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- PDB-8qav: Medicago truncatula HISN5 (IGPD) in complex with MN and IG2 -

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Basic information

Entry
Database: PDB / ID: 8qav
TitleMedicago truncatula HISN5 (IGPD) in complex with MN and IG2
ComponentsImidazoleglycerol-phosphate dehydratase
KeywordsLYASE / Medicago truncatula HISN5 IGPD histidine
Function / homology
Function and homology information


imidazoleglycerol-phosphate dehydratase / imidazoleglycerol-phosphate dehydratase activity / histidine biosynthetic process
Similarity search - Function
Imidazoleglycerol-phosphate dehydratase signature 1. / Imidazoleglycerol-phosphate dehydratase / Imidazoleglycerol-phosphate dehydratase, conserved site / Imidazole glycerol phosphate dehydratase domain superfamily / Imidazoleglycerol-phosphate dehydratase / Imidazoleglycerol-phosphate dehydratase signature 2. / Ribosomal protein S5 domain 2-type fold
Similarity search - Domain/homology
Chem-IG2 / : / Imidazoleglycerol-phosphate dehydratase
Similarity search - Component
Biological speciesMedicago truncatula (barrel medic)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.23 Å
AuthorsWitek, W. / Ruszkowski, M.
Funding support Poland, 1items
OrganizationGrant numberCountry
Polish National Science CentreSonata 2018/31/D/NZ1/03630 Poland
CitationJournal: Front Plant Sci / Year: 2024
Title: Targeting imidazole-glycerol phosphate dehydratase in plants: novel approach for structural and functional studies, and inhibitor blueprinting.
Authors: Wojciech Witek / Joanna Sliwiak / Michal Rawski / Milosz Ruszkowski /
Abstract: The histidine biosynthetic pathway (HBP) is targeted for herbicide design with preliminary success only regarding imidazole-glycerol phosphate dehydratase (IGPD, EC 4.2.1.19), or HISN5, as referred ...The histidine biosynthetic pathway (HBP) is targeted for herbicide design with preliminary success only regarding imidazole-glycerol phosphate dehydratase (IGPD, EC 4.2.1.19), or HISN5, as referred to in plants. HISN5 catalyzes the sixth step of the HBP, in which imidazole-glycerol phosphate (IGP) is dehydrated to imidazole-acetol phosphate. In this work, we present high-resolution cryoEM and crystal structures of HISN5 (HISN5) in complexes with an inactive IGP diastereoisomer and with various other ligands. HISN5 can serve as a new model for plant HISN5 structural studies, as it enables resolving protein-ligand interactions at high (2.2 Å) resolution using cryoEM. We identified ligand-binding hotspots and characterized the features of plant HISN5 enzymes in the context of the HISN5-targeted inhibitor design. Virtual screening performed against millions of small molecules not only revealed candidate molecules but also identified linkers for fragments that were experimentally confirmed to bind. Based on experimental and computational approaches, this study provides guidelines for designing symmetric HISN5 inhibitors that can reach two neighboring active sites. Finally, we conducted analyses of sequence similarity networks revealing that plant HISN5 enzymes derive from cyanobacteria. We also adopted a new approach to measure HISN5 enzymatic activity using isothermal titration calorimetry and enzymatically synthesized IGP.
History
DepositionAug 23, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 10, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Imidazoleglycerol-phosphate dehydratase
B: Imidazoleglycerol-phosphate dehydratase
C: Imidazoleglycerol-phosphate dehydratase
D: Imidazoleglycerol-phosphate dehydratase
E: Imidazoleglycerol-phosphate dehydratase
F: Imidazoleglycerol-phosphate dehydratase
G: Imidazoleglycerol-phosphate dehydratase
H: Imidazoleglycerol-phosphate dehydratase
I: Imidazoleglycerol-phosphate dehydratase
J: Imidazoleglycerol-phosphate dehydratase
K: Imidazoleglycerol-phosphate dehydratase
L: Imidazoleglycerol-phosphate dehydratase
M: Imidazoleglycerol-phosphate dehydratase
N: Imidazoleglycerol-phosphate dehydratase
O: Imidazoleglycerol-phosphate dehydratase
P: Imidazoleglycerol-phosphate dehydratase
Q: Imidazoleglycerol-phosphate dehydratase
R: Imidazoleglycerol-phosphate dehydratase
S: Imidazoleglycerol-phosphate dehydratase
T: Imidazoleglycerol-phosphate dehydratase
V: Imidazoleglycerol-phosphate dehydratase
W: Imidazoleglycerol-phosphate dehydratase
X: Imidazoleglycerol-phosphate dehydratase
Y: Imidazoleglycerol-phosphate dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)550,06396
Polymers541,71124
Non-polymers8,35272
Water20,3751131
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "L"
d_2ens_1chain "B"
d_3ens_1chain "C"
d_4ens_1chain "D"
d_5ens_1chain "Q"
d_6ens_1chain "F"
d_7ens_1chain "G"
d_8ens_1chain "H"
d_9ens_1chain "I"
d_10ens_1chain "J"
d_11ens_1chain "K"
d_12ens_1chain "E"
d_13ens_1chain "M"
d_14ens_1chain "N"
d_15ens_1chain "O"
d_16ens_1chain "P"
d_17ens_1chain "A"
d_18ens_1chain "R"
d_19ens_1chain "S"
d_20ens_1chain "T"
d_21ens_1chain "V"
d_22ens_1chain "W"
d_23ens_1chain "X"
d_24ens_1chain "Y"

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ALAALAARGARGLL78 - 2619 - 192
d_12MNMNMNMNJJB304
d_13MNMNMNMNJIB303
d_14IG2IG2IG2IG2JHB302
d_21ALAALAARGARGBB78 - 2619 - 192
d_22MNMNMNMNBCA301
d_23MNMNMNMNBDA302
d_24IG2IG2IG2IG2BEA303
d_31ALAALAARGARGCC78 - 2619 - 192
d_32IG2IG2IG2IG2BFA304
d_33MNMNMNMNCGA301
d_34MNMNMNMNCHA302
d_41ALAALAARGARGDD78 - 2619 - 192
d_42IG2IG2IG2IG2CIA303
d_43IG2IG2IG2IG2CJA304
d_44MNMNMNMNDKA301
d_51ALAALAARGARGQQ78 - 2619 - 192
d_52MNMNMNMNNVB303
d_53MNMNMNMNOWB301
d_54MNMNMNMNOXB302
d_61ALAALAARGARGFF78 - 2619 - 192
d_62MNMNMNMNEPA302
d_63IG2IG2IG2IG2EQA303
d_64IG2IG2IG2IG2ERA304
d_71ALAALAARGARGGG78 - 2619 - 192
d_72IG2IG2IG2IG2FSA301
d_73MNMNMNMNFTA302
d_74MNMNMNMNFUA303
d_81ALAALAARGARGHH78 - 2619 - 192
d_82IG2IG2IG2IG2FVA304
d_83MNMNMNMNGWA301
d_84MNMNMNMNGXA302
d_91ALAALAARGARGII78 - 2619 - 192
d_92IG2IG2IG2IG2GYA303
d_93IG2IG2IG2IG2GZA304
d_94MNMNMNMNHAB301
d_101ALAALAARGARGJJ78 - 2619 - 192
d_102MNMNMNMNHBB302
d_103IG2IG2IG2IG2HCB303
d_104IG2IG2IG2IG2IDB301
d_111ALAALAARGARGKK78 - 2619 - 192
d_112MNMNMNMNIEB302
d_113MNMNMNMNIFB303
d_114IG2IG2IG2IG2JGB301
d_121ALAALAARGARGEE78 - 2619 - 192
d_122MNMNMNMNDLA302
d_123IG2IG2IG2IG2DMA303
d_124IG2IG2IG2IG2DNA304
d_131ALAALAARGARGMM78 - 2619 - 192
d_132MNMNMNMNKKB301
d_133MNMNMNMNKLB302
d_134IG2IG2IG2IG2KMB303
d_141ALAALAARGARGNN78 - 2619 - 192
d_142IG2IG2IG2IG2LNB301
d_143MNMNMNMNLOB302
d_144IG2IG2IG2IG2ABA304
d_151ALAALAARGARGOO78 - 2619 - 192
d_152MNMNMNMNLPB303
d_153IG2IG2IG2IG2MQB301
d_154MNMNMNMNMRB302
d_161ALAALAARGARGPP78 - 2619 - 192
d_162MNMNMNMNMSB303
d_163IG2IG2IG2IG2NTB301
d_164MNMNMNMNNUB302
d_171ALAALAARGARGAA78 - 2619 - 192
d_172MNMNMNMNAY301
d_173MNMNMNMNAZ302
d_174IG2IG2IG2IG2AAA303
d_181ALAALAARGARGRR78 - 2619 - 192
d_182IG2IG2IG2IG2PYB301
d_183MNMNMNMNPZB302
d_184MNMNMNMNPAC303
d_191ALAALAARGARGSS78 - 2619 - 192
d_192MNMNMNMNQBC301
d_193MNMNMNMNQCC302
d_194MNMNMNMNRDC301
d_201ALAALAARGARGTT78 - 2619 - 192
d_202MNMNMNMNREC302
d_203IG2IG2IG2IG2SFC301
d_204MNMNMNMNSGC302
d_211ALAALAARGARGVU78 - 2619 - 192
d_212MNMNMNMNSHC303
d_213MNMNMNMNTIC301
d_214MNMNMNMNTJC302
d_221ALAALAARGARGWV78 - 2619 - 192
d_222MNMNMNMNVKC301
d_223MNMNMNMNVLC302
d_224MNMNMNMNWMC301
d_231ALAALAARGARGXW78 - 2619 - 192
d_232MNMNMNMNWNC302
d_233MNMNMNMNXOC301
d_234MNMNMNMNXPC302
d_241ALAALAARGARGYX78 - 2619 - 192
d_242MNMNMNMNYQC301
d_243MNMNMNMNYRC302
d_244MNMNMNMNEOA301

NCS oper:
IDCodeMatrixVector
1given(7.44465897218E-6, -0.999999990064, 0.000140773651889), (0.999999998226, 7.45297821592E-6, 5.90961645146E-5), (-5.90972131104E-5, 0.000140773211688, 0.999999988345)257.977132509, -0.00216260617495, -0.0104026930425
2given(-8.24383901554E-6, 0.999999997782, -6.60877803049E-5), (-0.999999957667, -8.22461663508E-6, 0.00029085633841), (0.000290855794218, 6.60901752801E-5, 0.999999955517)0.00290214384671, 257.96211472, -0.0516809233164
3given(-1.5952535519E-5, -7.23631227504E-5, -0.999999997255), (-0.999999996052, 8.74202012673E-5, 1.59462095008E-5), (8.74190471098E-5, 0.999999993561, -7.23645170388E-5)258.008076479, 257.983405119, -0.00254360675146
4given(-8.71846251885E-5, -8.70058115296E-5, -0.999999992414), (-8.5185361305E-5, -0.999999992586, 8.70132383984E-5), (-0.999999992571, 8.51929468754E-5, 8.71772129207E-5)258.019048125, 258.003204945, 257.974139299
5given(0.999999997412, 7.04486915536E-5, -1.46064306897E-5), (-1.4606251835E-5, -2.53930787597E-6, -0.99999999989), (-7.04487286361E-5, 0.999999997515, -2.53827887808E-6)-0.00703093272926, 258.005084587, 0.00890487762351
6given(7.68244840561E-5, -0.999999986915, 0.000142367852342), (7.02566633736E-5, -0.000142362454979, -0.999999987398), (0.999999994581, 7.6834485378E-5, 7.02457255324E-5)257.968379741, 258.012123167, -0.0128407904571
7given(0.999999996962, -1.7785638454E-5, -7.58925833002E-5), (7.58926316519E-5, 2.71791724327E-6, 0.999999997116), (-1.77854321329E-5, -0.999999999838, 2.71926703399E-6)0.0120832467427, -0.0100509241528, 258.004818769
8given(1.92025703658E-5, 0.000150877783043, 0.999999988434), (0.999999991373, 0.000129936766655, -1.9222174994E-5), (-0.000129939665351, 0.999999980176, -0.000150875286622)-0.0279527021176, -0.00758673359348, 0.0355760244341
9given(-0.999999929064, 0.000316875054446, 0.000203621519753), (0.000203637599454, 5.07131745922E-5, 0.99999997798), (0.000316864721175, 0.999999948509, -5.07776986707E-5)257.915871494, -0.0357256819506, -0.0498647536442
10given(7.28831425163E-5, 7.18425471138E-5, 0.999999994763), (-0.00011531419319, 0.999999990771, -7.18341423662E-5), (-0.999999990695, -0.000115308957088, 7.28914263091E-5)-0.0282745704899, 0.0232381036415, 258.002234764
11given(-0.999996463826, -0.00195377324346, 0.00180419100519), (0.00195163609837, -0.999997392794, -0.0011855466064), (0.00180650259053, -0.00118202128981, 0.999997669684)258.050476583, 257.789359563, -0.133975133868
12given(5.80160905495E-6, -0.000139847112708, -0.999999990205), (8.37881507139E-5, 0.999999986711, -0.000139846626113), (0.999999996473, -8.37873385577E-5, 5.81332650884E-6)258.013767589, 0.00718376451752, 0.0163683673073
13given(-0.000117693469723, -0.000150810496357, -0.999999981702), (0.999999993056, 5.98903705962E-6, -0.000117694374269), (6.00678649737E-6, -0.99999998861, 0.000150809790439)258.033738436, 0.0185277180657, 257.977201795
14given(7.57410257464E-5, 5.83060475861E-5, 0.999999995432), (-0.999999988806, -0.000129037274046, 7.57485488981E-5), (0.000129041690055, -0.999999989975, 5.82962735178E-5)-0.023453602169, 258.003403014, 257.979049937
15given(3.91070809629E-5, 0.999999989379, -0.000140399889538), (0.000224408613123, 0.000140391110144, 0.999999964966), (0.999999974056, -3.91385865376E-5, -0.000224403120453)0.00567393719783, -0.0504243394326, 0.0398259363488
16given(0.000109991421477, -0.999999988732, 0.000102164831713), (-0.999999987583, -0.000110002949517, -0.000112838889442), (0.000112850126604, -0.000102152419134, -0.999999988415)257.966527952, 258.026233079, 257.999361544
17given(-0.999999998536, -5.40469769304E-5, -2.46414952983E-6), (-5.40464578545E-5, 0.999999976454, -0.000210166776622), (2.47550835074E-6, -0.000210166643136, -0.999999977912)257.997478454, 0.0342284100149, 258.029087413
18given(-1.64036246013E-5, -0.999999996002, 8.79025264441E-5), (-7.11107844146E-5, 8.79036927084E-5, 0.999999993608), (-0.999999997337, 1.63973736789E-5, -7.11122260695E-5)257.987502465, -0.00181460528225, 258.003481901
19given(0.999999987222, 4.13769801413E-5, -0.000154414323031), (4.1375983576E-5, -0.999999999123, -6.45702859929E-6), (-0.000154414590068, 6.45063947229E-6, -0.999999988057)0.014349786476, 257.999083307, 258.024888032
20given(-2.33374376161E-5, 0.999999988832, -0.000147618120325), (0.999999973367, 2.33035419541E-5, -0.000229614764467), (-0.000229611321877, -0.000147623475014, -0.999999962743)0.0142287933123, 0.0330691789368, 258.054832406
21given(-0.999999982778, -0.000170658652131, 7.29315949798E-5), (-7.28130785553E-5, -0.000694367978367, -0.999999756276), (0.000170709251901, -0.999999744364, 0.000694355540226)258.001904152, 258.111294233, 257.900071652
22given(9.44929011306E-5, 0.000138637169482, 0.999999985925), (0.000129386550211, -0.999999982021, 0.00013862494283), (0.999999987165, 0.000129373449317, -9.45108372175E-5)-0.0363690553607, 257.969035488, 0.0019639517414
23given(-4.79997408316E-5, 0.999999995203, -8.53817092245E-5), (-0.000216091024397, -8.53920796424E-5, -0.999999973006), (-0.9999999755, -4.79812893149E-5, 0.000216095122159)0.00959882852882, 258.045154514, 257.974933133

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Components

#1: Protein ...
Imidazoleglycerol-phosphate dehydratase /


Mass: 22571.293 Da / Num. of mol.: 24
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Medicago truncatula (barrel medic) / Production host: Escherichia coli (E. coli)
References: UniProt: I3SDM5, imidazoleglycerol-phosphate dehydratase
#2: Chemical...
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 48 / Source method: obtained synthetically / Formula: Mn
#3: Chemical...
ChemComp-IG2 / (2S,3S)-2,3-dihydroxy-3-(1H-imidazol-5-yl)propyl dihydrogen phosphate


Mass: 238.135 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C6H11N2O6P / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1131 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: Complex of imidazole glycerol phosphate dehydratase (HISN5) with inhibitor 2S,3S-IGP (IG2)
Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 22.5 kDa/nm / Experimental value: NO
Source (natural)Organism: Medicago truncatula (barrel medic)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
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
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3500 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 40 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 3330

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2EPUimage acquisition
4cryoSPARCCTF correction
7Cootmodel fitting
10cryoSPARCfinal Euler assignment
11cryoSPARCclassification
12cryoSPARC3.3.23D reconstruction
13PHENIXmodel refinement
CTF correctionType: NONE
SymmetryPoint symmetry: O (octahedral)
3D reconstructionResolution: 2.23 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 605614 / Num. of class averages: 14 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model buildingPDB-ID: 7oj5

7oj5


Accession code: 7oj5 / Source name: PDB / Type: experimental model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 22.57 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00535352
ELECTRON MICROSCOPYf_angle_d0.85547856
ELECTRON MICROSCOPYf_dihedral_angle_d6.4294752
ELECTRON MICROSCOPYf_chiral_restr0.0585448
ELECTRON MICROSCOPYf_plane_restr0.0046264
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AELECTRON MICROSCOPYNCS constraints0.000714208077466
ens_1d_3CELECTRON MICROSCOPYNCS constraints0.000711444330581
ens_1d_4DELECTRON MICROSCOPYNCS constraints0.000704964269
ens_1d_5EELECTRON MICROSCOPYNCS constraints0.000709650966715
ens_1d_6FELECTRON MICROSCOPYNCS constraints0.000721104909416
ens_1d_7GELECTRON MICROSCOPYNCS constraints0.000712440932044
ens_1d_8HELECTRON MICROSCOPYNCS constraints0.000696372190731
ens_1d_9IELECTRON MICROSCOPYNCS constraints0.000686219507741
ens_1d_10JELECTRON MICROSCOPYNCS constraints0.000715125774431
ens_1d_11KELECTRON MICROSCOPYNCS constraints0.000705104726415
ens_1d_12LELECTRON MICROSCOPYNCS constraints0.000707657901849
ens_1d_13MELECTRON MICROSCOPYNCS constraints0.000703037173298
ens_1d_14NELECTRON MICROSCOPYNCS constraints0.000698967329069
ens_1d_15OELECTRON MICROSCOPYNCS constraints0.000707363549492
ens_1d_16PELECTRON MICROSCOPYNCS constraints0.000709133100164
ens_1d_17QELECTRON MICROSCOPYNCS constraints0.0958004017
ens_1d_18RELECTRON MICROSCOPYNCS constraints0.000706051144755
ens_1d_19SELECTRON MICROSCOPYNCS constraints0.000695565183181
ens_1d_20TELECTRON MICROSCOPYNCS constraints0.000704531683709
ens_1d_21VELECTRON MICROSCOPYNCS constraints0.000710473263838
ens_1d_22WELECTRON MICROSCOPYNCS constraints0.000714238728719
ens_1d_23XELECTRON MICROSCOPYNCS constraints0.000713415189023
ens_1d_24YELECTRON MICROSCOPYNCS constraints0.000714813250013

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  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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