Computational analysis of AnmK-like kinase: New insights into the cell wall metabolism of fungiby Jianghong Dai, Hong Qu, Zhisheng Yu, Jiangke Yang, Hongxun Zhang

Journal of Theoretical Biology

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Computational analysis of AnmK-like kinase: New insights into the cell wall metabolism of fungi

Jianghong Dai a,b,n, Hong Qu c,nn, Zhisheng Yu b, Jiangke Yang a, Hongxun Zhang bQ1 a School of Biology and Pharmaceutical Engineering, Wuhan Polytechnic University, No. 68 Xuefu Road (S), Evergreen Garden, Wuhan 430023, PR China b College of Resources & Environment, University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, PR China c Center for Bioinformatics, State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, No. 5 Yiheyuan Road,

Beijing 100871, PR China

H I G H L I G H T S  AnmK-like kinases were widely found in fungi.  The 3D structure of a fungal AnmK-like kinase: levoglucosan kinase, was modeled.  The catalytic mechanism of levoglucosan kinase was analyzed by computational method.  A putative recycling of anhydrosugars, which is associated with the metabolism of cell walls, exists in fungi. a r t i c l e i n f o

Article history:

Received 3 October 2014

Received in revised form 13 April 2015

Accepted 2 May 2015

Keywords:

Homology modeling

Molecular docking

Peptidoglycan

Chitin

Cell wall a b s t r a c t 1,6-Anhydro-N-acetylmuramic acid kinase (AnmK) is the unique enzyme that marks the recycling of the cell wall of Escherichia coli. Here, 81 fungal AnmK-like kinase sequences from 57 fungal species were searched in the NCBI database and a phylogenetic tree was constructed. The three-dimensional structure of an AnmK-like kinase, levoglucosan kinase (LGK) of the yeast Lipomyces starkeyi, was modeled; molecular docking revealed that AnmK and LGK are conserved proteins, and 187Asp, 212Asp are enzymatic residues, respectively. Analysis suggests that 1,6-anhydro-N-acetylglucosamine (anhGlcNAc) and/or 1,6-anhydro-β-D-glucosamine (anhGlcN) would be the appropriate substrates of AnmK-like kinases. Also, the counterparts of other characteristic enzymes of cell wall recycling of bacteria were found in fungi. Taken together, it is proposed that a putative recycling of anhGlcNAc/anhGlcN, which is associated with the hydrolysis of cell walls, exists in fungi. This computational analysis will provide new insights into the metabolism of fungal cell walls. & 2015 Published by Elsevier Ltd. 1. Introduction

The cell wall maintains the integrity of cells, making it an essential component of microorganisms. Characteristically, there is a resemblance between the bacterial and the fungal cell wall: both contain homologous β-1,4-linked polysaccharides. In bacteria, the polysaccharide is peptidoglycan (PG) that constitutes the skeleton of the wall (Vollmer and Seligman, 2009). The glycan strands of PG are heteropolymers of β-1,4-linked N-acetylglucosamine (GlcNAc) and N-acetylmuramic acid (MurNAc) (Park and Uehara, 2008). In fungi, the polysaccharide is mainly chitin, a linear homopolymers made of β-1,4-linked GlcNAc, in an average of about 20% of the wall between species of fungi; another polysaccharide is chitosan, partially deacetylated chitin (Ruiz-Herrera, 2012).

The cell wall behaves as a dynamic structure subject to synthesis and hydrolysis during cell growth and morphogenesis, including mycelial/cellular growth and spore germination (Adams, 2004;

Vollmer, 2012). In the hydrolytic metabolism of the abovementioned polysaccharides of bacterial walls, specifically in Gramnegative bacteria Escherichia coli, up to 45% of PG is turned over and recycled during each generation (Goodell, 1985; Reith and Mayer, 2011). PG turnover and recycling have two outstanding reactions: (1) glycan strands are degraded by lytic transglycosidases (LTs), which cleave the glycosidic bond between GlcNAc and MurNAc, simultaneously converting it into an intramolecular anhydro bond with the 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88

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Journal of Theoretical Biology http://dx.doi.org/10.1016/j.jtbi.2015.05.004 0022-5193/& 2015 Published by Elsevier Ltd. n CorrespondinQ2 g author at: School of Biology and Pharmaceutical Engineering,

Wuhan Polytechnic University, Wuhan 430023, PR China. Tel.: þ86 27 83953009; fax: þ86 27 83943875. nn Corresponding author.

E-mail addresses: daijh333@aliyun.com (J. Dai), quh@mail.cbi.pku.edu.cn (H. Qu).

Please cite this article as: Dai, J., et al., Computational analysis of AnmK-like kinase: New insights into the cell wall metabolism of fungi.

J. Theor. Biol. (2015), http://dx.doi.org/10.1016/j.jtbi.2015.05.004i

Journal of Theoretical Biology ∎ (∎∎∎∎) ∎∎∎–∎∎∎ formation of the anhydro-disaccharide-peptide GlcNAc-1,6-anhydroN-acetylmuramic acid-peptide (GlcNAc-anhMurNAc-peptide); (2) the 1,6-anhydro bond of anhMurNAc is split by a specific 1,6-anhydro-Nacetylmuramic acid kinase (AnmK), and the C6-OH of sugar is simultaneously phosphorylated, yielding MurNAc-6-P (Höltje et al., 1975; Park and Uehara, 2008; Uehara et al., 2005) (Fig. 1). In filamentous fungi, it is believed that partial chitin is degraded by chitinases to deliver the dimmer (GlcNAc)2, which subsequently is hydrolyzed by β-N-acetylglucosamidases to give GlcNAc during the growth; likewise, chitosan is hydrolyzed by chitosanases to release chito-oligosaccharides, chitobioses, which are then hydrolyzed to

GlcNAc and glucosamine (GlcN) by glucosaminidases (Adams, 2004;

Gooday, 1990; Hartl et al., 2012; Nguyen et al., 2014; Seidl, 2008).

Recently, a novel levoglucosan kinase (LGK) gene was isolated in the yeast Lipomyces starkeyi, and the deduced amino acid sequence showed that LGK is an AnmK-like kinase (Dai et al., 2009; Ning et al., 2008). Earlier studies demonstrated that LGK has a similar catalytic mechanism to AnmK (Fig. 1) (Kitamura et al., 1991; Zhuang and Zhang, 2002), and, surprisingly, all identified