Molecular basis of substrate recognition and specificity revealed in family 12 glycoside hydrolases.
Fungal GH12 enzymes are classified as xyloglucanases when they specifically target xyloglucans, or promiscuous endoglucanases when they exhibit catalytic activity against xyloglucan and β-glucan chains. Several structural and functional studies involving GH12 enzymes tried to explain the main patterns of xyloglucan activity, but what really determines xyloglucanase specificity remains elusive. Here, three fungal GH12 enzymes from Aspergillus clavatus (AclaXegA), A. zonatus (AspzoGH12), and A. terreus (AtEglD) were studied to unveil the molecular basis for substrate specificity. Using functional assays, site-directed mutagenesis, and molecular dynamics simulations, we demonstrated that three main regions are responsible for substrate selectivity: (i) the YSG group in loop 1; (ii) the SST group in loop 2; and (iii) loop A3-B3 and neighboring residues. Functional assays and sequence alignment showed that while AclaXegA is specific to xyloglucan, AtEglD cleaves β-glucan, and xyloglucan. However, AspzoGH12 was also shown to be promiscuous contrarily to a sequence alignment-based prediction. We find that residues Y111 and R93 in AtEglD harbor the substrate in an adequate orientation for hydrolysis in the catalytic cleft entrance and that residues Y19 in AclaXegA and Y30 in AspzoGH12 partially compensate the absence of the YSG segment, typically found in promiscuous enzymes. The results point out the multiple structural factors underlying the substrate specificity of GH12 enzymes. Biotechnol. Bioeng. 2016;113: 2577-2586. © 2016 Wiley Periodicals, Inc.
Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas-SP, Brazil.|Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas-SP, 13083862, Brazil.
Felipe
F
Calzado
Institute of Chemistry, University of Campinas (UNICAMP), Campinas-SP, Brazil.
Erica T
ET
Prates
Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas-SP, Brazil.|Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas-SP, 13083862, Brazil.
Thiago A
TA
Gonçalves
Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas-SP, Brazil.|Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas-SP, 13083862, Brazil.
Marcelo V
MV
Rubio
Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas-SP, Brazil.|Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas-SP, 13083862, Brazil.
Mariane P
MP
Zubieta
Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas-SP, Brazil.
Fabio M
FM
Squina
Institute of Chemistry, University of Campinas (UNICAMP), Campinas-SP, Brazil.
Munir S
MS
Skaf
Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas-SP, Brazil. adamasio@unicamp.br.|Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas-SP, 13083862, Brazil. adamasio@unicamp.br.
André R L
AR
Damásio
D001665:Binding Sites; D004789:Enzyme Activation; D005656:Fungal Proteins / Q000737:chemistry* / Q000378:metabolism / Q000648:ultrastructure; D005936:Glucans / Q000737:chemistry* / Q000378:metabolism / Q000648:ultrastructure*; D006026:Glycoside Hydrolases / Q000737:chemistry* / Q000378:metabolism / Q000648:ultrastructure*; D008956:Models, Chemical; D062105:Molecular Docking Simulation; D011485:Protein Binding; D011487:Protein Conformation; D013329:Structure-Activity Relationship; D013379:Substrate Specificity; D014990:Xylans / Q000737:chemistry* / Q000378:metabolism / Q000648:ultrastructure*
D005656:Fungal Proteins; D005936:Glucans; D014990:Xylans; C029353:xyloglucan; D006026:Glycoside Hydrolases
Aspergillus; GH12; fungal glucanases; xyloglucan specific; xyloglucanases