8YAG | pdb_00008yag

Cryo-electron microscopic structure of an amide hydrolase from Pseudoxanthomonas wuyuanensis


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.33 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Functional characterization and structural basis of an efficient ochratoxin A-degrading amidohydrolase.

Hu, Y.Dai, L.Xu, Y.Niu, D.Yang, X.Xie, Z.Shen, P.Li, X.Li, H.Zhang, L.Min, J.Guo, R.T.Chen, C.C.

(2024) Int J Biol Macromol 278: 134831-134831

  • DOI: https://doi.org/10.1016/j.ijbiomac.2024.134831
  • Primary Citation of Related Structures:  
    8YAG, 8YAK

  • PubMed Abstract: 

    Ochratoxin A (OTA) contamination in various agro-products poses a serious threat to the global food safety and human health, leading to enormous economic losses. Enzyme-mediated OTA degradation is an appealing strategy, and the search for more efficient enzymes is a prerequisite for achieving this goal. Here, a novel amidohydrolase, termed PwADH, was demonstrated to exhibit 7.3-fold higher activity than that of the most efficient OTA-degrading ADH3 previously reported. Cryo-electron microscopy structure analysis indicated that additional hydrogen-bond interactions among OTA and the adjacent residue H163, the more compact substrate-binding pocket, and the wider entry to the substrate-access cavity might account for the more efficient OTA-degrading activity of PwADH compared with that of ADH3. We conducted a structure-guided rational design of PwADH and obtained an upgraded variant, G88D, whose OTA-degrading activity was elevated by 1.2-fold. In addition, PwADH and the upgraded G88D were successfully expressed in the industrial yeast Pichia pastoris, and their catalytic activities were compared to those of their counterparts produced in E. coli, revealing the feasibility of producing PwADH and its variants in industrial yeast strains. These results illustrate the structural basis of a novel, efficient OTA-degrading amidohydrolase and will be beneficial for the development of high-efficiency OTA-degrading approaches.


  • Organizational Affiliation
    • State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Hongshan Laboratory, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan 430062, PR China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Imidazolonepropionase
A, B, C, D, E
A, B, C, D, E, F, G, H
408Pseudoxanthomonas wuyuanensisMutation(s): 0 
Gene Names: SAMN06296416_10433
UniProt
Find proteins for A0A286D6Z1 (Pseudoxanthomonas wuyuanensis)
Explore A0A286D6Z1 
Go to UniProtKB:  A0A286D6Z1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A286D6Z1
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
I [auth A]
J [auth A]
K [auth B]
L [auth B]
M [auth C]
I [auth A],
J [auth A],
K [auth B],
L [auth B],
M [auth C],
N [auth C],
O [auth D],
P [auth D],
Q [auth E],
R [auth E],
S [auth F],
T [auth F],
U [auth G],
V [auth G],
W [auth H],
X [auth H]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
KCX
Query on KCX
A, B, C, D, E
A, B, C, D, E, F, G, H
L-PEPTIDE LINKINGC7 H14 N2 O4LYS
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.33 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other government--

Revision History  (Full details and data files)

  • Version 1.0: 2024-10-09
    Type: Initial release
  • Version 1.1: 2025-06-25
    Changes: Data collection