The X-ray Crystallographic Structure ofEscherichia coli Branching Enzyme

Abad, M.C.; Binderup, Kim; Rios-Steiner, J.; Arni, Raghuvir K.; Preiss, Jack; Geiger, James H.

doi:10.1074/jbc.m205746200

Cited by 116 publications

(120 citation statements)

References 37 publications

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“…Analysis of SBE primary sequences indicates that SBEs belong to the a-amylase superfamily of enzymes (termed the glycoside hydrolase family 13 [GH13]) and structurally made up of three domains: a central (b/a)-barrel catalytic domain, or A-domain, an NH 2 -terminal domain, and a C-terminal domain (58,59). The central catalytic domain is highly conserved among the members of the a-amylase (GH13) superfamily, and only isoamylases share all three domains with the BEs and are able to bind sugars in the a-1,6-position (59).…”

Section: Structure-function Relationships Of Sbesmentioning

confidence: 99%

“…The sequences of the NH 2 -and C-terminal domains are highly variable, but nevertheless jointly contribute to catalytic activity with the Adomain. Various experimental approaches (discussed in the sections below) have been used to deduce the functions of the three domains of SBE, including analysis of amino acid sequence alignments, site-directed mutagenesis (60), domainswapping experiments (12), and utilizing available X-ray crystallographic structures (59,61,62).…”

Section: Structure-function Relationships Of Sbesmentioning

confidence: 99%

“…X-ray crystallographic structures of GBE and SBE allowed elucidation of the (b/a) 8 barrel structural domain (59,61) and showed that variations occur in SBEs where the a-helix 5 is missing and replaced by extra a-helices (59). Another conserved feature of the central catalytic A-domain of SBEs is a group of four conserved amino acid regions (termed 1 to 4, see Fig.…”

Section: The Central Catalytic A-domainmentioning

confidence: 99%

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A review of starch‐branching enzymes and their role in amylopectin biosynthesis

2014

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Starch-branching enzymes (SBEs) are one of the four major enzyme classes involved in starch biosynthesis in plants and algae, and their activities play a crucial role in determining the structure and physical properties of starch granules. SBEs generate a-1,6-branch linkages in a-glucans through cleavage of internal a-1,4 bonds and transfer of the released reducing ends to C-6 hydroxyls. Starch biosynthesis in plants and algae requires multiple isoforms of SBEs and is distinct from glycogen biosynthesis in both prokaryotes and eukaryotes which uses a single branching enzyme (BE) isoform. One of the unique characteristics of starch structure is the grouping of a-1,6-branch points in clusters within amylopectin. This is a feature of SBEs and their interplay with other starch biosynthetic enzymes, thus facilitating formation of the compact water-insoluble semicrystalline starch granule. In this respect, the activity of SBE isoforms is pivotal in starch granule assembly. SBEs are structurally related to the aamylase superfamily of enzymes, sharing three domains of secondary structure with prokaryotic Bes: the central (b/a) 8 -barrel catalytic domain, an NH 2 -terminal domain involved in determining the size of a-glucan chain transferred, and the C-terminal domain responsible for catalytic capacity and substrate preference. In addition, SBEs have conserved plant-specific domains, including phosphorylation sites which are thought to be involved in regulating starch metabolism. SBEs form heteromeric protein complexes with other SBE isoforms as well as other enzymes involved in starch synthesis, and assembly of these protein complexes is regulated by protein phosphorylation. Phosphorylated SBEIIb is found in multienzyme complexes with isoforms of glucan-elongating starch synthases, and these protein complexes are implicated in amylopectin cluster formation. This review presents a comparative overview of plant SBEs and includes a review of their properties, structural and functional characteristics, and recent developments on their posttranslational regulation.

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Section: Structure-function Relationships Of Sbesmentioning

confidence: 99%

Section: Structure-function Relationships Of Sbesmentioning

confidence: 99%

Section: The Central Catalytic A-domainmentioning

confidence: 99%

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A review of starch‐branching enzymes and their role in amylopectin biosynthesis

2014

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“…In addition to GBD represented by the β-subunit of the mammalian AMP-activated protein kinase (AMPK) (Polekhina et al 2005), the family CBM48 contains the putative SBDs present in the four enzyme specificities from the α-amylase enzyme family: pullulanase (PUL), isoamylase (IAM), maltooligosyl trehalohydrolase (MOTH), as well as the glycogen branching enzyme (GBE) and the starch branching enzyme (SBE). These enzymes have recently been revealed to constitute the so-called GH13 PUL subfamily (Janecek et al 2007); the SBD being found as a domain that precedes the catalytic (β/α) 8 -barrel (Katsuya et al 1998;Feese et al 2000;Abad et al 2002;Mikami et al 2006). Within the CAZy classification, these enzymes have been grouped in subfamilies as follows: GBE and SBE (GH13 8, GH13 9), MOTH (GH13 10), IAM (GH13 11) and PUL (GH13 12,GH13 13,GH13 14).…”

Section: Introductionmentioning

confidence: 99%

Domain evolution in the GH13 pullulanase subfamily with focus on the carbohydrate-binding module family 48

Martín

Janeček

2008

Biologia

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Glycoside hydrolase (GH) family 13 comprises about 30 different specificities. Four of them have been proposed to form the GH13 pullulanase subfamily: pullulanase, isoamylase, maltooligosyl trehalohydrolase and branching enzyme forming the seven CAZy GH13 subfamilies: GH13 8-GH13 14. Recently, a new family of carbohydrate-binding modules (CBMs), the family CBM48 has been established containing the putative starch-binding domains from the pullulanase subfamily, the β-subunit of AMP-activated protein kinase and some other GH13 enzymes with pullulanase and/or α-amylase-pullulanase specificity. Since all of these enzymes are multidomain proteins and the structure for at least one representative of each enzyme specificity has already been determined, the main goal of the present study was to elucidate domain evolution within this GH13 pullulanase subfamily (84 real enzymes) focusing on the CBM48 module. With regard to CBM48 positioning in the amino acid sequence, the N-terminal end of a protein appears to be a predominant position. This is especially true for isoamylases and maltooligosyl trehalohydrolases. Secondary structure-based alignment of CBM modules from CBM48, CBM20 and CBM21 revealed that several residues known as consensus for CBM20 and CBM21 could also be identified in CBM48, but only branching enzymes possess the aromatic residues that correspond with the two tryptophans forming the evolutionary conserved starch-binding site 1 in CBM20. The evolutionary trees constructed for the individual domains, complete alignment, and the conserved sequence regions of the α-amylase family were found to be comparable to each other (except for the C-domain tree) with two basic parts: (i) branching enzymes and maltooligosyl trehalohydrolases; and (ii) pullulanases and isoamylases. Taxonomy was respected only within clusters with pure specificity, i.e. the evolution of CBM48 reflects the evolution of specificities rather than evolution of species. This is a feature different from the one observed for the starch-binding domain of the family CBM20 where the starch-binding domain evolution reflects the evolution of species.

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“…The only exception is represented by the ␤-subunit of AMPK (37), which showed that CBM48 is a separate domain that binds cyclodextrin to increase its binding ability for the glucosyl polymeric structures commonly found in glycogen (62). Despite the wealth of structural information on CBM48 (36,52,55,(63)(64)(65)(66)(67) (for a review, see Ref. 68)), this paper is, to the best of our knowledge, the first to demonstrate that an independent CBM domain folds to interact with the catalytic domain and participates in substrate binding at the active site.…”

Section: Discussionmentioning

confidence: 99%

Association of Novel Domain in Active Site of Archaic Hyperthermophilic Maltogenic Amylase from Staphylothermus marinus

Jung

Park

et al. 2012

Journal of Biological Chemistry

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Background: Maltogenic amylases that are known to date form dimers to perform hydrolysis. Results: The structure of maltogenic amylase from Staphylothermus showed a novel domain at the N terminus associated with the active site. Conclusion:Staphylothermus amylase has all of its substrate-binding structural components in a single monomer. Significance: This is the first report of the newly observed domain arrangement adopted by hyperthermophilic archaic maltogenic amylase.

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The X-ray Crystallographic Structure ofEscherichia coli Branching Enzyme

Cited by 116 publications

References 37 publications

A review of starch‐branching enzymes and their role in amylopectin biosynthesis

A review of starch‐branching enzymes and their role in amylopectin biosynthesis

Domain evolution in the GH13 pullulanase subfamily with focus on the carbohydrate-binding module family 48

Association of Novel Domain in Active Site of Archaic Hyperthermophilic Maltogenic Amylase from Staphylothermus marinus

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