Role of N-terminal region of Escherichia coli maltodextrin glucosidase in folding and function of the protein

Pastor, Ashutosh; Singh, Amit Kumar; Shukla, Prakash; Equbal, Md. Javed; Malik, Shikha T.; Singh, T.P.; Chaudhuri, Tapan K.

doi:10.1016/j.bbapap.2016.06.008

Cited by 10 publications

(6 citation statements)

References 54 publications

(61 reference statements)

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“…Post-secretion, when no longer needed, rheostats may become stabilized in native states (e.g., in the PhoA dimer). Since N-terminal segments are first out of the ribosome, rheostats might have wider ramifications as generic controllers of protein folding, even in cytoplasmic folders (Buhr et al, 2016;Dumoulin et al, 1998;Pastor et al, 2016).…”

Section: Discussionmentioning

confidence: 99%

Preprotein Conformational Dynamics Drive Bivalent Translocase Docking and Secretion

et al. 2017

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Most bacterial secretory proteins destined beyond the plasma membrane are secreted post-translationally by the Sec translocase. In the first step of translocation, preproteins are targeted for binding to their 2-site receptor SecA, the peripheral ATPase subunit of the translocase. We now reveal that secretory preproteins use a dual-key mechanism to bridge the signal peptide and mature domain receptor sites and cooperatively enhance their affinities. Docking of targeting-competent mature domains requires that their extensive disorder is finely tuned. This is achieved through amino-terminal mature domain regions acting as conformational rheostats. By being linked to the rheostats, signal peptides regulate long-range preprotein disorder. Concomitant conformational changes in SecA sterically adapt its two receptor sites to optimally recognize hundreds of dissimilar preproteins. This novel intramolecular conformational crosstalk in the preprotein chains and the dynamic interaction with their receptor are mechanistically coupled to preprotein engagement in the translocase and essential for secretion.

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Section: Discussionmentioning

confidence: 99%

Preprotein Conformational Dynamics Drive Bivalent Translocase Docking and Secretion

et al. 2017

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“…WcAG acts on maltodextrin at the reducing end, similar to MalZ, a maltodextrin glucosidase from E. coli (Tapio et al, 1991;Dippel & Boos, 2005). WcAG and MalZ have low protein sequence similarity (29%) and MalZ is active in a monomeric form (Pastor et al, 2016). Moreover, the K m of MalZ was $3 times higher than that of WcAG when maltotriose was used as a substrate (Brunkhorst et al, 1999).…”

Section: Discussionmentioning

confidence: 99%

A GH13 α-glucosidase from Weissella cibaria uncommonly acts on short-chain maltooligosaccharides

Wangpaiboon

Laohawuttichai

Kim

et al. 2021

Acta Cryst Sect D Struct Biol

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α-Glucosidase (EC 3.2.1.20) is a carbohydrate-hydrolyzing enzyme which generally cleaves α-1,4-glycosidic bonds of oligosaccharides and starch from the nonreducing ends. In this study, the novel α-glucosidase from Weissella cibaria BBK-1 (WcAG) was biochemically and structurally characterized. WcAG belongs to glycoside hydrolase family 13 (GH13) and to the neopullanase subfamily. It exhibits distinct hydrolytic activity towards the α-1,4 linkages of short-chain oligosaccharides from the reducing end. The enzyme prefers to hydrolyse maltotriose and acarbose, while it cannot hydrolyse cyclic oligosaccharides and polysaccharides. In addition, WcAG can cleave pullulan hydrolysates and strongly exhibits transglycosylation activity in the presence of maltose. Size-exclusion chromatography and X-ray crystal structures revealed that WcAG forms a homodimer in which the N-terminal domain of one monomer is orientated in proximity to the catalytic domain of another, creating the substrate-binding groove. Crystal structures of WcAG in complexes with maltose, maltotriose and acarbose revealed a remarkable enzyme active site with accessible +2, +1 and −1 subsites, along with an Arg–Glu gate (Arg176–Glu296) in front of the active site. The −2 and −3 subsites were blocked by Met119 and Asn120 from the N-terminal domain of a different subunit, resulting in an extremely restricted substrate preference.

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“…A computational framework to differentiate destabilizing InDels from stabilizing ones will help in better understanding such backbone modifications and will help in the design of novel proteins with desirable functionalities. Several experimental studies − deal with the impact of domain deletions (mostly at the N-terminal and C-terminal) on the thermodynamic stability and functionality of proteins. Nevertheless, it is essential to note that most existing proteins have a modular design with independently stable subdomains .…”

Section: Introductionmentioning

confidence: 99%

Estimating Change in Foldability Due to Multipoint Deletions in Protein Structures

Banerjee

Kumar

Ghosh

et al. 2020

J. Chem. Inf. Model.

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Insertions/deletions of amino acids in the protein backbone potentially result in altered structural/functional specifications. They can either contribute positively to the evolutionary process or can result in disease conditions. Despite being the second most prevalent form of protein modification, there are no databases or computational frameworks that delineate harmful multipoint deletions (MPD) from beneficial ones. We introduce a positive unlabeled learning-based prediction framework (PROFOUND) that utilizes fold-level attributes, environment-specific properties, and deletion site-specific properties to predict the change in foldability arising from such MPDs, both in the non-loop and loop regions of protein structures. In the absence of any protein structure dataset to study MPDs, we introduce a dataset with 153 MPD instances that lead to native-like folded structures and 7650 unlabeled MPD instances whose effect on the foldability of the corresponding proteins is unknown. PROFOUND on 10-fold cross-validation on our newly introduced dataset reports a recall of 82.2% (86.6%) and a fall out rate (FR) of 14.2% (20.6%), corresponding to MPDs in the protein loop (non-loop) region. The low FR suggests that the foldability in proteins subject to MPDs is not random and necessitates unique specifications of the deleted region. In addition, we find that additional evolutionary attributes contribute to higher recall and lower FR. The first of a kind foldability prediction system owing to MPD instances and the newly introduced dataset will potentially aid in novel protein engineering endeavors.

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Role of N-terminal region of Escherichia coli maltodextrin glucosidase in folding and function of the protein

Cited by 10 publications

References 54 publications

Preprotein Conformational Dynamics Drive Bivalent Translocase Docking and Secretion

Preprotein Conformational Dynamics Drive Bivalent Translocase Docking and Secretion

A GH13 α-glucosidase from Weissella cibaria uncommonly acts on short-chain maltooligosaccharides

Estimating Change in Foldability Due to Multipoint Deletions in Protein Structures

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