9H4E | pdb_00009h4e

trans-aconitate decarboxylase Tad1- wild type binding with glycerol


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 
    0.253 (Depositor), 0.248 (DCC) 
  • R-Value Work: 
    0.227 (Depositor), 0.225 (DCC) 
  • R-Value Observed: 
    0.228 (Depositor) 

Starting Model: in silico
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Literature

Mechanistic and structural insights into the itaconate-producing trans -aconitate decarboxylase Tad1.

Zheng, L.Li, W.Christ, M.Paczia, N.Buckel, W.Mais, C.N.Bolker, M.Freitag, J.Bange, G.

(2025) PNAS Nexus 4: pgaf059-pgaf059

  • DOI: https://doi.org/10.1093/pnasnexus/pgaf059
  • Primary Citation of Related Structures:  
    9H3I, 9H4E, 9H4G, 9H4H

  • PubMed Abstract: 

    Itaconic acid belongs to the high-value precursors for the production of biomass-based industrial compounds. It originates from the tricarboxylic acid cycle, and depending on the organism, it is produced by different biosynthetic routes. The basidiomycete fungus Ustilago maydis synthesizes itaconic acid via isomerization of cis -aconitic acid to trans -aconitic acid, and subsequent decarboxylation catalyzed by the trans -aconitate decarboxylase Tad1, which belongs to the aspartase/fumarase superfamily. Since no other decarboxylase has been identified within this protein superfamily, Tad1 constitutes a novel type of decarboxylase. Here, we present high-resolution crystal structures of Tad1, which, together with mutational analysis and nuclear magnetic resonance spectroscopy measurements, provide insight into the molecular mechanism of Tad1-dependent decarboxylation. Specifically, our study shows that decarboxylation is favored in acidic conditions, requires protonation as well as migration of a double bond, and coincides with structural rearrangements in the catalytic center. In summary, our study elucidates the molecular mechanism underlying a novel type of enzymatic decarboxylation and provides a starting point for protein engineering aimed at optimizing the efficient production of itaconic acid.


  • Organizational Affiliation
    • Max-Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Strasse 14, Marburg 35043, Germany.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Trans-aconitate decarboxylase 1A [auth B],
B [auth A],
C,
D
493Mycosarcoma maydisMutation(s): 0 
Gene Names: TAD1UMAG_05076
EC: 4.1.1.113
UniProt
Find proteins for A0A0U2UYC4 (Mycosarcoma maydis)
Explore A0A0U2UYC4 
Go to UniProtKB:  A0A0U2UYC4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0U2UYC4
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free:  0.253 (Depositor), 0.248 (DCC) 
  • R-Value Work:  0.227 (Depositor), 0.225 (DCC) 
  • R-Value Observed: 0.228 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 153.67α = 90
b = 160.83β = 90
c = 209.56γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)Germany--

Revision History  (Full details and data files)

  • Version 1.0: 2025-03-19
    Type: Initial release