5C8Z

ZHD-ZGR complex after ZHD crystal soaking in ZEN for 30min

  • Classification: HYDROLASE
  • Organism(s): Clonostachys rosea
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2015-06-26 Released: 2016-06-29 
  • Deposition Author(s): Hu, X.-J., Qi, Q., Yang, W.-J.
  • Funding Organization(s): Chinese High-tech Research and Development program, the 973 Program of the Ministry of Science and Technology of China

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.168 
  • R-Value Work: 0.153 
  • R-Value Observed: 0.154 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 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 of 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Zearalenone hydrolase
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
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZGR
Query on ZGR

Download Ideal Coordinates CCD File 
C [auth A],
J [auth B]
2,4-dihydroxy-6-[(1E,10S)-10-hydroxy-6-oxoundec-1-en-1-yl]benzoic acid
C18 H24 O6
KZABMNZGZHPCFB-QBODLPLBSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
K [auth B],
L [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
FMT
Query on FMT

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A],
H [auth A]
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
K
Query on K

Download Ideal Coordinates CCD File 
I [auth A],
M [auth B]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.168 
  • R-Value Work: 0.153 
  • R-Value Observed: 0.154 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.9α = 90
b = 89.59β = 90
c = 113.79γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Chinese High-tech Research and Development programChina2013AA102803B
Chinese High-tech Research and Development programChina2014AA021301
the 973 Program of the Ministry of Science and Technology of ChinaChina2009CB918602

Revision History  (Full details and data files)

  • Version 1.0: 2016-06-29
    Type: Initial release
  • Version 1.1: 2018-04-25
    Changes: Data collection, Database references, Derived calculations
  • Version 1.2: 2023-11-08
    Changes: Data collection, Database references, Refinement description