5XMW | pdb_00005xmw

Selenomethionine-derivated ZHD


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 
    0.236 (Depositor), 0.249 (DCC) 
  • R-Value Work: 
    0.208 (Depositor), 0.218 (DCC) 
  • R-Value Observed: 
    0.209 (Depositor) 

wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history

Literature

The structure of a complex of the lactonohydrolase zearalenone hydrolase with the hydrolysis product of zearalenone at 1.60 angstrom resolution

Qi, Q.Yang, W.J.Zhou, H.J.Ming, D.M.Sun, K.L.Xu, T.Y.Hu, X.J.Lv, H.

(2017) Acta Crystallogr F Struct Biol Commun 73: 376-381

  • DOI: https://doi.org/10.1107/S2053230X17007713
  • Primary Citation Related Structures: 
    5C8Z, 5XMW

  • PubMed Abstract: 

    Zearalenone hydrolase (ZHD) is an α/β-hydrolase that detoxifies and degrades the lactone zearalenone (ZEN), a naturally occurring oestrogenic mycotoxin that contaminates crops. Several apoenzyme and enzyme-substrate complex structures have been reported in the resolution range 2.4-2.6 Å. However, the properties and mechanism of this enzyme are not yet fully understood. Here, a 1.60 Å resolution structure of a ZHD-product complex is reported which was determined from a C-terminally His 6 -tagged ZHD crystal soaked with 2 mM ZEN for 30 min. It shows that after the lactone-bond cleavage, the phenol-ring region moves closer to residues Leu132, Tyr187 and Pro188, while the lactone-ring region barely moves. Comparisons of the ZHD-substrate and ZHD-product structures show that the hydrophilic interactions change, especially Trp183 N ℇ1 , which shifts from contacting O2 to O12', suggesting that Trp183 is responsible for the unidirectional translational movement of the phenol ring. This structure provides information on the final stage of the catalytic mechanism of zearalenone hydrolysis.


  • Organizational Affiliation
    • State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200438, People's Republic of China.

Macromolecule Content 

  • Total Structure Weight: 62.69 kDa 
  • Atom Count: 4,142 
  • Modeled Residue Count: 538 
  • Deposited Residue Count: 568 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Zearalenone lactonase
A, B
284Clonostachys roseaMutation(s): 0 
Gene Names: ZHD101
EC: 3.1.1
UniProt
Find proteins for Q8NKB0 (Bionectria ochroleuca)
Explore Q8NKB0 
Go to UniProtKB:  Q8NKB0
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8NKB0
Sequence Annotations
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Reference Sequence

Small Molecules

Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free:  0.236 (Depositor), 0.249 (DCC) 
  • R-Value Work:  0.208 (Depositor), 0.218 (DCC) 
  • R-Value Observed: 0.209 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.924α = 90
b = 90.169β = 90
c = 113.056γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Released Date: 2018-04-25 
  • Deposition Author(s): Hu, X.J.

Revision History  (Full details and data files)

  • Version 1.0: 2018-04-25
    Type: Initial release
  • Version 1.1: 2024-10-30
    Changes: Data collection, Database references, Refinement description, Structure summary