4USC

Crystal structure of peroxidase from palm tree Chamaerops excelsa


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.220 

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This is version 2.0 of the entry. See complete history


Literature

Crystal Structure Analysis of Peroxidase from the Palm Tree Chamaerops Excelsa.

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.

(2015) Biochimie 111: 58

  • DOI: 10.1016/j.biochi.2015.01.014
  • Primary Citation of Related Structures:  
    4USC

  • 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 ...

    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.


    Organizational Affiliation

    Instituto de Física de São Carlos, Universidade de São Paulo, Av. Trabalhador Sãocarlense 400, São Carlos, SP 13560-970, Brazil. Electronic address: ipolikarpov@ifsc.usp.br.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PEROXIDASEA, B303Trachycarpus fortuneiMutation(s): 0 
EC: 1.11.1.7
UniProt
Find proteins for A0A0A0Y4H8 (Trachycarpus fortunei)
Explore A0A0A0Y4H8 
Go to UniProtKB:  A0A0A0Y4H8
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranoseC3N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G28524WC
GlyCosmos:  G28524WC
GlyGen:  G28524WC
Entity ID: 3
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranoseD, E3N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G11971MR
GlyCosmos:  G11971MR
GlyGen:  G11971MR
Small Molecules
Ligands 8 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM (Subject of Investigation/LOI)
Query on HEM

Download Ideal Coordinates CCD File 
N [auth A], V [auth B]PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
NAG (Subject of Investigation/LOI)
Query on NAG

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I [auth A], J [auth A], K [auth A], Q [auth B], R [auth B]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
MAN (Subject of Investigation/LOI)
Query on MAN

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H [auth A]alpha-D-mannopyranose
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
PEG
Query on PEG

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M [auth A]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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L [auth A], U [auth B]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
EDO
Query on EDO

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O [auth A], W [auth B]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

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F [auth A], G [auth A], S [auth B], T [auth B]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
PEO
Query on PEO

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P [auth A]HYDROGEN PEROXIDE
H2 O2
MHAJPDPJQMAIIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.220 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.18α = 90
b = 100.65β = 90
c = 132.31γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-05-27
    Type: Initial release
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Other, Structure summary