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- PDB-9d2s: Crystal structure of E. coli Threonine dehydratase regulatory dom... -

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Basic information

Entry
Database: PDB / ID: 9d2s
TitleCrystal structure of E. coli Threonine dehydratase regulatory domain F352A mutant in complex with isoleucine
ComponentsL-threonine dehydratase biosynthetic IlvA
KeywordsLYASE / Escherichia coli / threonine dehydratase / IlvA / isoleucine / branched-chain amino acids / regulation / allostery
Function / homology
Function and homology information


threonine ammonia-lyase / threonine deaminase activity / threonine metabolic process / L-serine ammonia-lyase activity / threonine catabolic process / L-serine catabolic process / branched-chain amino acid biosynthetic process / isoleucine biosynthetic process / amino acid binding / pyridoxal phosphate binding
Similarity search - Function
Threonine dehydratase, biosynthetic / Threonine dehydratase, ACT-like domain / Threonine dehydratase, ACT-like domain superfamily / C-terminal regulatory domain of Threonine dehydratase / ACT-like domain profile. / : / Serine/threonine dehydratase, pyridoxal-phosphate-binding site / Serine/threonine dehydratases pyridoxal-phosphate attachment site. / ACT-like domain / Pyridoxal-phosphate dependent enzyme ...Threonine dehydratase, biosynthetic / Threonine dehydratase, ACT-like domain / Threonine dehydratase, ACT-like domain superfamily / C-terminal regulatory domain of Threonine dehydratase / ACT-like domain profile. / : / Serine/threonine dehydratase, pyridoxal-phosphate-binding site / Serine/threonine dehydratases pyridoxal-phosphate attachment site. / ACT-like domain / Pyridoxal-phosphate dependent enzyme / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme
Similarity search - Domain/homology
ISOLEUCINE / L-threonine dehydratase biosynthetic IlvA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.22 Å
AuthorsRock, C.O. / Yun, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM034496 United States
CitationJournal: Biorxiv / Year: 2025
Title: Isoleucine binding and regulation of Escherichia coli and Staphylococcus aureus threonine dehydratase (IlvA).
Authors: Yun, M.D. / Subramanian, C. / Miller, K. / Jackson, P. / Radka, C.D. / Rock, C.O.
History
DepositionAug 9, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 9, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: L-threonine dehydratase biosynthetic IlvA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9393
Polymers22,7151
Non-polymers2232
Water2,684149
1
A: L-threonine dehydratase biosynthetic IlvA
hetero molecules

A: L-threonine dehydratase biosynthetic IlvA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,8776
Polymers45,4312
Non-polymers4474
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area3770 Å2
ΔGint-29 kcal/mol
Surface area15290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.376, 39.132, 56.631
Angle α, β, γ (deg.)90.000, 117.016, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein L-threonine dehydratase biosynthetic IlvA / Threonine deaminase


Mass: 22715.426 Da / Num. of mol.: 1 / Fragment: Regulatory domain / Mutation: F352A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ilvA, b3772, JW3745 / Production host: Escherichia coli (E. coli) / References: UniProt: P04968, threonine ammonia-lyase
#2: Chemical ChemComp-ILE / ISOLEUCINE


Type: L-peptide linking / Mass: 131.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 149 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.31 Å3/Da / Density % sol: 46.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4 / Details: Sodium acetate, ammonium acetate, PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 11, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.22→47.38 Å / Num. obs: 60600 / % possible obs: 97.9 % / Redundancy: 6.5 % / Biso Wilson estimate: 13.81 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.031 / Net I/σ(I): 28.4
Reflection shellResolution: 1.22→1.24 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.195 / Mean I/σ(I) obs: 7.1 / Num. unique obs: 2718 / CC1/2: 0.984 / % possible all: 89.5

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.22→47.38 Å / SU ML: 0.0882 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 15.3906 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.151 2000 3.3 %
Rwork0.1405 58587 -
obs0.1409 60587 97.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.83 Å2
Refinement stepCycle: LAST / Resolution: 1.22→47.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1456 0 15 149 1620
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01071508
X-RAY DIFFRACTIONf_angle_d1.06982037
X-RAY DIFFRACTIONf_chiral_restr0.0828212
X-RAY DIFFRACTIONf_plane_restr0.0082272
X-RAY DIFFRACTIONf_dihedral_angle_d3.2095893
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.22-1.250.21631330.16793886X-RAY DIFFRACTION91.86
1.25-1.280.17061450.14914244X-RAY DIFFRACTION98.87
1.28-1.320.18671430.14454208X-RAY DIFFRACTION98.84
1.32-1.360.15921420.14034157X-RAY DIFFRACTION98.17
1.36-1.410.16491430.1354187X-RAY DIFFRACTION98.1
1.41-1.470.16561440.13294210X-RAY DIFFRACTION99.02
1.47-1.540.15281430.13124207X-RAY DIFFRACTION98.57
1.54-1.620.13781430.12234172X-RAY DIFFRACTION97.4
1.62-1.720.14731440.13034235X-RAY DIFFRACTION99.03
1.72-1.850.16851430.13044178X-RAY DIFFRACTION98.56
1.85-2.040.1231420.12424166X-RAY DIFFRACTION96.7
2.04-2.330.14461450.12744244X-RAY DIFFRACTION98.61
2.33-2.940.13821420.14484165X-RAY DIFFRACTION96.48
2.94-47.380.15761480.15464328X-RAY DIFFRACTION97.96

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