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- PDB-9d2r: Crystal structure of E. coli Threonine dehydratase regulatory dom... -

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Basic information

Entry
Database: PDB / ID: 9d2r
TitleCrystal structure of E. coli Threonine dehydratase regulatory domain 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 / 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
ACETATE ION / ISOLEUCINE / L-threonine dehydratase biosynthetic IlvA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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: Biochemistry / Year: 2025
Title: Isoleucine Binding and Regulation of Escherichia coli and Staphylococcus aureus Threonine Dehydratase (IlvA).
Authors: Yun, M.K. / 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
Revision 1.1Jun 25, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_ASTM ..._citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jul 9, 2025Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)23,4428
Polymers22,7921
Non-polymers6517
Water3,567198
1
A: L-threonine dehydratase biosynthetic IlvA
hetero molecules

A: L-threonine dehydratase biosynthetic IlvA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,88416
Polymers45,5832
Non-polymers1,30114
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-1/31
Buried area6430 Å2
ΔGint-39 kcal/mol
Surface area15010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.357, 99.357, 50.061
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11A-807-

HOH

21A-847-

HOH

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Components

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


Mass: 22791.521 Da / Num. of mol.: 1 / Fragment: Regulatory domain
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.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 198 / 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: 3.13 Å3/Da / Density % sol: 60.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: Ammonium acetate, PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: May 27, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.6→28.68 Å / Num. obs: 37700 / % possible obs: 99.7 % / Redundancy: 8.2 % / Biso Wilson estimate: 21.8 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.05 / Net I/σ(I): 20.9
Reflection shellResolution: 1.6→1.64 Å / Rmerge(I) obs: 0.628 / Mean I/σ(I) obs: 2 / Num. unique obs: 2684 / CC1/2: 0.787

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→28.68 Å / SU ML: 0.1473 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 17.0624 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1663 1897 5.03 %
Rwork0.153 35782 -
obs0.1537 37679 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.33 Å2
Refinement stepCycle: LAST / Resolution: 1.6→28.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1442 0 43 198 1683
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01291527
X-RAY DIFFRACTIONf_angle_d1.15612056
X-RAY DIFFRACTIONf_chiral_restr0.0815211
X-RAY DIFFRACTIONf_plane_restr0.0089272
X-RAY DIFFRACTIONf_dihedral_angle_d10.835894
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.640.26511320.24462465X-RAY DIFFRACTION97.05
1.64-1.690.2451360.20892537X-RAY DIFFRACTION100
1.69-1.730.22611340.18252530X-RAY DIFFRACTION99.96
1.73-1.790.1741330.172553X-RAY DIFFRACTION100
1.79-1.850.20841340.16472540X-RAY DIFFRACTION100
1.85-1.930.20181300.16562535X-RAY DIFFRACTION100
1.93-2.020.17261350.15412540X-RAY DIFFRACTION100
2.02-2.120.16261360.1492539X-RAY DIFFRACTION100
2.12-2.260.19491340.15652552X-RAY DIFFRACTION100
2.26-2.430.16641390.15312571X-RAY DIFFRACTION100
2.43-2.670.17111350.1562558X-RAY DIFFRACTION100
2.67-3.060.17731380.14872572X-RAY DIFFRACTION100
3.06-3.850.13951360.13552612X-RAY DIFFRACTION100
3.85-28.680.14381450.14822678X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.681941354840.148816113786-0.2774436250173.172928856020.8189589897542.306803939780.05657880654630.0376258987598-0.1119869279280.0398057439190.03243058115640.01398637555540.101488206778-0.0386226283792-0.07376002538560.134928390773-0.00845226580375-0.01180715658550.1253838628850.01976944744830.124488165536-38.81635.274-8.222
22.15605441195-0.200202663798-0.2231235607773.003775212472.884499056692.766804067640.04171959786040.159185863816-0.13714539755-0.0546827127170.060815491591-0.00254834523770.083936679363-0.0686577319571-0.1015771188710.172412495312-0.00948650085084-0.0120728076980.1984589442930.02446743711460.161877600069-38.98932.506-14.711
32.011187979670.515796074573-0.2833007679361.07402400663-0.2976717782721.237961946910.0831751284173-0.11593908925-0.07689536953070.128563047186-0.04129516797230.007164941648070.003220923239-0.0288534946123-0.03793353861460.172432646695-0.0112298064924-0.006014075440480.1642221808090.00382879522020.181934647842-34.30839.333-3.604
43.771129953581.356971806571.068512016171.69008715875-2.242794128336.019977869230.221847371736-0.0631727747556-0.676023878945-0.20505613993-0.149536995492-0.184217526270.6253302949670.491385082359-0.06200133878570.226665208251-0.0226253672662-0.01411443146010.2171131291660.01953229860910.254729340112-30.45434.852.241
56.18455667513-3.07110727261-0.3769078338325.515449306471.974456463791.055567526220.153180020953-1.116661063570.1543165156671.39553266530.03299655150910.0273446652975-0.2099308802180.275579542962-0.2092812581210.550330860132-0.115926461320.08136376404320.613917304837-0.06359819824280.234000912242-39.54242.74714.197
68.536772448968.08438448326-2.815321693758.40080372642-3.222381527713.616990773520.578356191248-0.872238964222-0.3344646459830.795466379389-0.492266140256-0.3807265939490.03984772254960.17434464238-0.03968996933230.309614250462-0.0806825875042-0.04635226957450.3516413701450.02202859470920.201339800085-30.29639.91410.991
78.64443896433-0.732805469674.317475448084.26658833363-3.905073298175.134188213750.0200754632936-0.6637432534160.5460107940250.4067456951670.04065971206670.219608019823-0.619123712149-0.0910114706597-0.1294358647730.217073504334-0.03364988000690.02594479103130.198459113383-0.04902889090830.19015389342-24.68651.3071.476
84.29660421841-1.8178781015-2.462555695192.00004317892-0.5208781718198.15291898432-0.1217067744730.1824990824562.079915518680.04697710552521.632868772150.407299212350.79731243353-0.63296147943-1.986663205760.181370846867-0.009509121927870.02976859810610.1962914297980.008734840593040.208109160735-42.58743.039-2.652
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 335:370 )A335 - 370
2X-RAY DIFFRACTION2( CHAIN A AND RESID 371:401 )A371 - 401
3X-RAY DIFFRACTION3( CHAIN A AND RESID 402:466 )A402 - 466
4X-RAY DIFFRACTION4( CHAIN A AND RESID 467:480 )A467 - 480
5X-RAY DIFFRACTION5( CHAIN A AND RESID 481:494 )A481 - 494
6X-RAY DIFFRACTION6( CHAIN A AND RESID 495:505 )A495 - 505
7X-RAY DIFFRACTION7( CHAIN A AND RESID 506:514 )A506 - 514
8X-RAY DIFFRACTION8( CHAIN A AND RESID 601:601 )A601

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