4CUO

Banyan peroxidase with glycosylation


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.67 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.157 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Post-Translational Modification and Extended Glycosylation Pattern of a Plant Latex Peroxidase of Native Source Characterized by X-Ray Crystallography.

Palm, G.J.Sharma, A.Kumari, M.Panjikar, S.Albrecht, D.Jagannadham, M.V.Hinrichs, W.

(2014) FEBS J. 281: 4319

  • DOI: 10.1111/febs.12900

  • PubMed Abstract: 
  • The crystal structure of banyan peroxidase purified from the latex of Ficus benghalensis has been solved at 1.67 Å resolution by single-wavelength anomalous diffraction phasing. The refined structure includes 306 amino acid residues, a heme and two c ...

    The crystal structure of banyan peroxidase purified from the latex of Ficus benghalensis has been solved at 1.67 Å resolution by single-wavelength anomalous diffraction phasing. The refined structure includes 306 amino acid residues, a heme and two calcium ions. The protein belongs to class III peroxidases and is the first one from plant latex. Extensive glycosylation was observed with N-linked glycans attached to seven asparagine residues. The enzyme is stable with respect to a wide pH range, temperature, chemical denaturants and organic solvents, probably as a result of its high glycosylation. An unexpected post-translational modification of Asp290 was identified as succinimide moiety. Kinetic parameters of banyan peroxidase have been determined using various hydrogen donor substrates and hydrogen peroxide.


    Related Citations: 
    • Purification, Crystallization and Preliminary Crystallographic Analysis of Banyan Peroxidase.
      Sharma, A.,Palm, G.J.,Kumari, M.,Panjikar, S.,Jagannadham, M.V.,Hinrichs, W.
      (2012) Acta Crystallogr.,Sect.F 68: 931


    Organizational Affiliation

    Institut für Biochemie, Universität Greifswald, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
BANYAN PEROXIDASE
A
306Ficus benghalensisMutation(s): 0 
EC: 1.11.1.7
Find proteins for A0A087WNH2 (Ficus benghalensis)
Go to UniProtKB:  A0A087WNH2
Small Molecules
Ligands 11 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

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A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CL
Query on CL

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A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
CA
Query on CA

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A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
MAN
Query on MAN

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A
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
XYS
Query on XYS

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A
XYLOPYRANOSE
C5 H10 O5
SRBFZHDQGSBBOR-LECHCGJUSA-N
 Ligand Interaction
FUC
Query on FUC

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A
ALPHA-L-FUCOSE
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
 Ligand Interaction
BMA
Query on BMA

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A
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
HEM
Query on HEM

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A
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
NAG
Query on NAG

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A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
CO3
Query on CO3

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A
CARBONATE ION
C O3
BVKZGUZCCUSVTD-UHFFFAOYSA-L
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
SNN
Query on SNN
A
L-PEPTIDE LINKINGC4 H6 N2 O2ASN
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.67 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.157 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 73.115α = 90.00
b = 73.115β = 90.00
c = 164.596γ = 120.00
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling
Auto-Rickshawphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-07-23
    Type: Initial release
  • Version 1.1: 2014-10-01
    Type: Database references
  • Version 1.2: 2019-07-17
    Type: Data collection, Derived calculations