Dual biological role of glycoside hydrolase family fifty-seven glycogen branching enzymes

ABSTRACT The microbial degradation of xylan is a key biological process. Hardwood 4-O-methyl-d-glucuronoxylans are extensively decorated with 4-O-methyl-d-glucuronic acid, which is cleaved from the polysaccharides by α-glucuronidases. In this report we describe the primary structures of the α-glucuronidase from Cellvibrio mixtus (C. mixtus GlcA67A) and the α-glucuronidase from Pseudomonas cellulosa (P. cellulosa GlcA67A) and characterize P. cellulosa GlcA67A. The primary structures of C. mixtus GlcA67A and P. cellulosa GlcA67A, which are 76% identical, exhibit similarities with α-glucuronidases in glycoside hydrolase family 67. The membrane-associated pseudomonad α-glucuronidase released 4-O-methyl-d-glucuronic acid from 4-O-methyl-d-glucuronoxylooligosaccharides but not from 4-O-methyl-d-glucuronoxylan. We propose that the role of the glucuronidase, in combination with cell-associated xylanases, is to hydrolyze decorated xylooligosaccharides, generated by extracellular hemicellulases, to xylose and 4-O-methyl-d-glucuronic acid, enabling the pseudomonad to preferentially utilize the sugars derived from these polymers.

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The deduced role of a chitinase containing two nonsynergistic catalytic domains

Acta Crystallographica Section D Structural Biology ◽

10.1107/s2059798317018289 ◽

2018 ◽

Vol 74 (1) ◽

pp. 30-40 ◽

Cited By ~ 4

Author(s):

Tian Liu ◽

Weixing Zhu ◽

Jing Wang ◽

Yong Zhou ◽

Yanwei Duan ◽

...

Keyword(s):

Glycoside Hydrolase ◽

Gene Expression Pattern ◽

Physiological Data ◽

Glycoside Hydrolase Family ◽

Chitin Synthesis ◽

Group Iii ◽

Chitin Degradation ◽

Catalytic Domains ◽

Hydrolase Family

The glycoside hydrolase family 18 chitinases degrade or alter chitin. Multiple catalytic domains in a glycoside hydrolase family 18 chitinase function synergistically during chitin degradation. Here, an insect group III chitinase from the agricultural pestOstrinia furnacalis(OfChtIII) is revealed to be an arthropod-conserved chitinase that contains two nonsynergistic GH18 domains according to its catalytic properties. Both GH18 domains are active towards single-chained chitin substrates, but are inactive towards insoluble chitin substrates. The crystal structures of each unbound GH18 domain, as well as of GH18 domains complexed with hexa-N-acetyl-chitohexaose or penta-N-acetyl-chitopentaose, suggest that the two GH18 domains possess endo-specific activities. Physiological data indicated that the developmental stage-dependent gene-expression pattern ofOfChtIII was the same as that of the chitin synthaseOfChsA but significantly different from that of the chitinaseOfChtI, which is indispensable for cuticular chitin degradation. Additionally, immunological staining indicated thatOfChtIII was co-localized withOfChsA. Thus,OfChtIII is most likely to be involved in the chitin-synthesis pathway.

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Structural elements determining the transglycosylating activity of glycoside hydrolase family 57 glycogen branching enzymes

10.22541/au.162013331.11755851/v1 ◽

2021 ◽

Author(s):

Gang Xiang ◽

Hans Leemhuis ◽

Marc van der Maarel

Keyword(s):

Glycoside Hydrolase ◽

Bioinformatics Analysis ◽

Glycosidic Bond ◽

Glycoside Hydrolase Family ◽

Structural Elements ◽

Gene Sequences ◽

Flexible Loop ◽

Branching Enzymes ◽

Β Sheets ◽

Hydrolase Family

Glycoside hydrolase family 57 glycogen branching enzymes (GH57GBE) catalyze the formation of an α-1,6 glycosidic bond between α-1,4 linked glucooliogosaccharides. As an atypical family, a limited number of GH57GBEs have been biochemically characterized so far. This study aimed at acquiring a better understanding of the GH57GBE family by a systematic sequence-based bioinformatics analysis of almost 2,500 gene sequences and determining the branching activity of several native and mutant GH57GBEs. A correlation was found between a very low or even no branching activity with the absence of a flexible loop, a tyrosine at the loop tip, and two β-sheets.

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Role of a PA14 domain in determining substrate specificity of a glycoside hydrolase family 3 β-glucosidase from Kluyveromyces marxianus

Biochemical Journal ◽

10.1042/bj20100351 ◽

2010 ◽

Vol 431 (1) ◽

pp. 39-49 ◽

Cited By ~ 77

Author(s):

Erina Yoshida ◽

Masafumi Hidaka ◽

Shinya Fushinobu ◽

Takashi Koyanagi ◽

Hiromichi Minami ◽

...

Keyword(s):

Substrate Specificity ◽

Chain Length ◽

Kluyveromyces Marxianus ◽

Glycoside Hydrolase ◽

Critical Role ◽

Structural Basis ◽

Glycoside Hydrolase Family ◽

Catalytic Core ◽

Hydrolase Family

β-Glucosidase from Kluyveromyces marxianus (KmBglI) belongs to the GH3 (glycoside hydrolase family 3). The enzyme is particularly unusual in that a PA14 domain (pf07691), for which a carbohydrate-binding role has been claimed, is inserted into the catalytic core sequence. In the present study, we determined the enzymatic properties and crystal structure of KmBglI in complex with glucose at a 2.55 Å (1 Å=0.1 nm) resolution. A striking characteristic of KmBglI was that the enzyme activity is essentially limited to disaccharides, and when trisaccharides were used as the substrates the activity was drastically decreased. This chain-length specificity is in sharp contrast with the preferred action on oligosaccharides of barley β-D-glucan glucohydrolase (ExoI), which does not have a PA14 domain insertion. The structure of subsite (−1) of KmBglI is almost identical with that of Thermotoga neapolitana β-glucosidase and is also similar to that of ExoI, however, the structures of subsite (+1) significantly differ among them. In KmBglI, the loops extending from the PA14 domain cover the catalytic pocket to form subsite (+1), and hence simultaneously become a steric hindrance that could limit the chain length of the substrates to be accommodated. Mutational studies demonstrated the critical role of the loop regions in determining the substrate specificity. The active-site formation mediated by the PA14 domain of KmBglI invokes α-complementation of β-galactosidase exerted by its N-terminal domain, to which the PA14 domain shows structural resemblance. The present study is the first which reveals the structural basis of the interaction between the PA14 domain and a carbohydrate.

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Structural elements determining the transglycosylating activity of glycoside hydrolase family 57 glycogen branching enzymes

Proteins Structure Function and Bioinformatics ◽

10.1002/prot.26200 ◽

2021 ◽

Author(s):

Gang Xiang ◽

Hans Leemhuis ◽

Marc J. E. C. Maarel

Keyword(s):

Glycoside Hydrolase ◽

Glycoside Hydrolase Family ◽

Structural Elements ◽

Branching Enzymes ◽

Hydrolase Family

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Xylanases of glycoside hydrolase family 30 – An overview

Biotechnology Advances ◽

10.1016/j.biotechadv.2021.107704 ◽

2021 ◽

Vol 47 ◽

pp. 107704

Author(s):

Vladimír Puchart ◽

Katarína Šuchová ◽

Peter Biely

Keyword(s):

Glycoside Hydrolase ◽

Glycoside Hydrolase Family ◽

Hydrolase Family ◽

Glycoside Hydrolase Family 30

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Modeled 3D-Structures of Proteobacterial Transglycosylases from Glycoside Hydrolase Family 17 Give Insight in Ligand Interactions Explaining Differences in Transglycosylation Products

Applied Sciences ◽

10.3390/app11094048 ◽

2021 ◽

Vol 11 (9) ◽

pp. 4048

Author(s):

Javier A. Linares-Pastén ◽

Lilja Björk Jonsdottir ◽

Gudmundur O. Hreggvidsson ◽

Olafur H. Fridjonsson ◽

Hildegard Watzlawick ◽

...

Keyword(s):

Glycoside Hydrolase ◽

Ligand Docking ◽

Glycoside Hydrolase Family ◽

Ligand Interactions ◽

Tim Barrel ◽

Branching Point ◽

The Difference ◽

Dynamics Simulations ◽

And Function ◽

Hydrolase Family

The structures of glycoside hydrolase family 17 (GH17) catalytic modules from modular proteins in the ndvB loci in Pseudomonas aeruginosa (Glt1), P. putida (Glt3) and Bradyrhizobium diazoefficiens (previously B. japonicum) (Glt20) were modeled to shed light on reported differences between these homologous transglycosylases concerning substrate size, preferred cleavage site (from reducing end (Glt20: DP2 product) or non-reducing end (Glt1, Glt3: DP4 products)), branching (Glt20) and linkage formed (1,3-linkage in Glt1, Glt3 and 1,6-linkage in Glt20). Hybrid models were built and stability of the resulting TIM-barrel structures was supported by molecular dynamics simulations. Catalytic amino acids were identified by superimposition of GH17 structures, and function was verified by mutagenesis using Glt20 as template (i.e., E120 and E209). Ligand docking revealed six putative subsites (−4, −3, −2, −1, +1 and +2), and the conserved interacting residues suggest substrate binding in the same orientation in all three transglycosylases, despite release of the donor oligosaccharide product from either the reducing (Glt20) or non-reducing end (Glt1, Gl3). Subsites +1 and +2 are most conserved and the difference in release is likely due to changes in loop structures, leading to loss of hydrogen bonds in Glt20. Substrate docking in Glt20 indicate that presence of covalently bound donor in glycone subsites −4 to −1 creates space to accommodate acceptor oligosaccharide in alternative subsites in the catalytic cleft, promoting a branching point and formation of a 1,6-linkage. The minimum donor size of DP5, can be explained assuming preferred binding of DP4 substrates in subsite −4 to −1, preventing catalysis.

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