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PDBsum entry 3cu9
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References listed in PDB file
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Key reference
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Title
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Crystal structure of an inverting gh 43 1,5-Alpha-L-Arabinanase from geobacillus stearothermophilus complexed with its substrate.
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Authors
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A.Alhassid,
A.Ben-David,
O.Tabachnikov,
D.Libster,
E.Naveh,
G.Zolotnitsky,
Y.Shoham,
G.Shoham.
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Ref.
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Biochem J, 2009,
422,
73-82.
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PubMed id
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Abstract
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Arabinanases are glycosidases that hydrolyse alpha-(1-->5)-
arabinofuranosidic linkages found in the backbone of the pectic polysaccharide
arabinan. Here we describe the biochemical characterization and the
enzyme-substrate crystal structure of an inverting family 43 arabinanase from
Geobacillus stearothermophilus T-6 (AbnB). Based on viscosity and reducing power
measurements, and based on product analysis for the hydrolysis of linear
arabinan by AbnB, the enzyme works in an endo mode of action. Isothermal
titration calorimetry studies of a catalytic mutant with various
arabino-oligosaccharides suggested that the enzyme active site can accommodate
at least five arabinose units. The crystal structure of AbnB was determined at
1.06 A (1 A=0.1 nm) resolution, revealing a single five-bladed-beta-propeller
fold domain. Co-crystallization of catalytic mutants of the enzyme with
different substrates allowed us to obtain complex structures of AbnBE201A with
arabinotriose and AbnBD147A with arabinobiose. Based on the crystal structures
of AbnB together with its substrates, the position of the three catalytic
carboxylates: Asp27, the general base; Glu201, the general acid; and Asp147, the
pKa modulator, is in agreement with their putative catalytic roles. In the
complex structure of AbnBE201A with arabinotriose, a single water molecule is
located 2.8 A from Asp27 and 3.7 A from the anomeric carbon. The position of
this water molecule is kept via hydrogen bonding with a conserved tyrosine
(Tyr229) that is 2.6 A distant from it. The location of this molecule suggests
that it can function as the catalytic water molecule in the hydrolysis reaction,
resulting in the inversion of the anomeric configuration of the product.
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