4C65 | pdb_00004c65

Crystal structure of A. niger ochratoxinase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 
    0.245 (Depositor), 0.250 (DCC) 
  • R-Value Work: 
    0.213 (Depositor), 0.217 (DCC) 
  • R-Value Observed: 
    0.215 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history

Literature

Structural and Functional Characterization of Ochratoxinase, a Novel Mycotoxin Degrading Enzyme.

Dobritzsch, D.Wang, H.Schneider, G.Yu, S.

(2014) Biochem J 462: 441

  • DOI: https://doi.org/10.1042/BJ20140382
  • Primary Citation Related Structures: 
    4C5Y, 4C5Z, 4C60, 4C65

  • PubMed Abstract: 

    Ochratoxin, with ochratoxin A as the dominant form, is one of the five major mycotoxins most harmful to humans and animals. It is produced by Aspergillus and Penicillium species and occurs in a wide range of agricultural products. Detoxification of contaminated food is a challenging health issue. In the present paper we report the identification, characterization and crystal structure (at 2.2 Å) of a novel microbial ochratoxinase from Aspergillus niger. A putative amidase gene encoding a 480 amino acid polypeptide was cloned and homologously expressed in A. niger. The recombinant protein is N-terminally truncated, thermostable, has optimal activity at pH ~6 and 66°C, and is more efficient in ochratoxin A hydrolysis than carboxypeptidase A and Y, the two previously known enzymes capable of degrading this mycotoxin. The subunit of the homo-octameric enzyme folds into a two-domain structure characteristic of a metal dependent amidohydrolase, with a twisted TIM (triosephosphateisomerase)-barrel and a smaller β-sandwich domain. The active site contains an aspartate residue for acid-base catalysis, and a carboxylated lysine and four histidine residues for binding of a binuclear metal centre.


  • Organizational Affiliation
    • *Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-17177 Stockholm, Sweden.

Macromolecule Content 

  • Total Structure Weight: 373.17 kDa 
  • Atom Count: 27,300 
  • Modeled Residue Count: 3,463 
  • Deposited Residue Count: 3,504 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
OCHRATOXINASE
A, B, C, D, E
A, B, C, D, E, F, G, H
438Aspergillus nigerMutation(s): 0 
EC: 3.4.13.9 (PDB Primary Data), 3.5.1 (PDB Primary Data), 3.4.17 (UniProt)
UniProt
Find proteins for A2R2V4 (Aspergillus niger (strain ATCC MYA-4892 / CBS 513.88 / FGSC A1513))
Explore A2R2V4 
Go to UniProtKB:  A2R2V4
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA2R2V4
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free:  0.245 (Depositor), 0.250 (DCC) 
  • R-Value Work:  0.213 (Depositor), 0.217 (DCC) 
  • R-Value Observed: 0.215 (Depositor) 
Space Group: I 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 210.855α = 90
b = 78.92β = 105.05
c = 217γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
REFMACphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-07-02
    Type: Initial release
  • Version 1.1: 2014-09-03
    Changes: Database references
  • Version 1.2: 2023-12-20
    Changes: Data collection, Database references, Other, Refinement description