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Predicting the functionally distinct residues in the heme, cation, and substrate-binding sites of peroxidase from stress-tolerant mangrove specie, Avicennia marina

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Cell Stress and Chaperones Aims and scope

Abstract

Recent work was conducted to predict the structure of functionally distinct regions of Avicennia marina peroxidase (AP) by using the structural coordinates of barley grains peroxidase as the template. This enzyme is utilized by all living organisms in many biosynthetic or degradable processes and in defense against oxidative stress. The homology model showed some distinct structural changes in the heme, calcium, and substrate-binding regions. Val53 was found to be an important coordinating residue between distal calcium ion and the distal heme site while Ser176 is coordinated to the proximal histidine through Ala174 and Leu172. Different ionic and hydrogen-bonded interactions were also observed in AP. Analyses of various substrate–enzyme interactions revealed that the substrate-binding pocket is provided by the residues, His41, Phe70, Gly71, Asp138, His139, and Lys176; the later three residues are not conserved in the peroxidase family. We have also performed structural comparison of the A. marina peroxidase with that of two class III salt-sensitive species, peanut and soybean. Four loop regions were found to have largest structural deviation. The overall protein sequence was also analyzed for the presence of probable post-translational modification sites and the functional significance of these sites were outlined.

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Abbreviations

AP:

Avicennia marina peroxidase

BGP:

Barley grain peroxidase

PNP:

Peanut peroxidase

SBP:

Soybean peroxidase

HRP:

Horseradish peroxidase

BHA:

Benzhydroxamate

FCN:

Ferulic acid-cyanide

FA:

Formic acid

CO:

Carbon monoxide

TRIS:

Tris (hydroxy methyl) aminomethane

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Authors and Affiliations

  1. H.E.J. Research Institute of Chemistry, University of Karachi, Karachi, 75270, Pakistan

    Uzma Jabeen & Atiya Abbasi

  2. Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270, Pakistan

    Asmat Salim

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  1. Uzma Jabeen
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  2. Atiya Abbasi
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Correspondence to Asmat Salim.

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Jabeen, U., Abbasi, A. & Salim, A. Predicting the functionally distinct residues in the heme, cation, and substrate-binding sites of peroxidase from stress-tolerant mangrove specie, Avicennia marina . Cell Stress and Chaperones 16, 585–605 (2011). https://doi.org/10.1007/s12192-011-0269-3

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