4USC

Crystal structure of peroxidase from palm tree Chamaerops excelsa

Summary for 4USC

• Entry DOI: 10.2210/pdb4usc/pdb
• Descriptor: PEROXIDASE, 1,2-ETHANEDIOL, HYDROGEN PEROXIDE, ... (12 entities in total)
• Functional Keywords: oxidoreductase, plant peroxidase, glycosylation
• Biological source: TRACHYCARPUS FORTUNEI (WINDMILL PALM)
• Total number of polymer chains: 2
• Total formula weight: 68784.86

Authors

Bernardes, A.,Santos, J.C.,Textor, L.C.,Cuadrado, N.H.,Kostetsky, E.Y.,Roig, M.G.,Muniz, J.R.C.,Shnyrov, V.L.,Polikarpov, I. (deposition date: 2014-07-07, release date: 2015-05-27, Last modification date: 2024-10-09)

Primary citation

Bernardes, A.,Textor, L.C.,Santos, J.C.,Cuadrado, N.H.,Kostetsky, E.Y.,Roig, M.G.,Bavro, V.N.,Muniz, J.R.C.,Shnyrov, V.L.,Polikarpov, I.
Crystal Structure Analysis of Peroxidase from the Palm Tree Chamaerops Excelsa.
Biochimie, 111:58-, 2015

PubMed 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.

PubMed: 25660651
DOI: 10.1016/J.BIOCHI.2015.01.014

Experimental method

X-RAY DIFFRACTION (2.6 Å)