Computational modeling and functional characterization of a GgChi: A class III chitinase from corms of Gladiolus grandiflorus

Maria Rafiq; Ashiq Hussain; Kausar Hussain Shah; Qamar Saeed; Muhammad Umair Sial; Zahid Ali; Friedrich Buck; Richard E. Goodman; Binish Khaliq; Uzma Ishaq; Mirza Ahsen Baig; Aisha Munawar; Seema Mahmood; Ahmed Akrem

doi:10.1016/j.kjms.2018.08.003

Computational modeling and functional characterization of a GgChi: A class III chitinase from corms of Gladiolus grandiflorus

Maria Rafiq, Ashiq Hussain, Kausar Hussain Shah, Qamar Saeed, Muhammad Umair Sial, Zahid Ali, Friedrich Buck, Richard E. Goodman, Binish Khaliq, Uzma Ishaq, Mirza Ahsen Baig, Aisha Munawar, Seema Mahmood, Ahmed Akrem^*

^*Corresponding author for this work

1 Citation (Scopus)

Abstract

The present study describes the predicted model and functional characterization of an endochitinase (30 kDa) from corms of Gladiolus grandiflorus. ESI-QTOF-MS generated peptide showed 96% sequence homology with family 18, Class III acidic endochitinase of Gladiolus gandavensis. Purified G. grandiflorus chitinase (GgChi) hydrolyzed 4-methylumbelliferyl β-D-N,N′,N′′-triacetylchitotriose substrate showing specific endochitinase activity. Since no structural details of GgChi were available in the Protein Data Bank (PDB), a homology model was predicted using the coordinate information of Crocus vernus chitinase (PDB ID: 3SIM). Ramachandran plot indicated 84.5% in most favored region, 14.8% in additional and 0.6% in generously allowed region while no residue in disallowed region. The predicted structure indicated a highly conserved (β/α)₈ (TIM barrel) structure similar to the family 18, class III chitinases. The GgChi also showed sequence and structural homologies with other active chitinases. The GgChi (50 μg/disc) showed no antibacterial activity, but did provide mild growth inhibition of phytopathogenic fungus Fusarium oxysporum at a concentration of 500 μg/well Similarly, insect toxicity bioassays of GgChi (50 μg) against nymphs of Bemisia tabaci showed 14% reduction in adult emergence and 14% increase in mortality rate in comparison to control values. The GgChi (1.5 mg) protein showed significant reduction in a population of flour beetle (Tribolium castaneum) after 35 days, but lower reactivity against rice weevil (Sitophilus oryzae). The results of this study provide detai.led insight on functional characterization of a family 18 class III acidic plant endochitinase.

Original language	English
Journal	Kaohsiung Journal of Medical Sciences
ISSN	1607-551X
DOIs	https://doi.org/10.1016/j.kjms.2018.08.003
Publication status	Published - Dec 2018
Externally published	Yes

Keywords

Antibacterial
Antifungal
Endochitinase
Gladiolus grandiflorus
TIM barrel

Access to Document

10.1016/j.kjms.2018.08.003Licence: CC BY-NC-ND

j.kjms.2018.08.003Final published version, 2.11 MBLicence: CC BY-NC-ND

Cite this

Rafiq, M., Hussain, A., Shah, K. H., Saeed, Q., Sial, M. U., Ali, Z., Buck, F., Goodman, R. E., Khaliq, B., Ishaq, U., Baig, M. A., Munawar, A., Mahmood, S., & Akrem, A. (2018). Computational modeling and functional characterization of a GgChi: A class III chitinase from corms of Gladiolus grandiflorus. Kaohsiung Journal of Medical Sciences. https://doi.org/10.1016/j.kjms.2018.08.003

@article{582b7d14624c4f368c208f1c4d19ef82,

title = "Computational modeling and functional characterization of a GgChi: A class III chitinase from corms of Gladiolus grandiflorus",

abstract = "The present study describes the predicted model and functional characterization of an endochitinase (30 kDa) from corms of Gladiolus grandiflorus. ESI-QTOF-MS generated peptide showed 96% sequence homology with family 18, Class III acidic endochitinase of Gladiolus gandavensis. Purified G. grandiflorus chitinase (GgChi) hydrolyzed 4-methylumbelliferyl β-D-N,N′,N′′-triacetylchitotriose substrate showing specific endochitinase activity. Since no structural details of GgChi were available in the Protein Data Bank (PDB), a homology model was predicted using the coordinate information of Crocus vernus chitinase (PDB ID: 3SIM). Ramachandran plot indicated 84.5% in most favored region, 14.8% in additional and 0.6% in generously allowed region while no residue in disallowed region. The predicted structure indicated a highly conserved (β/α)8 (TIM barrel) structure similar to the family 18, class III chitinases. The GgChi also showed sequence and structural homologies with other active chitinases. The GgChi (50 μg/disc) showed no antibacterial activity, but did provide mild growth inhibition of phytopathogenic fungus Fusarium oxysporum at a concentration of 500 μg/well Similarly, insect toxicity bioassays of GgChi (50 μg) against nymphs of Bemisia tabaci showed 14% reduction in adult emergence and 14% increase in mortality rate in comparison to control values. The GgChi (1.5 mg) protein showed significant reduction in a population of flour beetle (Tribolium castaneum) after 35 days, but lower reactivity against rice weevil (Sitophilus oryzae). The results of this study provide detai.led insight on functional characterization of a family 18 class III acidic plant endochitinase.",

keywords = "Antibacterial, Antifungal, Endochitinase, Gladiolus grandiflorus, TIM barrel",

author = "Maria Rafiq and Ashiq Hussain and Shah, {Kausar Hussain} and Qamar Saeed and Sial, {Muhammad Umair} and Zahid Ali and Friedrich Buck and Goodman, {Richard E.} and Binish Khaliq and Uzma Ishaq and Baig, {Mirza Ahsen} and Aisha Munawar and Seema Mahmood and Ahmed Akrem",

year = "2018",

month = dec,

doi = "10.1016/j.kjms.2018.08.003",

language = "English",

journal = "Kaohsiung Journal of Medical Sciences",

issn = "1607-551X",

publisher = "Elsevier (Singapore) Pte Ltd",

}

TY - JOUR

T1 - Computational modeling and functional characterization of a GgChi

T2 - A class III chitinase from corms of Gladiolus grandiflorus

AU - Rafiq, Maria

AU - Hussain, Ashiq

AU - Shah, Kausar Hussain

AU - Saeed, Qamar

AU - Sial, Muhammad Umair

AU - Ali, Zahid

AU - Buck, Friedrich

AU - Goodman, Richard E.

AU - Khaliq, Binish

AU - Ishaq, Uzma

AU - Baig, Mirza Ahsen

AU - Munawar, Aisha

AU - Mahmood, Seema

AU - Akrem, Ahmed

PY - 2018/12

Y1 - 2018/12

N2 - The present study describes the predicted model and functional characterization of an endochitinase (30 kDa) from corms of Gladiolus grandiflorus. ESI-QTOF-MS generated peptide showed 96% sequence homology with family 18, Class III acidic endochitinase of Gladiolus gandavensis. Purified G. grandiflorus chitinase (GgChi) hydrolyzed 4-methylumbelliferyl β-D-N,N′,N′′-triacetylchitotriose substrate showing specific endochitinase activity. Since no structural details of GgChi were available in the Protein Data Bank (PDB), a homology model was predicted using the coordinate information of Crocus vernus chitinase (PDB ID: 3SIM). Ramachandran plot indicated 84.5% in most favored region, 14.8% in additional and 0.6% in generously allowed region while no residue in disallowed region. The predicted structure indicated a highly conserved (β/α)8 (TIM barrel) structure similar to the family 18, class III chitinases. The GgChi also showed sequence and structural homologies with other active chitinases. The GgChi (50 μg/disc) showed no antibacterial activity, but did provide mild growth inhibition of phytopathogenic fungus Fusarium oxysporum at a concentration of 500 μg/well Similarly, insect toxicity bioassays of GgChi (50 μg) against nymphs of Bemisia tabaci showed 14% reduction in adult emergence and 14% increase in mortality rate in comparison to control values. The GgChi (1.5 mg) protein showed significant reduction in a population of flour beetle (Tribolium castaneum) after 35 days, but lower reactivity against rice weevil (Sitophilus oryzae). The results of this study provide detai.led insight on functional characterization of a family 18 class III acidic plant endochitinase.

AB - The present study describes the predicted model and functional characterization of an endochitinase (30 kDa) from corms of Gladiolus grandiflorus. ESI-QTOF-MS generated peptide showed 96% sequence homology with family 18, Class III acidic endochitinase of Gladiolus gandavensis. Purified G. grandiflorus chitinase (GgChi) hydrolyzed 4-methylumbelliferyl β-D-N,N′,N′′-triacetylchitotriose substrate showing specific endochitinase activity. Since no structural details of GgChi were available in the Protein Data Bank (PDB), a homology model was predicted using the coordinate information of Crocus vernus chitinase (PDB ID: 3SIM). Ramachandran plot indicated 84.5% in most favored region, 14.8% in additional and 0.6% in generously allowed region while no residue in disallowed region. The predicted structure indicated a highly conserved (β/α)8 (TIM barrel) structure similar to the family 18, class III chitinases. The GgChi also showed sequence and structural homologies with other active chitinases. The GgChi (50 μg/disc) showed no antibacterial activity, but did provide mild growth inhibition of phytopathogenic fungus Fusarium oxysporum at a concentration of 500 μg/well Similarly, insect toxicity bioassays of GgChi (50 μg) against nymphs of Bemisia tabaci showed 14% reduction in adult emergence and 14% increase in mortality rate in comparison to control values. The GgChi (1.5 mg) protein showed significant reduction in a population of flour beetle (Tribolium castaneum) after 35 days, but lower reactivity against rice weevil (Sitophilus oryzae). The results of this study provide detai.led insight on functional characterization of a family 18 class III acidic plant endochitinase.

KW - Antibacterial

KW - Antifungal

KW - Endochitinase

KW - Gladiolus grandiflorus

KW - TIM barrel

UR - http://www.scopus.com/inward/record.url?scp=85054617816&partnerID=8YFLogxK

U2 - 10.1016/j.kjms.2018.08.003

DO - 10.1016/j.kjms.2018.08.003

M3 - Journal article

AN - SCOPUS:85054617816

SN - 1607-551X

JO - Kaohsiung Journal of Medical Sciences

JF - Kaohsiung Journal of Medical Sciences

ER -

Computational modeling and functional characterization of a GgChi: A class III chitinase from corms of Gladiolus grandiflorus

Abstract

Keywords

Access to Document

Other files and links

Fingerprint

Cite this