Crystal structure and statistical coupling analysis of highly glycosylated peroxidase from royal palm tree (Roystonea regia).
Royal palm tree peroxidase (RPTP) is a very stable enzyme in regards to acidity, temperature, H(2)O(2), and organic solvents. Thus, RPTP is a promising candidate for developing H(2)O(2)-sensitive biosensors for diverse applications in industry and analytical chemistry. RPTP belongs to the family of class III secretory plant peroxidases, which include horseradish peroxidase isozyme C, soybean and peanut peroxidases. Here we report the X-ray structure of native RPTP isolated from royal palm tree (Roystonea regia) refined to a resolution of 1.85A. RPTP has the same overall folding pattern of the plant peroxidase superfamily, and it contains one heme group and two calcium-binding sites in similar locations. The three-dimensional structure of RPTP was solved for a hydroperoxide complex state, and it revealed a bound 2-(N-morpholino) ethanesulfonic acid molecule (MES) positioned at a putative substrate-binding secondary site. Nine N-glycosylation sites are clearly defined in the RPTP electron-density maps, revealing for the first time conformations of the glycan chains of this highly glycosylated enzyme. Furthermore, statistical coupling analysis (SCA) of the plant peroxidase superfamily was performed. This sequence-based method identified a set of evolutionarily conserved sites that mapped to regions surrounding the heme prosthetic group. The SCA matrix also predicted a set of energetically coupled residues that are involved in the maintenance of the structural folding of plant peroxidases. The combination of crystallographic data and SCA analysis provides information about the key structural elements that could contribute to explaining the unique stability of RPTP.
Watanabe
Leandra
L
Instituto de Física de São Carlos, Departamento de Física e Informática, Universidade de São Paulo, Avenida Trabalhador São Carlense 400, CEP 13566-590 São Carlos, SP, Brazil.
de Moura
Patricia Ribeiro
PR
Bleicher
Lucas
L
Nascimento
Alessandro S
AS
Zamorano
Laura S
LS
Calvete
Juan J
JJ
Sanz
Libia
L
Pérez
Alicia
A
Bursakov
Sergey
S
Roig
Manuel G
MG
Shnyrov
Valery L
VL
Polikarpov
Igor
I
D000595:Amino Acid Sequence; D029064:Araceae / Q000201:enzymology*; D001483:Base Sequence; D003460:Crystallization; D017931:DNA Primers / Q000235:genetics; D018076:DNA, Complementary / Q000235:genetics; D006031:Glycosylation; D007700:Kinetics; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009195:Peroxidase / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D011487:Protein Conformation; D017422:Sequence Analysis, DNA; D053719:Tandem Mass Spectrometry
D017931:DNA Primers; D018076:DNA, Complementary; D009195:Peroxidase