8XOD | pdb_00008xod

ThDP-dependent HKA synthase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 
    0.286 (Depositor), 0.283 (DCC) 
  • R-Value Work: 
    0.203 (Depositor), 0.221 (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
BbmA-G484F complex with CBOA
A, B, C, D
584BrevibacillusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1LX0 (Subject of Investigation/LOI)
Query on A1LX0

Download Ideal Coordinates CCD File 
F [auth A],
K [auth C],
N [auth D]
2-[3-[(4-azanyl-2-methyl-pyrimidin-5-yl)methyl]-2-[(~{R})-cyclobutyl(oxidanyl)methyl]-4-methyl-1,3-thiazol-5-yl]ethyl phosphono hydrogen phosphate
C17 H27 N4 O8 P2 S
FVAVQECWBZFMTG-OAHLLOKOSA-O
ADP (Subject of Investigation/LOI)
Query on ADP

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B],
J [auth C],
M [auth D]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
TPP (Subject of Investigation/LOI)
Query on TPP

Download Ideal Coordinates CCD File 
I [auth B]THIAMINE DIPHOSPHATE
C12 H19 N4 O7 P2 S
AYEKOFBPNLCAJY-UHFFFAOYSA-O
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
G [auth A],
L [auth C],
O [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free:  0.286 (Depositor), 0.283 (DCC) 
  • R-Value Work:  0.203 (Depositor), 0.221 (DCC) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 95.935α = 90
b = 116.695β = 90
c = 201.61γ = 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: 2025-01-01
    Type: Initial release
  • Version 1.1: 2025-06-04
    Changes: Database references
  • Version 1.2: 2025-07-16
    Changes: Database references