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Comparative structural modeling of six old yellow enzymes (OYEs) from the necrotrophic fungus Ascochyta rabiei: Insight into novel OYE classes with differences in cofactor binding, organization of active site residues and stereopreferences

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Title Comparative structural modeling of six old yellow enzymes (OYEs) from the necrotrophic fungus Ascochyta rabiei: Insight into novel OYE classes with differences in cofactor binding, organization of active site residues and stereopreferences
 
Creator Nizam, Shadab
Gazara, Rajesh Kumar
Verma, Sandhya
Singh, Kunal
Verma, Praveen K.
 
Subject Ascochyta rabiei
Necrotrophic Fungus
Cofactor Binding
 
Description Accepted date: April 2, 2014
Old Yellow Enzyme (OYE1) was the first flavin-dependent enzyme identified and characterized in detail by the entire range of physical techniques. Irrespective of this scrutiny, true physiological role of the enzyme remains a mystery. In a recent study, we systematically identified OYE proteins from various fungi and classified them into three classes viz. Class I, II and III. However, there is no information about the structural organization of Class III OYEs, eukaryotic Class II OYEs and Class I OYEs of filamentous fungi. Ascochyta rabiei, a filamentous phytopathogen which causes Ascochyta blight (AB) in chickpea possesses six OYEs (ArOYE1-6) belonging to the three OYE classes. Here we carried out comparative homology modeling of six ArOYEs representing all the three classes to get an in depth idea of structural and functional aspects of fungal OYEs. The predicted 3D structures of A. rabiei OYEs were refined and evaluated using various validation tools for their structural integrity. Analysis of FMN binding environment of Class III OYE revealed novel residues involved in interaction. The ligand para-hydroxybenzaldehyde (PHB) was docked into the active site of the enzymes and interacting residues were analyzed. We observed a unique active site organization of Class III OYE in comparison to Class I and II OYEs. Subsequently, analysis of stereopreference through structural features of ArOYEs was carried out, suggesting differences in R/S selectivity of these proteins. Therefore, our comparative modeling study provides insights into the FMN binding, active site organization and stereopreference of different classes of ArOYEs and indicates towards functional differences of these enzymes. This study provides the basis for future investigations towards the biochemical and functional characterization of these enigmatic enzymes.
This work was supported by research grant from Department of Biotechnology, Government of India (File No: BT/PR10605/PBD/16/791/2008) and a
core grant from National Institute of Plant Genome Research. The funders had no role in study design, data collection and analysis, decision to publish, or
preparation of the manuscript.
 
Date 2015-12-21T07:18:07Z
2015-12-21T07:18:07Z
2014
 
Type Article
 
Identifier PLoS One, 9(4): e95989
1932-6203
http://172.16.0.77:8080/jspui/handle/123456789/439
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0095989
10.1371/journal.pone.0095989
 
Language en_US
 
Publisher PLOS