9XB2 | pdb_00009xb2

trans-Aconitate Decarboxylase Tad1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 
    0.250 (Depositor) 
  • R-Value Work: 
    0.196 (Depositor) 
  • R-Value Observed: 
    0.199 (Depositor) 

Starting Model: in silico
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wwPDB Validation

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Literature

Biochemical characterization and molecular mechanism study of trans-aconitate decarboxylase Tad1.

Lu, Y.Zhang, K.Wang, C.Wu, D.Huang, X.Xu, H.Ma, H.Lu, X.

(2026) Enzyme Microb Technol 199: 110875-110875

  • DOI: https://doi.org/10.1016/j.enzmictec.2026.110875
  • Primary Citation Related Structures: 
    9XB2

  • PubMed Abstract: 

    Trans-aconitate decarboxylase (Tad1) catalyzes the conversion of trans-aconitate to itaconate, a compound of growing interest in biotechnology owing to its diverse applications as a platform chemical. Despite this potential, detailed biochemical and mechanistic insights into Tad1 remain incomplete. This study presents the heterologous expression, purification, and comprehensive biochemical characterization of Tad1 from Ustilago maydis. We determined its optimal pH and temperature, and cofactor requirements. Furthermore, we employed X-ray crystallography, molecular docking, and site-directed mutagenesis to elucidate key residues involved in substrate binding and catalysis, thereby establishing a molecular basis for its decarboxylase activity. Elucidating Tad1's catalytic mechanism and active site architecture is essential for overcoming current limitations in itaconate biosynthesis and advancing sustainable chemical production.


  • Organizational Affiliation
    • Key Laboratory of Photoelectric Conversion and Utilization of Solar Energy, Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Songling Rd 189, Qingdao 266101, China; Shandong Energy Institute, Songling Rd 189, Qingdao 266101, China.

Macromolecule Content 

  • Total Structure Weight: 264.93 kDa 
  • Atom Count: 13,378 
  • Modeled Residue Count: 1,697 
  • Deposited Residue Count: 2,396 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Ubiquitin-like protein SMT3,Trans-aconitate decarboxylase 1
A, B, C, D
599Saccharomyces cerevisiae S288CMycosarcoma maydis
This entity is chimeric
Mutation(s): 0 
Gene Names: SMT3YDR510WD9719.15TAD1UMAG_05076
EC: 4.1.1.113
UniProt
Find proteins for Q12306 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q12306 
Go to UniProtKB:  Q12306
Find proteins for A0A0U2UYC4 (Mycosarcoma maydis)
Explore A0A0U2UYC4 
Go to UniProtKB:  A0A0U2UYC4
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsQ12306A0A0U2UYC4
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free:  0.250 (Depositor) 
  • R-Value Work:  0.196 (Depositor) 
  • R-Value Observed: 0.199 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 154.114α = 90
b = 160.008β = 90
c = 208.209γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-3000data scaling
PHENIXphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China32271358

Revision History  (Full details and data files)

  • Version 1.0: 2026-09-09
    Type: Initial release