1uhv: Difference between revisions

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Crystal structure of beta-D-xylosidase from Thermoanaerobacterium saccharolyticum, a family 39 glycoside hydrolase

OverviewOverview

1,4-beta-D-Xylan is the major component of plant cell-wall hemicelluloses. beta-D-Xylosidases are involved in the breakdown of xylans into xylose and belong to families 3, 39, 43, 52, and 54 of glycoside hydrolases. Here, we report the first crystal structure of a member of family 39 glycoside hydrolase, i.e. beta-D-xylosidase from Thermoanaerobacterium saccharolyticum strain B6A-RI. This study also represents the first structure of any beta-xylosidase of the above five glycoside hydrolase families. Each monomer of T. saccharolyticum beta-xylosidase comprises three distinct domains; a catalytic domain of the canonical (beta/alpha)(8)-barrel fold, a beta-sandwich domain, and a small alpha-helical domain. We have determined the structure in two forms: D-xylose-bound enzyme and a covalent 2-deoxy-2-fluoro-alpha-D-xylosyl-enzyme intermediate complex, thus providing two snapshots in the reaction pathway. This study provides structural evidence for the proposed double displacement mechanism that involves a covalent intermediate. Furthermore, it reveals possible functional roles for His228 as the auxiliary acid/base and Glu323 as a key residue in substrate recognition.

About this StructureAbout this Structure

1UHV is a Single protein structure of sequence from Thermoanaerobacterium saccharolyticum with as ligand. Active as Xylan 1,4-beta-xylosidase, with EC number 3.2.1.37 Full crystallographic information is available from OCA.

ReferenceReference

Crystal structure of beta-D-xylosidase from Thermoanaerobacterium saccharolyticum, a family 39 glycoside hydrolase., Yang JK, Yoon HJ, Ahn HJ, Lee BI, Pedelacq JD, Liong EC, Berendzen J, Laivenieks M, Vieille C, Zeikus GJ, Vocadlo DJ, Withers SG, Suh SW, J Mol Biol. 2004 Jan 2;335(1):155-65. PMID:14659747

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 '''Crystal structure of beta-D-xylosidase from Thermoanaerobacterium saccharolyticum, a family 39 glycoside hydrolase'''<br />
 ==Overview==
-,4-beta-D-Xylan is the major component of plant cell-wall hemicelluloses., beta-D-Xylosidases are involved in the breakdown of xylans into xylose and, belong to families 3, 39, 43, 52, and 54 of glycoside hydrolases. Here, we, report the first crystal structure of a member of family 39 glycoside, hydrolase, i.e. beta-D-xylosidase from Thermoanaerobacterium, saccharolyticum strain B6A-RI. This study also represents the first, structure of any beta-xylosidase of the above five glycoside hydrolase, families. Each monomer of T. saccharolyticum beta-xylosidase comprises, three distinct domains; a catalytic domain of the canonical, (beta/alpha)(8)-barrel fold, a beta-sandwich domain, and a small, alpha-helical domain. We have determined the structure in two forms:, D-xylose-bound enzyme and a covalent, 2-deoxy-2-fluoro-alpha-D-xylosyl-enzyme intermediate complex, thus, providing two snapshots in the reaction pathway. This study provides, structural evidence for the proposed double displacement mechanism that, involves a covalent intermediate. Furthermore, it reveals possible, functional roles for His228 as the auxiliary acid/base and Glu323 as a key, residue in substrate recognition.
+,4-beta-D-Xylan is the major component of plant cell-wall hemicelluloses. beta-D-Xylosidases are involved in the breakdown of xylans into xylose and belong to families 3, 39, 43, 52, and 54 of glycoside hydrolases. Here, we report the first crystal structure of a member of family 39 glycoside hydrolase, i.e. beta-D-xylosidase from Thermoanaerobacterium saccharolyticum strain B6A-RI. This study also represents the first structure of any beta-xylosidase of the above five glycoside hydrolase families. Each monomer of T. saccharolyticum beta-xylosidase comprises three distinct domains; a catalytic domain of the canonical (beta/alpha)(8)-barrel fold, a beta-sandwich domain, and a small alpha-helical domain. We have determined the structure in two forms: D-xylose-bound enzyme and a covalent 2-deoxy-2-fluoro-alpha-D-xylosyl-enzyme intermediate complex, thus providing two snapshots in the reaction pathway. This study provides structural evidence for the proposed double displacement mechanism that involves a covalent intermediate. Furthermore, it reveals possible functional roles for His228 as the auxiliary acid/base and Glu323 as a key residue in substrate recognition.
 ==About this Structure==
-UHV is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Thermoanaerobacterium_saccharolyticum Thermoanaerobacterium saccharolyticum] with DFX as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/Xylan_1,4-beta-xylosidase Xylan 1,4-beta-xylosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.37 3.2.1.37] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1UHV OCA].
+UHV is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Thermoanaerobacterium_saccharolyticum Thermoanaerobacterium saccharolyticum] with <scene name='pdbligand=DFX:'>DFX</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/Xylan_1,4-beta-xylosidase Xylan 1,4-beta-xylosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.37 3.2.1.37] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UHV OCA].
 ==Reference==
@@ Line 14: / Line 14: @@
 [[Category: Thermoanaerobacterium saccharolyticum]]
 [[Category: Xylan 1,4-beta-xylosidase]]
-[[Category: Ahn, H.J.]]
+[[Category: Ahn, H J.]]
 [[Category: Berendzen, J.]]
 [[Category: Laivenieks, M.]]
-[[Category: Lee, B.Il.]]
+[[Category: Lee, B Il.]]
-[[Category: Liong, E.C.]]
+[[Category: Liong, E C.]]
-[[Category: Pedelacq, J.D.]]
+[[Category: Pedelacq, J D.]]
-[[Category: Suh, S.W.]]
+[[Category: Suh, S W.]]
 [[Category: Vieille, C.]]
-[[Category: Vocadlo, D.J.]]
+[[Category: Vocadlo, D J.]]
-[[Category: Withers, S.G.]]
+[[Category: Withers, S G.]]
-[[Category: Yang, J.K.]]
+[[Category: Yang, J K.]]
-[[Category: Yoon, H.J.]]
+[[Category: Yoon, H J.]]
-[[Category: Zeikus, G.J.]]
+[[Category: Zeikus, G J.]]
 [[Category: DFX]]
 [[Category: covalent glycosyl-enzyme intermediate]]
@@ Line 34: / Line 34: @@
 [[Category: xylosidase]]
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