New Ulvan-Degrading Polysaccharide Lyase Family: Structure and Catalytic Mechanism Suggests Convergent Evolution of Active Site Architecture

Ulaganathan, ThirumalaiSelvi; Boniecki, Michal T.; Foran, Elizabeth; Buravenkov, Vitaliy; Mizrachi, Naama; Banin, Ehud; Helbert, William; Cygler, Mirosław

doi:10.1021/acschembio.7b00126

Cited by 56 publications

(43 citation statements)

References 31 publications

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“…PLSV (PLSV_3936) belonging to PL25 was identified. 24) This new ulvan lyase could be secreted, although no direct evidence has been demonstrated so far. We have found the homologous gene in KUL17 (unpublished data).…”

Section: Discussionmentioning

confidence: 94%

Characterization of an Alteromonas long-type ulvan lyase involved in the degradation of ulvan extracted from Ulva ohnoi

Muramatsu

Kato

et al. 2017

Bioscience, Biotechnology, and Biochemistry

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Ulvan is a sulfated polysaccharide found in the cell wall of the green algae Ulva. We first isolated several ulvan-utilizing Alteromonas sp. from the feces of small marine animals. The strain with the highest ulvan-degrading activity, KUL17, was analyzed further. We identified a 55-kDa ulvan-degrading protein secreted by this strain and cloned the gene encoding for it. The deduced amino acid sequence indicated that the enzyme belongs to polysaccharide lyase family 24 and thus the protein was named ulvan lyase. The predicted molecular mass of this enzyme is 110 kDa, which is different from that of the identified protein. By deletion analysis, the catalytic domain was proven to be located on the N-terminal half of the protein. KUL17 contains two ulvan lyases, one long and one short, but the secreted and cleaved long ulvan lyase was demonstrated to be the major enzyme for ulvan degradation.

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Section: Discussionmentioning

confidence: 94%

Characterization of an Alteromonas long-type ulvan lyase involved in the degradation of ulvan extracted from Ulva ohnoi

Muramatsu

Kato

et al. 2017

Bioscience, Biotechnology, and Biochemistry

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“…Both enzymes harbor bound ions, Ca 2+ in the case of LOR_107 and Zn 2+ for PLSV_3936. The Ca 2+ ions in LOR_107 play strictly structural roles and are distant from the active site, while the Zn 2+ ion in PLSV_3936 is located much closer to the active site and likely contributes not only to the stabilization of one of the loops but also rigidifies the active site area (16).…”

Section: Comparison Of Lor_107 and Plsv_3936mentioning

confidence: 99%

“…strain PLSV, called PLSV_3936. This enzyme belongs to another new polysaccharide lyase family, PL25 (16). PLSV_3936 is folded into a seven bladed β-propeller and utilizes the His/Tyr mediated elimination mechanism for catalysis.…”

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confidence: 99%

Structure–function analyses of a PL24 family ulvan lyase reveal key features and suggest its catalytic mechanism

Ulaganathan

Helbert

Kopel

et al. 2018

Journal of Biological Chemistry

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Ulvan is a major cell wall component of green algae of the genus Ulva and some marine bacteria encode enzymes that can degrade this polysaccharide. The first ulvan degrading lyases have been recently characterized and several putative ulvan lyases have been recombinantly expressed, confirmed as ulvan lyases and partially characterized. Two families of ulvan degrading lyases, PL24 and PL25, have recently been established. The PL24 lyase LOR_107 from the bacterial Alteromonadales sp. strain LOR degrades ulvan endolytically, cleaving the bond at the C4 of a glucuronic acid. However, the mechanism and LOR_107 structural features involved are unknown. We present here the crystal structure of LOR_107, representing the first PL24 family structure. We found that LOR_107 adopts a seven-bladed β-propeller fold with a deep canyon on one side of the protein. Comparative sequence analysis revealed a cluster of conserved residues within this canyon, and site-directed mutagenesis disclosed several residues essential for catalysis. We also found that LOR_107 uses the His/Tyr catalytic mechanism, common to several PL families. We captured a tetrasaccharide substrate in the structures of two inactive mutants, which indicated a two-step binding event, with the first substrate interaction near the top of the canyon coordinated by Arg-320, followed by sliding of the substrate into the canyon toward the active-site residues. Surprisingly, the LOR_107 structure was very similar to that of PL25 family PLSV_3936, despite only ~14% sequence identity between the two enzymes. On the basis of our structural and mutational analyses, we propose a catalytic mechanism for LOR_107 that differs from the typical His/Tyr mechanism.Ulvan is one of the two major cell wall components of marine green algae (genus Ulva and Enteromorpha). It is a complex sulfated polysaccharide composed mainly of 3-sulfated rhamnose (Rha3S), glucuronic acid (GlcA), iduronic acid (IdoA) and xylose (1). The common disaccharide repetitive units within the ulvan polysaccharides are [→4)-β-D-GlcA-(1→4)-α-LRha3S-(1→] called type A ulvanobiourinic-3-sulfate (A 3S ) and [→4)-α-L-IdoA-(1→4)-α-LRha3S(1→] called type B ulvanobiouronic-3-sulfate (B 3S ) (1) (Schema 1). The presence of iduronic acid and sulfated rhamnose differentiates ulvan from other polysaccharides of marine origin and displays similarity with mammalian glycosaminoglycans such as chondroitin sulfate and hyaluronic acid. This distinctive chemical feature makes ulvan an attractive candidate for various biomedical, nanobiotechnological and drug delivery applications (2-6).Polysaccharides containing uronic acid sugars can be degraded by enzymes utilizing a β-http://www.jbc.org/cgi/doi/10.1074/jbc.RA117. (PLs). They utilize a β-elimination mechanism to cleave the oxygenaglycone bond by abstracting the C5 proton, which results in the formation of an unsaturated 4-deoxy-L-threo-hex-4-enopyranosiduronic acid (ΔUA) at the non-reducing end of the oligosaccharide product (7). These enzymes are presently classified into 26 s...

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“…Glycosyl hydrolases, detailed information which are available in Carbohydrate-Active Enzymes (CAZy) Database, utilize the linkage between anomeric carbon and the bridging oxygen of glycosidic bond. Polysaccharides containing uronic acid residues are depolymerised through O-C4 bond cleavage via an elimination reaction to produce an α,β-unsaturated residue at the newly created non-reducing end of the sugar (Garron and Cygler, 2014;Ulaganathan et al, 2017).…”

Section: In Vitro Enzymatic Degradation Of Marine Sulfated Polysacchamentioning

confidence: 99%

“…These enzymes cleave glycosidic linkage between sulfated rhamnose and GlcA or IduA and the endproducts of lyase-mediated β-elimination reaction are unsaturated oligosaccharides with degree of polymerization greater than 2, terminal positions being occupied by uronyl residues at the non-reducing end e.g. Δ, 4-deoxy-L-threohex-4-enopyranosiduronic acid (Collen et al, 2014;He et al, 2017;Ulaganathan et al, 2017). Complex nature of ulvanolytic degradation into monosaccharides indicates participation of other lyases such as 6S-rhamnosidases, xylanases, and sulfatases (Collen et al, 2011).…”

Section: In Vitro Enzymatic Degradation Of Marine Sulfated Polysacchamentioning

confidence: 99%

Absorption, distribution, metabolism and elimination (ADME) and toxicity profile of marine sulfated polysaccharides used in bionanotechnology

Majee¹,

Avlani²,

Ghosh³

et al. 2018

Afr. J. Pharm. Pharmacol.

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Sulfated polysaccharides extracted from marine algae and bacteria constitute an important class of biomacromolecules as they are characterized by biocompatibility, biodegradability and low immunogenicity. Recent advances in bionanotechnology are attributed to identification of marine sulfated polysaccharides of unique composition and functional properties. Promising results obtained so far justify the need for additional research in the study of absorption, distribution, metabolism and elimination (ADME) of these novel biopolymer-based nanomaterials in human body after administration by oral or parenteral route for therapeutic or diagnostic purpose. In vitro enzymatic degradation pathways should be investigated in order to yield commercially valuable oligomers. The goal of the present review is to enlighten on the ADME, cytotoxicity and in vitro enzymatic degradation of three marine sulfated polysaccharides, fucoidan, ulvan and mauran, obtained from brown seaweeds or macroalgae in the class of Phaeophyceae, members of Ulvales (green algae) and halophilic bacteria, respectively. They are presently being exploited in fabrication of nanoplatforms with novel applications in the field of controlled drug delivery, tissue regeneration scaffolds, cancer therapy, and bioimaging. However, significant research still needs to be carried out to characterize ADME of mauran and to improve production of the biopolymers on a large scale in order to find out clinically relevant solutions to establish these sulfated polysachharide-based nanotools as novel bionanotechnology strategies in future.

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New Ulvan-Degrading Polysaccharide Lyase Family: Structure and Catalytic Mechanism Suggests Convergent Evolution of Active Site Architecture

Cited by 56 publications

References 31 publications

Characterization of an Alteromonas long-type ulvan lyase involved in the degradation of ulvan extracted from Ulva ohnoi

Characterization of an Alteromonas long-type ulvan lyase involved in the degradation of ulvan extracted from Ulva ohnoi

Structure–function analyses of a PL24 family ulvan lyase reveal key features and suggest its catalytic mechanism

Absorption, distribution, metabolism and elimination (ADME) and toxicity profile of marine sulfated polysaccharides used in bionanotechnology

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