Database of articles cited by EMDB/PDB/SASBDB data

Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
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Journal
IF	>30 >20 >10 >5 all

Title	α-Hydrazino Acids Inhibit Pyridoxal Phosphate-Dependent Decarboxylases via "Catalytically Correct" Ketoenamine Tautomers: A Special Motif for Chemical Biology and Drug Discovery?
Journal, issue, pages	ACS Catal, Vol. 15, Issue 10, Page 8204-8218, Year 2025
Publish date	May 16, 2025
Authors	Jonathan M Baine / Yoan Duhoo / Tzanko Doukov / Ambroise Desfosses / Giovanni Bisello / Matthew L Beio / Olivia Bauer / Massimiliano Perduca / Maria Bacia-Verloop / Mariarita Bertoldi / Robert S Phillips / Irina Gutsche / David B Berkowitz /
PubMed Abstract	We present evidence that supports a 'correct hydrazone tautomer/Dunathan alignment model' for how α-hydrazino analogues of α-amino acids inhibit PLP enzymes. Described is the asymmetric synthesis ...We present evidence that supports a 'correct hydrazone tautomer/Dunathan alignment model' for how α-hydrazino analogues of α-amino acids inhibit PLP enzymes. Described is the asymmetric synthesis of l- and d-α-hydrazino acid l-lysine analogues and their inhibition of lysine decarboxylase (LdcI) via kinetic analysis, stopped-flow spectrophotometry, and cryo-EM. We describe a similar investigation of the important anti-Parkinsonism drug, carbidopa, with its human DOPA decarboxylase (hDdc) target. Evidence is consistent with these three hydrazino analogues forming the catalytically relevant ketoenamine PLP-hydrazone tautomer in their target active sites, with the α-carboxylate groups, though insulated, aligning with the PLP-π-system in a Dunathan-model-like orientation. High-resolution cryo-EM structures of the LdcI holoenzyme (pdb 9E0M-2.1Å) and LdcI-bound l- and d-hydrazones (pdb 9E0O-2.0 Å; pdb 9E0Q-2.3Å) and the first X-ray crystal structure of hDdc-bound carbidopa (pdb 9GNS-1.93Å) support this 'correct tautomer' model. These insights are expected to guide future PLP enzyme inhibitor development.
External links	ACS Catal / PubMed:40401103 / PubMed Central
Methods	EM (single particle) / X-ray diffraction
Resolution	1.93 - 2.3 Å
Structure data	47362 9e0m EMDB-47362, PDB-9e0m: CryoEM structure of holoenzyme of inducible Lysine decarboxylase from Hafnia alvei holoenzyme at 2.19 Angstrom resolution Method: EM (single particle) / Resolution: 2.2 Å 47364 9e0o EMDB-47364, PDB-9e0o: CryoEM structure of inducible Lysine decarboxylase from Hafnia alvei L-hydrazino-Lysine analog at 2.04 Angstrom resolution Method: EM (single particle) / Resolution: 2.0 Å 47366 9e0q EMDB-47366, PDB-9e0q: CryoEM structure of inducible Lysine decarboxylase from Hafnia alvei D-hydrazino-Lysine analog at 2.3 Angstrom resolution Method: EM (single particle) / Resolution: 2.3 Å PDB-9dui: Re-refined of Crystal structure of dopa decarboxylase in complex with the inhibitor carbidopa (1JS3) with ketoenamine form of carbidopa Method: X-RAY DIFFRACTION / Resolution: 2.25 Å PDB-9gns: X-ray structure of Human holo aromatic L-amino acid decarboxylase (AADC) complex with Carbidopa at physiological pH Method: X-RAY DIFFRACTION / Resolution: 1.93 Å
Chemicals	PDB-1bcs: COMPLEX OF THE WHEAT SERINE CARBOXYPEPTIDASE, CPDW-II, WITH THE MICROBIAL PEPTIDE ALDEHYDE INHIBITOR, CHYMOSTATIN, AND ARGININE AT 100 DEGREES KELVIN ChemComp-SO4: SULFATE ION ChemComp-HOH: WATER PDB-1bd1: CRYSTALLOGRAPHIC STUDY OF ONE TURN OF G/C-RICH B-DNA PDB-1bd0: ALANINE RACEMASE COMPLEXED WITH ALANINE PHOSPHONATE ChemComp-PLP: PYRIDOXAL-5'-PHOSPHATE ChemComp-142: CARBIDOPA / medicationYM ChemComp-PG4: TETRAETHYLENE GLYCOL / precipitantYM
Source	hafnia alvei atcc 51873 (bacteria) sus scrofa (pig) homo sapiens (human)
Keywords	LYASE / DOPA decarboxylase / carbiDOPA / Parkinson's disease / Vitamin B6 / L-lysine carboxylyase / pH homeostasis / cadaverine / pyridoxal-phosphate protein / L-Lysine decarboxylase / alpha-hydrazone inhibitor / D-alpha-hydrazone inhibitor / BIOSYNTHETIC PROTEIN / DDC / aromatic L-amino acid decarboxylase / AADC