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Computational Molecular Biology 2014, Vol. 4, No. 15, 1-5
http://cmb.biopublisher.ca
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Research Report Open Access
An in-silico analysis showing the interaction of FAD ligand with cytokinin
dehydrogenase enzyme and with its domain part in rice
Pranati Swain , Lambodar Behera
Central rice research institute, India
Corresponding author email
Computational Molecular Biology, 2014, Vol.4, No.15 doi: 10.5376/cmb.2014.04.0015
Received: 10 Dec., 2014
Accepted: 26 Dec., 2014
Published: 30 Dec., 2014
© 2014
Swain and Behera, This is an open access article published under the terms of the Creative Commons Attribution License, which permits unrestricted
use, distribution, and reproduction in any medium, provided the original work is properly cited.
Preferred citation for this article:
Swain and Behera, 2014,
An in-silico analysis showing the interaction of FAD ligand with cytokinin dehydrogenase enzyme and with its domain
part in rice
, Computational Molecular Biology, Vol.4, No.15, 1-5
(doi
Abstract
The cytokinin dehydrogenase enzyme plays an important role in the high grain production of rice. This enzyme interacts
with the FAD ligand. This study shows the domain region of the enzyme which was identified by protparam tool, generated
homology models using modeller9.12 tool, models were validated using errat, procheck saves server, prosa and anolea server. Then
the active sites were predicted by using castP server. Finally the interaction was studied between the FAD and cytokinin
dehydrogenase and with its domain part. The stronger interaction was found between the FAD and the domain of the cytokinin
degydrogenase with the binding enegy of -10.91. ALA6, ARG1, AR536, TYR10, ASP55, ALA57, CYS38 of FAD is binding to the
domain part of cytokinin degydrogenase in rice.
Keywords
FAD Ligand; Cytokinin dehydrogenase enzyme; Interaction between ligand and enzyme; Functional domain
Introduction
Cytokinin dehydrogenase of
Oryza sativa (japonica)
plays an important role in high grain production. The
cytokinin dehydrogenase helps in
the oxidation of
cytokinins. This protein belongs to the family of
N(6)-substituted adenine derivatives, which is a plant
hormone having isopentenyl group. This protein helps
in modulating the number of reproductive organs by
regulating the cytokinin accumulation in inflorescence
meristems. The CKX2 is also known as OsCKX2. The
CKX2 is generally located on Os01g0197700. FAD or
flavoprotein is the ligand of Cytokinin dehydrogenase
2 proteins in
O.sativa.CKX2 is located on chromosome
number 1. CKX2 has 5137 basepairs. Cytokinin
positively regulates the growth of shoot apical
meristem that helps in more seed production. The
Gn1a gene of rice encodes
cytokinin oxidase as a
major quantitative trait locus. zinc finger transcription
factor directly regulates the OsCKX2 expression in
the reproductive meristem (Li et al., 2013)
Reduced
expression of OsCKX2 causes cytokinin accumulation
in inflorescence meristems leading to the increase in
number of reproductive organs which results more
grain production (Ashikari et al., 2005). CKX helps
for high grain production in wheat, maize, barely,
sorghum, foxtail millet (Mameaux et al., 2011).
Cytokinin dehydrogenase plays an important role in the
formation of crown root system in rice, which helps in
high grain production (Gao et al., 2014). The main
objective of this study is to find out the best interaction
among the ligand FAD and enzyme. Here the
interaction is studied by considering the whole amino
acid sequence and then only the domain part. Domain
is the function region of a protein or domain. So
generally the binding is more stronger at domain part.
This study involves retrieval of amino acid sequence,
predicting the domain region of enzyme, finding the
common residues among domain part and the whole
sequence, generating homologous models, validating
and evaluating models, predicting the active site,
interaction of FAD with the enzyme.
1 Material and Methods
1.1 Sequence retrieval
The amino acid sequences of cytokinin dehydrogenase
was retrieved from uniprot in fasta format.
1.2 Finding the domain part
The sequence of domain in the protein was retrieved