Functional Roles of Starch Binding Domains and Surface Binding Sites in Enzymes Involved in Starch Biosynthesis

Wilkens, Casper; Svensson, Birte; Møller, Marie Sofie

doi:10.3389/fpls.2018.01652

Cited by 24 publications

(23 citation statements)

References 80 publications

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“…The binding site is at a distance of approximately 25 Å from the active site. Recently, it has been reported that a large number of enzymes catalysing starch degradation or biosynthesis possess surface binding sites (SBSs), which are involved in carbohydrate interaction and are located on the protein surface at a distance from the active site (Møller & Svensson, 2016;Wilkens et al, 2018). The SBSs in some enzymes are proposed to play roles in the recognition of parts of starch chains and also to transfer chains entering or exiting the active site.…”

Section: Substrate Recognition In Ef-amy Imentioning

confidence: 99%

X-ray crystallographic structural studies of α-amylase I from Eisenia fetida

Hirano¹,

Tsukamoto²,

Ariki³

et al. 2020

Acta Cryst Sect D Struct Biol

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The earthworm Eisenia fetida possesses several cold-active enzymes, including α-amylase, β-glucanase and β-mannanase. E. fetida possesses two isoforms of α-amylase (Ef-Amy I and II) to digest raw starch. Ef-Amy I retains its catalytic activity at temperatures below 10°C. To identify the molecular properties of Ef-Amy I, X-ray crystal structures were determined of the wild type and of the inactive E249Q mutant. Ef-Amy I has structural similarities to mammalian α-amylases, including the porcine pancreatic and human pancreatic α-amylases. Structural comparisons of the overall structures as well as of the Ca2+-binding sites of Ef-Amy I and the mammalian α-amylases indicate that Ef-Amy I has increased structural flexibility and more solvent-exposed acidic residues. These structural features of Ef-Amy I may contribute to its observed catalytic activity at low temperatures, as many cold-adapted enzymes have similar structural properties. The structure of the substrate complex of the inactive mutant of Ef-Amy I shows that a maltohexaose molecule is bound in the active site and a maltotetraose molecule is bound in the cleft between the N- and C-terminal domains. The recognition of substrate molecules by Ef-Amy I exhibits some differences from that observed in structures of human pancreatic α-amylase. This result provides insights into the structural modulation of the recognition of substrates and inhibitors.

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Section: Substrate Recognition In Ef-amy Imentioning

confidence: 99%

X-ray crystallographic structural studies of α-amylase I from Eisenia fetida

Hirano¹,

Tsukamoto²,

Ariki³

et al. 2020

Acta Cryst Sect D Struct Biol

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“…citreum NRRL B-1299 (17)(18)(19). Surprisingly, additional surface (or secondary) binding sites more distant from the active site were never described in the domains A, B or IV of GH70 dextransucrases contrary to what was observed for GH13 enzymes, which belong to the same clan as the GH70 enzymes and for which the distant surface binding sites were found to play a role in substrate targeting, allosteric regulation and also processivity (20)(21)(22)(23)(24).…”

Section: Introductionmentioning

confidence: 99%

A specific oligosaccharide-binding site in the alternansucrase catalytic domain mediates alternan elongation

Molina

Moulis

Monties

et al. 2020

Journal of Biological Chemistry

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Microbial α-glucans produced by GH70 (glycoside hydrolase family 70) glucansucrases are gaining importance because of the mild conditions for their synthesis from sucrose, their biodegradability, and their current and anticipated applications that largely depend on their molar mass. Focusing on the alternansucrase (ASR) from Leuconostoc citreum NRRL B-1355, a well-known glucansucrase catalyzing the synthesis of both high- and low-molar-mass alternans, we searched for structural traits in ASR that could be involved in the control of alternan elongation. The resolution of five crystal structures of a truncated ASR version (ASRΔ2) in complex with different gluco-oligosaccharides pinpointed key residues in binding sites located in the A and V domains of ASR. Biochemical characterization of three single mutants and three double mutants targeting the sugar-binding pockets identified in domain V revealed an involvement of this domain in alternan binding and elongation. More strikingly, we found an oligosaccharide-binding site at the surface of domain A, distant from the catalytic site and not previously identified in other glucansucrases. We named this site surface-binding site (SBS) A1. Among the residues lining the SBS-A1 site, two (Gln700 and Tyr717) promoted alternan elongation. Their substitution to alanine decreased high-molar-mass alternan yield by a third, without significantly impacting enzyme stability or specificity. We propose that the SBS-A1 site is unique to alternansucrase and appears to be designed to bind alternating structures, acting as a mediator between the catalytic site and the sugar-binding pockets of domain V and contributing to a processive elongation of alternan chains.

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“…Synthesis of this sugar nucleotide takes place from glucose-1-phosphate (Glc1P) and ATP in a reaction catalyzed by ADP-Glc pyrophosphorylase (EC 2.7.7.27, ADP-Glc PPase) ( Ballicora et al., 2003 ; Ballicora et al., 2004 ). The metabolic route follows by the action of enzymes implicated in branching, debranching, phosphorylation, and de-phosphorylation of the polymer under formation ( Wilkens et al., 2018 ). Most of these enzymes arise in isoforms exhibiting changes in specificity and ability to interact with different partners forming multi-protein complexes of functional relevance for the production of the polysaccharide ( Crofts et al., 2017 ; Wilkens et al., 2018 ).…”

Section: Introductionmentioning

confidence: 99%

“…The metabolic route follows by the action of enzymes implicated in branching, debranching, phosphorylation, and de-phosphorylation of the polymer under formation ( Wilkens et al., 2018 ). Most of these enzymes arise in isoforms exhibiting changes in specificity and ability to interact with different partners forming multi-protein complexes of functional relevance for the production of the polysaccharide ( Crofts et al., 2017 ; Wilkens et al., 2018 ). The step producing ADP-Glc is rate-limiting in the starch biosynthetic pathway ( Kavakli et al., 2001b ; Ballicora et al., 2003 ; Ballicora et al., 2004 ; Tuncel and Okita, 2013 ).…”

Section: Introductionmentioning

confidence: 99%

Phosphorylation of ADP-Glucose Pyrophosphorylase During Wheat Seeds Development

et al. 2020

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Starch is the dominant reserve polysaccharide accumulated in the seed of grasses (like wheat). It is the most common carbohydrate in the human diet and a material applied to the bioplastics and biofuels industry. Hence, the complete understanding of starch metabolism is critical to design rational strategies to improve its allocation in plant reserve tissues. ADP-glucose pyrophosphorylase (ADP-Glc PPase) catalyzes the key (regulated) step in the synthetic starch pathway. The enzyme comprises a small (S) and a large (L) subunit forming an S 2 L 2 heterotetramer, which is allosterically regulated by orthophosphate, fructose-6P, and 3P-glycerate. ADP-Glc PPase was found in a phosphorylated state in extracts from wheat seeds. The amount of the phosphorylated protein increased along with the development of the seed and correlated with relative increases of the enzyme activity and starch content. Conversely, this post-translational modification was absent in seeds from Ricinus communis . In vitro , the recombinant ADP-Glc PPase from wheat endosperm was phosphorylated by wheat seed extracts as well as by recombinant Ca 2+ -dependent plant protein kinases. Further analysis showed that the preferential phosphorylation takes place on the L subunit. Results suggest that the ADP-Glc PPase is a phosphorylation target in seeds from grasses but not from oleaginous plants. Accompanying seed maturation and starch accumulation, a combined regulation of ADP-Glc PPase by metabolites and phosphorylation may provide an enzyme with stable levels of activity. Such concerted modulation would drive carbon skeletons to the synthesis of starch for its long-term storage, which later support seed germination.

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Functional Roles of Starch Binding Domains and Surface Binding Sites in Enzymes Involved in Starch Biosynthesis

Cited by 24 publications

References 80 publications

X-ray crystallographic structural studies of α-amylase I from Eisenia fetida

X-ray crystallographic structural studies of α-amylase I from Eisenia fetida

A specific oligosaccharide-binding site in the alternansucrase catalytic domain mediates alternan elongation

Phosphorylation of ADP-Glucose Pyrophosphorylase During Wheat Seeds Development

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