Molecular phylogeny, 3D-structural insights, docking and mechanisms of action of plant beta-galactosidases

Md Anowar Hossain, Hairul Azman Roslan, Md Rezaul Karim, Yoshinobu Kimura

Research output: Contribution to journalArticle

1 Citation (Scopus)

Abstract

Beta-galactosidase (BGAL) is an exoglycosidase that catalyses the hydrolysis of terminal β-linked galactose residues. To better understand the molecular characteristics and structural insights of mango BGAL (MiBGAL), we performed the sequence analyses, reconstruction of the evolutionary tree, homology modelling and molecular docking. BGALs are widely distributed enzymes that evolved from a common bacterial ancestor. Plant BGALs (pBGALs) belong to glycosyl hydrolase-35(GH35) family and had close similarities with fungi BGALs. Three conserved motifs and GH35 putative active site with a consensus sequence G-G-P-[LIVM](2)-x(2)-Q-x-E-N-E-[FY] were identified in 67 BGAL sequences. Modelled 3D structure of MiBGAL is composed of a catalytic TIM barrel domain (domain-I) and three other β-domains, II, III &IV. Structural studies identified the residues Glu182 and Glu251 as the proton donor and nucleophile, respectively in pBGALs that could function through retaining mechanism. p-nitrophenyl-β-Dgalactopyranoside and 2-[4-(2-hydroxyethyl)piperazin-1-yl]ethanesulfonic acid could be potential substrate and inhibitor, respectively among the dockedligands for both tomato BGAL4 and MiBGAL.

Original languageEnglish
Pages (from-to)149-179
Number of pages31
JournalInternational Journal of Bioinformatics Research and Applications
Volume12
Issue number2
DOIs
Publication statusPublished - 2016

Fingerprint

Phylogeny
beta-Galactosidase
Hydrolases
Mangifera
Nucleophiles
Glycoside Hydrolases
Consensus Sequence
Lycopersicon esculentum
Fungi
Galactose
Sequence Analysis
Protons
Hydrolysis
Catalytic Domain
Enzymes
Acids
Substrates
Galactosidases

Keywords

  • Beta-galactosidase
  • Homology modelling
  • Ligands
  • Molecular docking
  • Phylogenetics

ASJC Scopus subject areas

  • Health Informatics
  • Health Information Management
  • Biomedical Engineering
  • Clinical Biochemistry

Cite this

Molecular phylogeny, 3D-structural insights, docking and mechanisms of action of plant beta-galactosidases. / Hossain, Md Anowar; Roslan, Hairul Azman; Karim, Md Rezaul; Kimura, Yoshinobu.

In: International Journal of Bioinformatics Research and Applications, Vol. 12, No. 2, 2016, p. 149-179.

Research output: Contribution to journalArticle

@article{0d6dec7ecc59415e98c0b59dd60115e1,
title = "Molecular phylogeny, 3D-structural insights, docking and mechanisms of action of plant beta-galactosidases",
abstract = "Beta-galactosidase (BGAL) is an exoglycosidase that catalyses the hydrolysis of terminal β-linked galactose residues. To better understand the molecular characteristics and structural insights of mango BGAL (MiBGAL), we performed the sequence analyses, reconstruction of the evolutionary tree, homology modelling and molecular docking. BGALs are widely distributed enzymes that evolved from a common bacterial ancestor. Plant BGALs (pBGALs) belong to glycosyl hydrolase-35(GH35) family and had close similarities with fungi BGALs. Three conserved motifs and GH35 putative active site with a consensus sequence G-G-P-[LIVM](2)-x(2)-Q-x-E-N-E-[FY] were identified in 67 BGAL sequences. Modelled 3D structure of MiBGAL is composed of a catalytic TIM barrel domain (domain-I) and three other β-domains, II, III &IV. Structural studies identified the residues Glu182 and Glu251 as the proton donor and nucleophile, respectively in pBGALs that could function through retaining mechanism. p-nitrophenyl-β-Dgalactopyranoside and 2-[4-(2-hydroxyethyl)piperazin-1-yl]ethanesulfonic acid could be potential substrate and inhibitor, respectively among the dockedligands for both tomato BGAL4 and MiBGAL.",
keywords = "Beta-galactosidase, Homology modelling, Ligands, Molecular docking, Phylogenetics",
author = "Hossain, {Md Anowar} and Roslan, {Hairul Azman} and Karim, {Md Rezaul} and Yoshinobu Kimura",
year = "2016",
doi = "10.1504/IJBRA.2016.077125",
language = "English",
volume = "12",
pages = "149--179",
journal = "International Journal of Bioinformatics Research and Applications",
issn = "1744-5485",
publisher = "Inderscience Enterprises Ltd",
number = "2",

}

TY - JOUR

T1 - Molecular phylogeny, 3D-structural insights, docking and mechanisms of action of plant beta-galactosidases

AU - Hossain, Md Anowar

AU - Roslan, Hairul Azman

AU - Karim, Md Rezaul

AU - Kimura, Yoshinobu

PY - 2016

Y1 - 2016

N2 - Beta-galactosidase (BGAL) is an exoglycosidase that catalyses the hydrolysis of terminal β-linked galactose residues. To better understand the molecular characteristics and structural insights of mango BGAL (MiBGAL), we performed the sequence analyses, reconstruction of the evolutionary tree, homology modelling and molecular docking. BGALs are widely distributed enzymes that evolved from a common bacterial ancestor. Plant BGALs (pBGALs) belong to glycosyl hydrolase-35(GH35) family and had close similarities with fungi BGALs. Three conserved motifs and GH35 putative active site with a consensus sequence G-G-P-[LIVM](2)-x(2)-Q-x-E-N-E-[FY] were identified in 67 BGAL sequences. Modelled 3D structure of MiBGAL is composed of a catalytic TIM barrel domain (domain-I) and three other β-domains, II, III &IV. Structural studies identified the residues Glu182 and Glu251 as the proton donor and nucleophile, respectively in pBGALs that could function through retaining mechanism. p-nitrophenyl-β-Dgalactopyranoside and 2-[4-(2-hydroxyethyl)piperazin-1-yl]ethanesulfonic acid could be potential substrate and inhibitor, respectively among the dockedligands for both tomato BGAL4 and MiBGAL.

AB - Beta-galactosidase (BGAL) is an exoglycosidase that catalyses the hydrolysis of terminal β-linked galactose residues. To better understand the molecular characteristics and structural insights of mango BGAL (MiBGAL), we performed the sequence analyses, reconstruction of the evolutionary tree, homology modelling and molecular docking. BGALs are widely distributed enzymes that evolved from a common bacterial ancestor. Plant BGALs (pBGALs) belong to glycosyl hydrolase-35(GH35) family and had close similarities with fungi BGALs. Three conserved motifs and GH35 putative active site with a consensus sequence G-G-P-[LIVM](2)-x(2)-Q-x-E-N-E-[FY] were identified in 67 BGAL sequences. Modelled 3D structure of MiBGAL is composed of a catalytic TIM barrel domain (domain-I) and three other β-domains, II, III &IV. Structural studies identified the residues Glu182 and Glu251 as the proton donor and nucleophile, respectively in pBGALs that could function through retaining mechanism. p-nitrophenyl-β-Dgalactopyranoside and 2-[4-(2-hydroxyethyl)piperazin-1-yl]ethanesulfonic acid could be potential substrate and inhibitor, respectively among the dockedligands for both tomato BGAL4 and MiBGAL.

KW - Beta-galactosidase

KW - Homology modelling

KW - Ligands

KW - Molecular docking

KW - Phylogenetics

UR - http://www.scopus.com/inward/record.url?scp=84976878455&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84976878455&partnerID=8YFLogxK

U2 - 10.1504/IJBRA.2016.077125

DO - 10.1504/IJBRA.2016.077125

M3 - Article

AN - SCOPUS:84976878455

VL - 12

SP - 149

EP - 179

JO - International Journal of Bioinformatics Research and Applications

JF - International Journal of Bioinformatics Research and Applications

SN - 1744-5485

IS - 2

ER -