8</scene>, <scene name='pdbsite=AC9:Gol+Binding+Site+For+Chain+A'>AC9</scene>, <scene name='pdbsite=BC1:Xyp+Binding+Site+For+Chain+A'>BC1</scene> and <scene name='pdbsite=BC2:Xyp+Binding+Site+For+Chain+A'>BC2</scene>. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VGD OCA].
 ==Reference==
-Understanding the Structural Basis for Substrate and Inhibitor Recognition in Eukaryotic GH11 Xylanases., Vardakou M, Dumon C, Murray JW, Christakopoulos P, Weiner DP, Juge N, Lewis RJ, Gilbert HJ, Flint JE, J Mol Biol. 2007 Nov 12;. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=18078955 18078955]
+Understanding the structural basis for substrate and inhibitor recognition in eukaryotic GH11 xylanases., Vardakou M, Dumon C, Murray JW, Christakopoulos P, Weiner DP, Juge N, Lewis RJ, Gilbert HJ, Flint JE, J Mol Biol. 2008 Feb 1;375(5):1293-305. Epub 2007 Nov 12. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=18078955 18078955]
 [[Category: Endo-1,4-beta-xylanase]]
 [[Category: Escherichia coli]]
@@ Line 16: / Line 16: @@
 [[Category: Christakopoulos, P.]]
 [[Category: Dumon, C.]]
-[[Category: Flint, J.E.]]
+[[Category: Flint, J E.]]
-[[Category: Gilbert, H.J.]]
+[[Category: Gilbert, H J.]]
 [[Category: Juge, N.]]
-[[Category: Lewis, R.J.]]
+[[Category: Lewis, R J.]]
-[[Category: Murray, J.W.]]
+[[Category: Murray, J W.]]
 [[Category: Vardakou, M.]]
-[[Category: Weiner, D.P.]]
+[[Category: Weiner, D P.]]
 [[Category: FX3]]
 [[Category: GOL]]
@@ Line 31: / Line 31: @@
 [[Category: xylanase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jan 23 10:46:03 2008''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 18:55:42 2008''