Structural and biochemical characterization of a carbohydrate acetylesterase from <i>Sinorhizobium meliloti 1021</i>

Kim, Kyungmin; Ryu, Bum Han; Kim, Sung Soo; An, Deu Rae; Ngo, Tri Duc; Pandian, Ramesh; Kim, Kyeong Kyu; Kim, T. Doohun

doi:10.1016/j.febslet.2014.11.033

Cited by 18 publications

(25 citation statements)

References 36 publications

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“…5 and Additional file 8). Furthermore, the 3D structure of Sinorhizobium meliloti, Sm23, carbohydrate esterase of family 3 (CE3) belonging, like CE13, to the SGNH superfamily, showed that an asparagine residue (N) contributes to stabilizing the active site geometry and is located close to the aspartic amino acid residue involved in the catalytic triad [40]. Hence, the asparagine residue found in the NxayDxwQ motif could also contribute to the stability of the active site.…”

Section: Resultsmentioning

confidence: 99%

Plant pectin acetylesterase structure and function: new insights from bioinformatic analysis

2017

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BackgroundPectins are plant cell wall polysaccharides that can be acetylated on C2 and/or C3 of galacturonic acid residues. The degree of acetylation of pectin can be modulated by pectin acetylesterase (EC 3.1.1.6, PAE). The function and structure of plant PAEs remain poorly understood and the role of the fine-tuning of pectin acetylation on cell wall properties has not yet been elucidated.ResultsIn the present study, a bioinformatic approach was used on 72 plant PAEs from 16 species among 611 plant PAEs available in plant genomic databases. An overview of plant PAE proteins, particularly Arabidopsis thaliana PAEs, based on phylogeny analysis, protein motif identification and modeled 3D structure is presented. A phylogenetic tree analysis using protein sequences clustered the plant PAEs into five clades. AtPAEs clustered in four clades in the plant kingdom PAE tree while they formed three clades when a phylogenetic tree was performed only on Arabidopsis proteins, due to isoform AtPAE9. Primitive plants that display a smaller number of PAEs clustered into two clades, while in higher plants, the presence of multiple members of PAE genes indicated a diversification of AtPAEs. 3D homology modeling of AtPAE8 from clade 2 with a human Notum protein showed an α/β hydrolase structure with the hallmark Ser-His-Asp of the active site. A 3D model of AtPAE4 from clade 1 and AtPAE10 from clade 3 showed a similar shape suggesting that the diversification of AtPAEs is unlikely to arise from the shape of the protein. Primary structure prediction analysis of AtPAEs showed a specific motif characteristic of each clade and identified one major group of AtPAEs with a signal peptide and one group without a signal peptide. A multiple sequence alignment of the putative plant PAEs revealed consensus sequences with important putative catalytic residues: Ser, Asp, His and a pectin binding site. Data mining of gene expression profiles of AtPAE revealed that genes from clade 2 including AtPAE7, AtPAE8 and AtPAE11, which are duplicated genes, are highly expressed during plant growth and development while AtPAEs without a signal peptide, including AtPAE2 and AtPAE4, are more regulated in response to plant environmental conditions.ConclusionBioinformatic analysis of plant, and particularly Arabidopsis, AtPAEs provides novel insights, including new motifs that could play a role in pectin binding and catalytic sites. The diversification of AtPAEs is likely to be related to neofunctionalization of some AtPAE genes.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-017-3833-0) contains supplementary material, which is available to authorized users.

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Section: Resultsmentioning

confidence: 99%

Plant pectin acetylesterase structure and function: new insights from bioinformatic analysis

2017

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“…The substrate specificity of CcEstA was assessed using p -nitrophenyl esters with different acyl chain lengths28. As shown in Fig.…”

Section: Resultsmentioning

confidence: 99%

“…6B). The ability of CcEstA to hydrolyze tertiary alcohol esters (TAEs) was examined using tert -butyl acetate, α-terpinyl acetate, and linalyl acetate as substrates28. As shown in Fig.…”

Section: Resultsmentioning

confidence: 99%

Biochemical and Structural Analysis of a Novel Esterase from Caulobacter crescentus related to Penicillin-Binding Protein (PBP)

Ryu

Ngo

Yoo

et al. 2016

Sci Rep

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Considering that the prevalence of antibiotic-resistant pathogenic bacteria is largely increasing, a thorough understanding of penicillin-binding proteins (PBPs) is of great importance and crucial significance because this enzyme family is a main target of β-lactam-based antibiotics. In this work, combining biochemical and structural analysis, we present new findings that provide novel insights into PBPs. Here, a novel PBP homologue (CcEstA) from Caulobacter crescentus CB15 was characterized using native-PAGE, mass spectrometry, gel filtration, CD spectroscopy, fluorescence, reaction kinetics, and enzyme assays toward various substrates including nitrocefin. Furthermore, the crystal structure of CcEstA was determined at a 1.9 Å resolution. Structural analyses showed that CcEstA has two domains: a large α/β domain and a small α-helix domain. A nucleophilic serine (Ser68) residue is located in a hydrophobic groove between the two domains along with other catalytic residues (Lys71 and Try157). Two large flexible loops (UL and LL) of CcEstA are proposed to be involved in the binding of incoming substrates. In conclusion, CcEstA could be described as a paralog of the group that contains PBPs and β-lactamases. Therefore, this study could provide new structural and functional insights into the understanding this protein family.

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“…However, the mutant SmAcE1 (SmAcE1 S15A) did not show any color changes ( Figure 5C,F). From the functional and structural analyses of Sm23 and Est24, their substrate specificity has not been well understood in atomic levels due to the lack of the substrate-bound structures [25,26,29]. On the other hand, the crystal structure of CtCE2 in a complex with β-D-glucose chain (PDB code: 2WAO) showed how CEs recognize their carbohydrate substrates.…”

Section: Resultsmentioning

confidence: 99%

“…Sm23 (PDB code: 4TX1, [25]), Est24 (PDB code: 5HOE [26]), TcAE206 (PDB code: 5B5S [27]), and CtCES3-1 (PDB code: 2TVP [28]) were used. Furthermore, CtCE2 from Clostridium thermocellum (PDB code: 2WAO [29]) that belongs to the CE2 was also included for the sequence alignment [30,31].…”

Section: Sequence Alignment Of Smace1 With Other Cesmentioning

confidence: 99%

Identification and Crystallographic Analysis of a New Carbohydrate Acetylesterase (SmAcE1) from Sinorhizobium meliloti

Ryu

Yoo

et al. 2018

Crystals

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Carbohydrate-active enzymes (CAZymes) regulate the synthesis, degradation, and modification of the poly-and oligosaccharides in all three kingdoms of life. A novel carbohydrate acetylesterase from Sinorhizobium meliloti, designated SmAcE1, was identified, characterized, and crystallized. This SmAcE1 is classified into the carbohydrate esterase family 3 (CE3) based on the sequence alignments with other currently known carbohydrate esterase (CE) family enzymes. The SmAcE1 was crystallized as a hexamer in a space group P2 1 2 1 2 1 with the unit cell parameters: a = 99.12 Å, b = 148.88 Å, c = 149.84 Å, and α = β = γ = 90.00 • . The diffraction data set was collected up to a 2.05 Å resolution. Hydrolysis activity of SmAcE1 towards glucose pentaacetate and cellulose acetate was further confirmed using acetic acid release assay. Further crystallographic and functional analyses studies on SmAcE1 would be followed to fully understand the reaction mechanisms of CEs.

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Structural and biochemical characterization of a carbohydrate acetylesterase from Sinorhizobium meliloti 1021

Cited by 18 publications

References 36 publications

Plant pectin acetylesterase structure and function: new insights from bioinformatic analysis

Plant pectin acetylesterase structure and function: new insights from bioinformatic analysis

Biochemical and Structural Analysis of a Novel Esterase from Caulobacter crescentus related to Penicillin-Binding Protein (PBP)

Identification and Crystallographic Analysis of a New Carbohydrate Acetylesterase (SmAcE1) from Sinorhizobium meliloti

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