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PDBsum entry 3hdl
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Oxidoreductase
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PDB id
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3hdl
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Contents |
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* Residue conservation analysis
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PDB id:
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| Name: |
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Oxidoreductase
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Title:
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Crystal structure of highly glycosylated peroxidase from royal palm tree
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Structure:
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Royal palm tree peroxidase. Chain: a. Ec: 1.11.1.-
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Source:
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Roystonea regia. Organism_taxid: 145709
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Resolution:
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1.85Å
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R-factor:
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0.177
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R-free:
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0.187
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Authors:
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L.Watanabe,P.R.Moura,L.Bleicher,A.S.Nascimento,L.S.Zamorano, J.J.Calvete,S.Bursakov,M.G.Roig,V.L.Shnyrov,I.Polikarpov
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Key ref:
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L.Watanabe
et al.
(2010).
Crystal structure and statistical coupling analysis of highly glycosylated peroxidase from royal palm tree (Roystonea regia).
J Struct Biol,
169,
226-242.
PubMed id:
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Date:
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07-May-09
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Release date:
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24-Nov-09
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PROCHECK
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Headers
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References
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D1MPT2
(D1MPT2_ROYRE) -
Peroxidase from Roystonea regia
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Seq:
Struc:
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304 a.a.
304 a.a.
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Key: |
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PfamA domain |
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Secondary structure |
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CATH domain |
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Enzyme class:
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E.C.1.11.1.7
- peroxidase.
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Reaction:
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2 a phenolic donor + H2O2 = 2 a phenolic radical donor + 2 H2O
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2
×
a phenolic donor
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+
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H2O2
Bound ligand (Het Group name = )
corresponds exactly
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=
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2
×
a phenolic radical donor
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+
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2
×
H2O
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Cofactor:
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Heme
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Heme
Bound ligand (Het Group name =
HEM)
matches with 95.45% similarity
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Molecule diagrams generated from .mol files obtained from the
KEGG ftp site
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J Struct Biol
169:226-242
(2010)
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PubMed id:
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Crystal structure and statistical coupling analysis of highly glycosylated peroxidase from royal palm tree (Roystonea regia).
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L.Watanabe,
P.R.de Moura,
L.Bleicher,
A.S.Nascimento,
L.S.Zamorano,
J.J.Calvete,
L.Sanz,
A.Pérez,
S.Bursakov,
M.G.Roig,
V.L.Shnyrov,
I.Polikarpov.
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ABSTRACT
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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.
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