Glycoside Hydrolase Family 25

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• Author: ^^^Ed Taylor^^^
• Responsible Curator: ^^^Gideon Davies^^^

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Glycoside Hydrolase Family GHnn
Clan	GH-K
Mechanism	retaining
Active site residues	Asp/Gul
CAZy DB link
http://www.cazy.org/fam/GHnn.html

Substrate specificities

Family GH25 lysozymes otherwise known as Chalaropsis (CH) type of lysozymes (from is initial characterisation from Chalaropsis species of fungus[1, 2, 3, 3, 3, 4, 5, 6, 6, 7, 8, 9, 10, 10, 11, 11, 12, 12, 13, 13, 13, 14, 14, 15, 15, 15, 16, 16, 17, 17, 18, 18, 19, 19, 20, 21, 21, 21, 21, 21, 21, 22, 23, 24, 24, 25, 26, 27, 28, 29, 29, 30, 30, 31, 31, 31, 31, 32, 32, 32, 33, 34, 35, 36, 37, 37, 38, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 49, 50, 50, 51, 51, 52, 52, 53, 53, 54, 54, 55, 56, 56, 57, 58, 58, 59, 60, 60, 61, 62, 62, 63, 63, 64, 64, 64, 64, 64, 64, 64, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 74, 74, 74, 75, 76, 76, 77, 77, 78, 78, 79, 79, 80, 81, 81, 82, 83, 84, 84, 85, 85, 86, 86, 87, 87, 88, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 105, 106]</EndNote>(Hash & Rothlauf, 1967)pmid=12325376) cleaves the β-1,4-glycosidic bond between N-acetylmuramic acid (NAM) and N-acetylglucosamine (NAG) in the carbohydrate backbone of bacterial peptidoglycan. The characterized lysozymes from this family exhibit both β-1,4-N-acetyl- and β-1,4- N ,6-O-diacetylmuramidase activities and are able to degrade O-acetylated peptidoglycan present in Staphylococcus aureus and other pathogens[107]. The activity of GH25 enzymes appears to fulfil two main biological roles in bacteria. These roles are the re-modelling of peptidoglycan in cellular process such as division and promoting the dissemination of phage progeny toward the end of the phage lytic cycle, which is achieved by bacterial cell lysis. For this reason many GH25 proteins are found to be either chromosomal, phage or prophage encoded. The majority of the GH25 family is comprised of bacterial or prokaryotic viral (phage) members. There are however a few eukaryotic representatives, but these are so far restricted to the fungal kingdom. The roles of these fungal enzymes are less clear, many possess signal secretion peptides indicating a likely extracellular location, possibly for the purpose of obtaining or gaining assess to nutrients or even as a selective agent against bacteria.

Kinetics and Mechanism

The lack of activity on chitooligosaccharides and complexity in producing defined synthetic peptidoglycan substrates, has inevitably hampered the determination of kinetic parameters. Structural studies have shown the active-centre is extremely similar to those from GH18, 20, 56, 84 and 85 implying that, in the absence of evidence to the contrary, GH25 enzymes act with net retention of anomeric configuration using a neighboring-group catalytic mechanism common to this “super-family” of enzymes[108].

Catalytic Residues

This super-family has been shown to use an active site DE or DXE sequence motif ( or exceptionally in the case of GH85 a DXN moitif[109],[110] ). This carboxylate pair promotes a double displacement mechanism in which the nucleophile is not enzyme-derived but is provided by the substrate in an intramolecular “neighboring group” attack of the N-acetyl carbonyl group[111]. Thus catalysis occurs via the formation, and subsequent breakdown of a covalent oxazoline intermediate.

Three-dimensional structures

So far four members of this family of enzymes have been structural characterized, that of the Streptomyces coelicolor enzyme “cellosyl”[112], the bacteriophage lysine PlyB[113], and Clp-1lysozyme from a Streptococcus pneumoniae phage [114],[62], whose structure was also obtained in complex with fragments of peptidoglycan analogues 10 and BaGh25c from Bacillus anthracis str. Ames[108]. The GH25 lysozymes, are structurally unrelated to the GH22-24, 73 and 108 lysozyme folds and instead these enzymes display a modified α -barrel-like fold that, like the classical “TIM-barrel” is composed of a eight-stranded β-barrel, but which is flanked by just three (as opposed to the normal eight) α-helices 7.There is a prominent, long groove, very likely the substrate binding site, located on the C-terminal face. This groove culminates in a deep hole of a highly negative electrostatic potential forming the catalytic site[115].

Family Firsts

First sterochemistry determination

Cite some reference here, with a short (1-2 sentence) explanation.

First catalytic nucleophile identification

Cite some reference here, with a short (1-2 sentence) explanation.

First general acid/base residue identification

Cite some reference here, with a short (1-2 sentence) explanation.

First 3-D structure

Cite some reference here, with a short (1-2 sentence) explanation [112].

References

62. Perez-Dorado I, Campillo NE, Monterroso B, Hesek D, Lee M, Paez JA, Garcia P, Martinez-Ripoll M, Garcia JL, Mobashery S, Menendez M, Hermoso JA. Elucidation of the molecular recognition of bacterial cell wall by modular pneumococcal phage endolysin CPL-1. J Biol Chem 2007;282(34):24990-24999.

107. Vollmer W. Structural variation in the glycan strands of bacterial peptidoglycan. FEMS Microbiol Rev 2008;32(2):287-306.

108. Martinez-Fleites C, Korczynska JE, Davies GJ, Cope MJ, Turkenburg JP, Taylor EJ. The crystal structure of a family GH25 lysozyme from Bacillus anthracis implies a neighboring-group catalytic mechanism with retention of anomeric configuration. Carbohydr Res 2009;344(13):1753-1757.

109. Ling Z, Suits MD, Bingham RJ, Bruce NC, Davies GJ, Fairbanks AJ, Moir JW, Taylor EJ. The X-ray crystal structure of an Arthrobacter protophormiae endo-beta-N-acetylglucosaminidase reveals a (beta/alpha)(8) catalytic domain, two ancillary domains and active site residues key for transglycosylation activity. J Mol Biol 2009;389(1):1-9.

110. Abbott DW, Macauley MS, Vocadlo DJ, Boraston AB. Streptococcus pneumoniae endohexosaminidase D, structural and mechanistic insight into substrate-assisted catalysis in family 85 glycoside hydrolases. J Biol Chem 2009;284(17):11676-11689.

111. Vocadlo D, Davies GJ. Mechanistic Insights into Glycosidase Chemistry. Curr Opin Chem Biol 2008;12:539-555

112. Rau A, Hogg T, Marquardt R, Hilgenfeld R. A new lysozyme fold. Crystal structure of the muramidase from Streptomyces coelicolor at 1.65 A resolution. J Biol Chem 2001;276(34):31994-31999.

113. Porter CJ, Schuch R, Pelzek AJ, Buckle AM, McGowan S, Wilce MC, Rossjohn J, Russell R, Nelson D, Fischetti VA, Whisstock JC. The 1.6 A crystal structure of the catalytic domain of PlyB, a bacteriophage lysin active against Bacillus anthracis. J Mol Biol 2007;366(2):540-550.

114. Hermoso JA, Monterroso B, Albert A, Galan B, Ahrazem O, Garcia P, Martinez-Ripoll M, Garcia JL, Menendez M. Structural basis for selective recognition of pneumococcal cell wall by modular endolysin from phage Cp-1. Structure 2003;11(10):1239-1249.

115. Vollmer W, Joris B, Charlier P, Foster S. Bacterial peptidoglycan (murein) hydrolases. FEMS Microbiol Rev 2008;32(2):259-286.

116. Hash JH, Rothlauf MV. The N,O-diacetylmuramidase of Chalaropsis species. I. Purification and crystallization. J Biol Chem 1967;242(23):5586-5590.