8X3Z | pdb_00008x3z

ThDP-dependent HKA synthase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 
    0.219 (Depositor), 0.220 (DCC) 
  • R-Value Work: 
    0.172 (Depositor), 0.179 (DCC) 

Starting Model: in silico
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Structural insights into two thiamine diphosphate-dependent enzymes and their synthetic applications in carbon-carbon linkage reactions.

Liu, T.Wang, G.Yu, J.Li, M.Peng, T.Wang, J.Li, H.Su, X.D.Jiang, C.Ye, M.Yang, D.Ma, M.

(2025) Nat Chem 17: 1107-1118

  • DOI: https://doi.org/10.1038/s41557-025-01822-y
  • Primary Citation of Related Structures:  
    8X3X, 8X3Y, 8X3Z, 8XOD

  • PubMed Abstract: 

    The α-hydroxy-β-keto acid synthases are thiamine diphosphate-dependent enzymes catalysing carbon-carbon linkage reactions in the biosynthesis of primary metabolites and various secondary metabolites. However, the substrate selectivity and catalytic stereoselectivity of α-hydroxy-β-keto acid synthases are poorly understood, greatly hindering their synthetic application in generating diverse carbon frameworks. We here report the discovery of two new α-hydroxy-β-keto acid synthases CsmA and BbmA, which show different substrate selectivities in catalysing carbon-carbon coupling reactions between two β-keto acids. Four crystal structures of CsmA or BbmA complexed with thiamine diphosphate and their substrates were determined, clearly revealing their structural bases of substrate selectivity and catalytic stereoselectivity. Substrate scope expansion enables us to generate 120 α-hydroxy-β-keto acids together with 240 NaBH 4 -reduction products. Furthermore, we applied CsmA and BbmA into enzymatic total synthesis, generating 36 γ-butyrolactone-containing furanolides. These results provide new structural insights into the catalyses of α-hydroxy-β-keto acid synthases and highlight their great potential in carboligation catalysis and synthetic applications.


  • Organizational Affiliation
    • State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CsmA
A, B
552Chryseomicrobium sp.Mutation(s): 0 
UniProt
Find proteins for A0A264W1B9 (Tetzosporium hominis)
Explore A0A264W1B9 
Go to UniProtKB:  A0A264W1B9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A264W1B9
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free:  0.219 (Depositor), 0.220 (DCC) 
  • R-Value Work:  0.172 (Depositor), 0.179 (DCC) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.916α = 90
b = 129.734β = 90
c = 220.675γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2024-11-20
    Type: Initial release
  • Version 1.1: 2025-06-04
    Changes: Database references
  • Version 1.2: 2025-07-16
    Changes: Database references