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- PDB-9e0m: CryoEM structure of holoenzyme of inducible Lysine decarboxylase ... -

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Basic information

Entry
Database: PDB / ID: 9e0m
TitleCryoEM structure of holoenzyme of inducible Lysine decarboxylase from Hafnia alvei holoenzyme at 2.19 Angstrom resolution
ComponentsLysine decarboxylase, inducible
KeywordsLYASE / L-lysine carboxylyase / pH homeostasis / cadaverine / pyridoxal-phosphate protein
Function / homology
Function and homology information


arginine decarboxylase activity / L-arginine catabolic process / pyridoxal phosphate binding / cytosol
Similarity search - Function
Orn/Lys/Arg decarboxylase, N-terminal / Ornithine/lysine/arginine decarboxylase / Orn/Lys/Arg decarboxylase, N-terminal domain / Orn/Lys/Arg decarboxylases family 1 pyridoxal-P attachment site. / Orn/Lys/Arg decarboxylase, major domain / Orn/Lys/Arg decarboxylase, C-terminal / Orn/Lys/Arg decarboxylase, C-terminal domain superfamily / Orn/Lys/Arg decarboxylase, major domain / Orn/Lys/Arg decarboxylase, C-terminal domain / Pyridoxal phosphate-dependent transferase, small domain ...Orn/Lys/Arg decarboxylase, N-terminal / Ornithine/lysine/arginine decarboxylase / Orn/Lys/Arg decarboxylase, N-terminal domain / Orn/Lys/Arg decarboxylases family 1 pyridoxal-P attachment site. / Orn/Lys/Arg decarboxylase, major domain / Orn/Lys/Arg decarboxylase, C-terminal / Orn/Lys/Arg decarboxylase, C-terminal domain superfamily / Orn/Lys/Arg decarboxylase, major domain / Orn/Lys/Arg decarboxylase, C-terminal domain / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
Lysine decarboxylase, inducible
Similarity search - Component
Biological speciesHafnia alvei ATCC 51873 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.2 Å
AuthorsDuhoo, Y. / Desfosses, A. / Gutsche, I. / Doukov, T.I. / Berkowitz, D.B.
Funding support France, United States, 4items
OrganizationGrant numberCountry
French National Research AgencyANR-10-INBS-0005-02 France
French National Research AgencyANR-17-EURE-0003 France
National Science Foundation (NSF, United States)NSF-2102705 United States
National Science Foundation (NSF, United States)NSF-2400333 United States
CitationJournal: ACS Catal / Year: 2025
Title: α-Hydrazino Acids Inhibit Pyridoxal Phosphate-Dependent Decarboxylases via "Catalytically Correct" Ketoenamine Tautomers: A Special Motif for Chemical Biology and Drug Discovery?
Authors: Jonathan M Baine / Yoan Duhoo / Tzanko Doukov / Ambroise Desfosses / Giovanni Bisello / Matthew L Beio / Olivia Bauer / Massimiliano Perduca / Maria Bacia-Verloop / Mariarita Bertoldi / ...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 /
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.
History
DepositionOct 18, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 4, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lysine decarboxylase, inducible
B: Lysine decarboxylase, inducible
C: Lysine decarboxylase, inducible
D: Lysine decarboxylase, inducible
E: Lysine decarboxylase, inducible
F: Lysine decarboxylase, inducible
G: Lysine decarboxylase, inducible
H: Lysine decarboxylase, inducible
I: Lysine decarboxylase, inducible
J: Lysine decarboxylase, inducible


Theoretical massNumber of molelcules
Total (without water)804,33410
Polymers804,33410
Non-polymers00
Water34,6071921
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, similarity with 3N75 homologous protein entry
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Lysine decarboxylase, inducible


Mass: 80433.406 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hafnia alvei ATCC 51873 (bacteria) / Gene: HMPREF0454_03276
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: G9Y9L1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1921 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Lysine decarboxylase / Type: COMPLEX / Details: Holo form / Entity ID: #1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Hafnia alvei ATCC 51873 (bacteria)
Source (recombinant)Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Buffer solutionpH: 8 / Details: 50 mM Tris (pH8.0), 300 mM NaCl, 30 microM PLP
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMTris1
2300 mMSodium ChloridNaCl1
330 microMPLP1
41
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil Active R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 295 K
Details: 3 microL sample was applied to a glow-discharged R2/1 300 mesh holey carbon copper grid (Quantifoil Micro Tools GmbH) and plunge-frozen in liquid ethane at 100% humidity at room temperature.

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 700 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARC3.1particle selection
7Coot0.9.8.95ELmodel fitting
9PHENIX1.21.2_5419model refinement
11cryoSPARC3.1final Euler assignment
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: D5 (2x5 fold dihedral)
3D reconstructionResolution: 2.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 500000 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 18.84 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.003458461
ELECTRON MICROSCOPYf_angle_d0.586979437
ELECTRON MICROSCOPYf_chiral_restr0.04438689
ELECTRON MICROSCOPYf_plane_restr0.004510268
ELECTRON MICROSCOPYf_dihedral_angle_d4.94278106

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