Backbone and side-chain assignments for a novel CBM69 starch binding domain AmyP-SBD

Li, Xinxin; Yu, Jigang; Zhang, Jiahai; Sun, Hongbin; Zhang, Xuecheng

doi:10.1007/s12104-017-9755-6

Cited by 5 publications

(3 citation statements)

References 12 publications

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“…All remaining individual CBM families of SBDs share a β‐barrel fold of a β‐sandwich although their sequences are, in general, poorly conserved . Although there are no clans of CBMs in CAZy , several related SBDs are classified in different CBM families, for example, CBM20, CBM48 and CBM69 . They also exhibit a striking sequence‐structural similarity suggesting a conserved mode of carbohydrate binding and often involve corresponding amino acid residues for carbohydrate binding.…”

mentioning

confidence: 99%

The unique evolution of the carbohydrate‐binding module CBM20 in laforin

2018

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Laforin catalyses glycogen dephosphorylation. Mutations in its gene result in Lafora disease, a fatal progressive myoclonus epilepsy, the hallmark being water-insoluble, hyperphosphorylated carbohydrate inclusions called Lafora bodies. Human laforin consists of an N-terminal carbohydrate-binding module (CBM) from family CBM20 and a C-terminal dual-specificity phosphatase domain. Laforin is conserved in all vertebrates, some basal metazoans and a small group of protozoans. The present in silico study defines the evolutionary relationships among the CBM20s of laforin with an emphasis on newly identified laforin orthologues. The study reveals putative laforin orthologues in Trichinella, a parasitic nematode, and identifies two sequence inserts in the CBM20 of laforin from parasitic coccidia. Finally, we identify that the putative laforin orthologues from some protozoa and algae possess more than one CBM20.

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confidence: 99%

The unique evolution of the carbohydrate‐binding module CBM20 in laforin

2018

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“…In 1997, Spiess demonstrated that The CBM69 that has been characterized so far is the one found in AmyP [20,36]. The structure of recombinant CBM69, which was produced independently, was elucidated using NMR techniques [37]. This CBM69 partially unfolds in its free form, resembling a compact molten globule.…”

Section: Essentials Of Calcium Ion Binding To Malsmentioning

confidence: 99%

The Distinctive Permutated Domain Structure of Periplasmic α-Amylase (MalS) from Glycoside Hydrolase Family 13 Subfamily 19

Tran

Yoo

et al. 2023

Molecules

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Periplasmic α-amylase MalS (EC. 3.2.1.1), which belongs to glycoside hydrolase (GH) family 13 subfamily 19, is an integral component of the maltose utilization pathway in Escherichia coli K12 and used among Ecnterobacteriaceae for the effective utilization of maltodextrin. We present the crystal structure of MalS from E. coli and reveal that it has unique structural features of circularly permutated domains and a possible CBM69. The conventional C-domain of amylase consists of amino acids 120–180 (N-terminal) and 646–676 (C-terminal) in MalS, and the whole domain architecture shows the complete circular permutation of C-A-B-A-C in domain order. Regarding substrate interaction, the enzyme has a 6-glucosyl unit pocket binding it to the non-reducing end of the cleavage site. Our study found that residues D385 and F367 play important roles in the preference of MalS for maltohexaose as an initial product. At the active site of MalS, β-CD binds more weakly than the linear substrate, possibly due to the positioning of A402. MalS has two Ca2+ binding sites that contribute significantly to the thermostability of the enzyme. Intriguingly, the study found that MalS exhibits a high binding affinity for polysaccharides such as glycogen and amylopectin. The N domain, of which the electron density map was not observed, was predicted to be CBM69 by AlphaFold2 and might have a binding site for the polysaccharides. Structural analysis of MalS provides new insight into the structure–evolution relationship in GH13 subfamily 19 enzymes and a molecular basis for understanding the details of catalytic function and substrate binding of MalS.

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“…The sequence alignment of the N1 domain of Gt-apu with CBM20 of gt-apu, CBM48 of the α-amylasepullulanase of Bacillus sp. XAL601 and the CBM69 of AmyP [69][70][71] has helped in identifying the amino acid residues of the starch-binding sites 1 and 2. The homology model of G. thermoleovorans NP33 amylopullulanase and its N1 domain built using Thermoactinomyces vulgaris α-amylase II (PDB code: 1BVZA) and B. acidopullulyticus pullulanase (PDB code: 2WANA) as templates suggested that the N1 domain (residues 1-257) of Gt-apu is positioned as a flexible region away from the rest of the structure (Fig.…”

Section: N-domainmentioning

confidence: 99%

Archaeal and bacterial thermostable amylopullulanases: characteristic features and biotechnological applications

Satyanarayana

Mohanan²

2018

Amylase

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Amylopullulanases are endoacting bifunctional enzymes capable of hydrolyzing α-1,4- and α-1,6-glycosidic linkages in starch, amylose, pullulan, amylopectin and related oligosaccharides. These enzymes possess single or dual active site(s) for cleaving α-1,4- and α-1,6-glycosidic bonds; the former are called amylopullulanases, and the latter, α-amylase-pullulanases. These are grouped into GH13 and GH57 families based on the architecture of the catalytic domain and the number of conserved sequence regions. The amylopullulanases/α-amylasepullulanases are produced by bacteria as well as archaea, and among them, thermophilic and hyperthermophilic species are the major producers. The thermostable amylopullulanases find application in one-step starch liquefaction-saccharification to form various sugar syrups and maltooligosaccharides. The starch saccharification process catalysed by amylopullulanases minimizes the use of other amylolytic enzymes, like α-amylase and glucoamylase, thereby reducing the cost of sugar syrups. The enzymes also find applications in bread making as an anti-stale and as a detergent additive.

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Backbone and side-chain assignments for a novel CBM69 starch binding domain AmyP-SBD

Cited by 5 publications

References 12 publications

The unique evolution of the carbohydrate‐binding module CBM20 in laforin

The unique evolution of the carbohydrate‐binding module CBM20 in laforin

The Distinctive Permutated Domain Structure of Periplasmic α-Amylase (MalS) from Glycoside Hydrolase Family 13 Subfamily 19

Archaeal and bacterial thermostable amylopullulanases: characteristic features and biotechnological applications

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