Crystal structure analysis of peroxidase from the palm tree Chamaerops excelsa

Published Date
Biochimie
April 2015, Vol.111:58–69, doi:10.1016/j.biochi.2015.01.014
Research paper

• Author 

• Amanda Bernardes ^a,1
 
• Larissa C. Textor ^a,1
 
• Jademilson C. Santos ^a,1
 
• Nazaret Hidalgo Cuadrado^b,2
 
• Eduard Ya. Kostetsky ^c
 
• Manuel G. Roig ^b
 
• Vassiliy N. Bavro ^e
 
• João R.C. Muniz ^a
 
• Valery L. Shnyrov ^d
 
• Igor Polikarpov ^a,,

• aInstituto de Física de São Carlos, Universidade de São Paulo, Av. Trabalhador Sãocarlense 400, São Carlos, SP 13560-970, Brazil
• bDepartamento de Química Física, Facultad de Química, Universidad de Salamanca, 37008 Salamanca, Spain
• cDepartament of Biochemistry, Microbiology and Biotechnology, Far Eastern Federal University, 690600 Vladivostok, Russia
• dDepartamento de Bioquímica y Biología Molecular, Facultad de Biología, Universidad de Salamanca, 37007 Salamanca, Spain
• eInstitute of Microbiology and Infection, University of Birmingham, Birmingham B152TT, United Kingdom

Received 29 July 2014. Accepted 25 January 2015. Available online 7 February 2015. 

Highlights

• •
  We solved an X-ray structure of native peroxidase from the Chamaerops excelsa.
• •
  The investigation of the structure revealed putative functional homodimer.
• •
  Morphology of the enzyme active site might help to alleviate inhibition.
• •
  High glycosylation and dimerization of the enzyme explain its high stability.

Abstract

Palm tree peroxidases are known to be very stable enzymes and the peroxidase from the Chamaerops excelsa (CEP), which has a high pH and thermal stability, is no exception. To date, the structural and molecular events underscoring such biochemical behavior have not been explored in depth. In order to identify the structural characteristics accounting for the high stability of palm tree peroxidases, we solved and refined the X-ray structure of native CEP at a resolution of 2.6 Å. The CEP structure has an overall fold typical of plant peroxidases and confirmed the conservation of characteristic structural elements such as the heme group and calcium ions. At the same time the structure revealed important modifications in the amino acid residues in the vicinity of the exposed heme edge region, involved in substrate binding, that could account for the morphological variations among palm tree peroxidases through the disruption of molecular interactions at the second binding site. These modifications could alleviate the inhibition of enzymatic activity caused by molecular interactions at the latter binding site. Comparing the CEP crystallographic model described here with other publicly available peroxidase structures allowed the identification of a noncovalent homodimer assembly held together by a number of ionic and hydrophobic interactions. We demonstrate, that this dimeric arrangement results in a more stable protein quaternary structure through stabilization of the regions that are highly dynamic in other peroxidases. In addition, we resolved five N-glycosylation sites, which might also contribute to enzyme stability and resistance against proteolytic cleavage.

Graphical abstract

Keywords

• Plant peroxidase
• Chamaerops excelsa
• Oxidoreductases
• Protein crystallography
• Protein oligomerization

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• ∗ 
  Corresponding author.

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