9DRI | pdb_00009dri

Crystal structure of SphA in complex with VGQ intermedaite


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 
    0.230 (Depositor), 0.230 (DCC) 
  • R-Value Work: 
    0.194 (Depositor), 0.194 (DCC) 
  • R-Value Observed: 
    0.196 (Depositor) 

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Pyridoxal 5'-Phosphate-Dependent Enzymatic Decarboxylative Annulation.

Chai, W.Luo, S.Xi, W.He, X.Zhang, T.Zou, Y.Hai, Y.

(2026) J Am Chem Soc 148: 9709-9719

  • DOI: https://doi.org/10.1021/jacs.5c20979
  • Primary Citation Related Structures: 
    9DRI, 9PEP

  • PubMed Abstract: 

    Pyridoxal 5'-phosphate (PLP)-dependent enzymes are among the most versatile biocatalysts, yet transformations involving the Cγ-nucleophilic vinylglycine quinonoid (VGQ) intermediate remain exceptionally rare. Understanding the untapped reactivity of VGQ could open new avenues for developing PLP-dependent biocatalysts. Here, we establish a biocatalytic platform that artificially accesses and exploits the reactivity of this high-energy intermediate. By reprogramming SphA, a PLP-dependent enzyme that natively catalyzes decarboxylative Claisen condensation, to generate VGQ in situ through facile decarboxylation of vinylaminomalonate, we enable a decarboxylative [3 + 2] annulation between vinylaminomalonate and electron-deficient alkenes. Crystallographic, computational, and mutagenesis studies reveal the key mechanistic features underlying this abiotic transformation. Our findings demonstrate the latent [3 + 2] annulating potential of VGQ and expand the catalytic repertoire of PLP-dependent enzymes, establishing a new strategy for the enzymatic construction of complex carbocyclic architectures.


  • Organizational Affiliation
    • Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, California 93106, United States.

Macromolecule Content 

  • Total Structure Weight: 108.05 kDa 
  • Atom Count: 7,478 
  • Modeled Residue Count: 920 
  • Deposited Residue Count: 974 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
8-amino-7-oxononanoate synthaseA [auth B],
B [auth C]
487Aspergillus fumigatusMutation(s): 0 
Gene Names: KXV57_002439
EC: 2.3.1.47
UniProt
Find proteins for A0A8H4HX52 (Aspergillus fumigatus)
Explore A0A8H4HX52 
Go to UniProtKB:  A0A8H4HX52
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A8H4HX52
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1BC7
(Subject of Investigation/LOI)

Query on A1BC7



Download:Ideal Coordinates CCD File
D [auth B],
E [auth C]
(2E)-2-{[(Z)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4(1H)-ylidene}methyl]imino}but-3-enoic acid
C12 H15 N2 O7 P
LEPXTPTVSFKGPT-HMHNAJCMSA-N
TRS

Query on TRS



Download:Ideal Coordinates CCD File
C [auth B]2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free:  0.230 (Depositor), 0.230 (DCC) 
  • R-Value Work:  0.194 (Depositor), 0.194 (DCC) 
  • R-Value Observed: 0.196 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.2α = 90
b = 71.873β = 113.813
c = 90.531γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data

  • Released Date: 2025-10-22 
  • Deposition Author(s): Xi, W., Hai, Y.

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM151205

Revision History  (Full details and data files)

  • Version 1.0: 2025-10-22
    Type: Initial release
  • Version 1.1: 2026-03-11
    Changes: Database references
  • Version 1.2: 2026-03-18
    Changes: Database references
  • Version 1.3: 2026-03-25
    Changes: Database references