Approaches to labeling and identification of active site residues in glycosidases

Withers, Stephen G.; Aebersold, Ruedi

doi:10.1002/pro.5560040302

Cited by 157 publications

(44 citation statements)

References 71 publications

(61 reference statements)

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“…MeGlcA-␤-1,6-Gal-␤-1,6-Gal (MeGlcA-␤-1,6-Gal 2 ) was prepared as described previously (6), and 2Ј,4Ј-dinitrophenyl 2-deoxy-2-fluoro-␤-D-glucuronide (DNP-2FGlcA) was synthesized according to a method described previously (18).…”

Section: Methodsmentioning

confidence: 99%

Structural and Biochemical Characterization of Glycoside Hydrolase Family 79 β-Glucuronidase from Acidobacterium capsulatum

Michikawa

Ichinose

Momma

et al. 2012

Journal of Biological Chemistry

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Background:The three-dimensional structures of ␤-glucuronidase have been solved only for the GH2 enzymes. Results: AcGlcA79A is composed of a (␤/␣) 8 -barrel domain and a ␤-domain. Conclusion:The substrate binding site of AcGlcA79A is adapted for recognition of GlcA as a substrate. Significance: This is the first report describing the crystal structure, mechanism, and catalytic residues of a GH79 enzyme.

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Section: Methodsmentioning

confidence: 99%

Structural and Biochemical Characterization of Glycoside Hydrolase Family 79 β-Glucuronidase from Acidobacterium capsulatum

Michikawa

Ichinose

Momma

et al. 2012

Journal of Biological Chemistry

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“…Thus,glycosidasesare (Rye and WitherS,2000).Alltheenzyrnes of GH family 13 retain the anomeric configuration and work according to the double displacement mechanism (MacGregor, 1993;van del' Maarel el al., 2002). This is an acid-base catalysed reaction, requiring a proton donor and a nucleophile, in which a glucosyl-enzyme intermediate is formed (Withers and Aebersold, 1995 (Withers and Aebersold,1995).…”

Section: Mechanismforalpha-amylaseactionmentioning

confidence: 99%

The impact of heat-moisture treatment on the molecular structure and physicochemical properties of normal and waxy potato starches

Varatharajan

Hoover

Liu

et al. 2010

Carbohydrate Polymers

148

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Heat-moisture treatment (HMT) is a physical modification technique that modifies starch structure and properties without destroying its granular structure. HMT has been shown to cause starch chain interactions and crystallite disruption/reorientation within the amorphous and crystalline domains. However, the part played by amylose (AM) during HMT of starches is not properly understood. Furthermore, a systematic study has not been carried out to examine how variations in HMT temperatures influence molecular structure, physicochemical properties and digestibility of normal potato (NP) and waxy potato (WP) starches. Thus, the objective of this study was to determine changes to molecular structure, physicochemical properties and digestibility ofNP and WP starches on HMT at different temperatures (80,100,120 and l30°C) for 16 h at 27% moisture. Structural changes on HMT were monitored by scanning electron microscopy (SEM), confocal laser scanning microscopy (CLSM), polarized light microscopy (pLM), wide angle X-ray scattering (WAXS), attenuated total reflection-Fourier transform infrared (ATR-FTIR) spectroscopy, fluorophore assisted capillary electrophoresis (FACE) and KlS spectra. Changes to physicochemical properties on HMT were determined by granular swelling, amylose leaching, gelatinization parameters and pasting properties. Digestibility of normal and waxy potato starches before and after HMT by porcine pancreatic a-amylase (PPA) was monitored by measuring initial velocity and by exarninationofthe granular structure at different stages of hydrolysis by SEM, CLSM and PLM. The results showed that structural changes on HMT were influenced by differences in starch chain mobility at different temperatures of HMT. Starch chain mobility, in turn, was influenced by the interplay between the extent to which B-type crystallites were transformed into A+B-type crystallites, kinetic energy imparted to starch chains and amylose content. The main type of structural changes influencing physicochemical properties at different temperatures of HMT were starch chain interactions (at 80 and IOO°C), disruption of hydrogen bonds between amylose-amylopectin and amylopectin-amylopectin (at 120 and l30°C), disorganization of amylopectin chains near the vicinity of the hilum (at 100, 120 and l30°C)andformationofinterruptedhelices(atl30°C).The susceptibility ofNP and WP starches towards a-amylase decreased at 80°C, but increased in the range 100 to l30°C. NPand WPstarches exhibited heterogeneity in degradation (NP>WP) Most studies have been on the impact ofHMT on the thermal properties, crystallinity and pasting propertiesofnorrnalstarches. Some researchers (Hoover and Manuel, 1996; Kweon el al., 2000;Zavareze et al., 2010) have attempted to explain the impact of HMT on the structure and physicochemical properties of starches varying in amylose content. However, the part played by amylose during HMT of starches is still not properly understood. Unlike in cereal starches, amylose has been shown to be co-crystallized with amylopectin...

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“…All the enzymes of GH family 13 retain the anomeric configuration and work according to the double displacement mechanism (MacGregor 1993;van der Maarel et al 2002). This is an acid-base catalysed reaction, requiring a proton donor and a nucleophile, in which a glycosyl-enzyme intermediate is formed (Withers & Aebersold 1995). Typically, all endo-acting amylases work according to this action mechanism.…”

Section: Action Pattern Of Amylasesmentioning

confidence: 99%

“…In contrast, exo-acting amylases, such as β-amylases, are inverting amylases and work through the single displacement mechanism . The reaction proceeds through an oxocarbenium ion-like transition state (Withers & Aebersold 1995).…”

Section: Action Pattern Of Amylasesmentioning

confidence: 99%

Amylase action pattern on starch polymers

2008

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Several decades ago, the first reports on differences in action pattern between amylases from different sources indicated that the starch polymers are not degraded in a completely random manner. We here give an overview of different action patterns of amylases on amylose and amylopectin, focusing on the so-called multiple attack action of the enzymes. Nowadays, the multiple attack action is generally an accepted concept to explain the differences in amylase action pattern. However, the pancreatic α-amylase remains one of the few enzymes known with a considerable level of multiple attack action. Despite some recent studies, the molecular mechanism of the multiple attack action is still largely unclear. Probably, the degree to which the active site architecture and binding properties allow both the reorganization (sliding) of the substrate in the active site and the stabilisation of the productive enzyme/substrate complex mainly determine the multiple attack action of amylases.

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Approaches to labeling and identification of active site residues in glycosidases

Cited by 157 publications

References 71 publications

Structural and Biochemical Characterization of Glycoside Hydrolase Family 79 β-Glucuronidase from Acidobacterium capsulatum

Structural and Biochemical Characterization of Glycoside Hydrolase Family 79 β-Glucuronidase from Acidobacterium capsulatum

The impact of heat-moisture treatment on the molecular structure and physicochemical properties of normal and waxy potato starches

Amylase action pattern on starch polymers

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