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- PDB-9eej: Crystal structure of E. coli aspartate transcarbamoylase in the R... -

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Basic information

Entry
Database: PDB / ID: 9eej
TitleCrystal structure of E. coli aspartate transcarbamoylase in the R-state complexed with CP, succinate, ATP, and Mg2+
Components
  • Aspartate carbamoyltransferase
  • Aspartate carbamoyltransferase regulatory chain
KeywordsCYTOSOLIC PROTEIN / Complex / Allostery / ATCase / R-state / CP / succinate / ATP
Function / homology
Function and homology information


aspartate carbamoyltransferase complex / pyrimidine nucleotide biosynthetic process / aspartate carbamoyltransferase / aspartate carbamoyltransferase activity / amino acid metabolic process / amino acid binding / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / transferase activity / metal ion binding / cytosol
Similarity search - Function
Aspartate transcarbamylase regulatory subunit / Aspartate carbamoyltransferase regulatory subunit, C-terminal / Aspartate carbamoyltransferase regulatory subunit, N-terminal / Aspartate carbamoyltransferase regulatory subunit, C-terminal domain superfamily / Aspartate carbamoyltransferase regulatory subunit, N-terminal domain superfamily / Aspartate carbamoyltransferase regulatory chain, allosteric domain / Aspartate carbamoyltransferase regulatory chain, metal binding domain / Aspartate carbamoyltransferase / Aspartate and ornithine carbamoyltransferases signature. / Aspartate/ornithine carbamoyltransferase ...Aspartate transcarbamylase regulatory subunit / Aspartate carbamoyltransferase regulatory subunit, C-terminal / Aspartate carbamoyltransferase regulatory subunit, N-terminal / Aspartate carbamoyltransferase regulatory subunit, C-terminal domain superfamily / Aspartate carbamoyltransferase regulatory subunit, N-terminal domain superfamily / Aspartate carbamoyltransferase regulatory chain, allosteric domain / Aspartate carbamoyltransferase regulatory chain, metal binding domain / Aspartate carbamoyltransferase / Aspartate and ornithine carbamoyltransferases signature. / Aspartate/ornithine carbamoyltransferase / Aspartate/ornithine carbamoyltransferase, Asp/Orn-binding domain / Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding / Aspartate/ornithine carbamoyltransferase superfamily / Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain / Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / PHOSPHORIC ACID MONO(FORMAMIDE)ESTER / SUCCINIC ACID / Aspartate carbamoyltransferase / Aspartate carbamoyltransferase regulatory chain
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsPatterson, M.G. / Miller, R.C. / Ando, N.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM124847 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30 GM124165 United States
Department of Energy (DOE, United States)DE-AC02-06CH11357 United States
Citation
Journal: Nat Commun / Year: 2026
Title: Cooperativity in E. coli aspartate transcarbamoylase is tuned by allosteric breathing.
Authors: Robert C Miller / Michael G Patterson / Neti Bhatt / Xiaokun Pei / Nozomi Ando /
Abstract: Aspartate transcarbamoylase (ATCase) from Escherichia coli catalyzes a key step in pyrimidine nucleotide biosynthesis and has long served as a model for allosteric regulation. Despite decades of ...Aspartate transcarbamoylase (ATCase) from Escherichia coli catalyzes a key step in pyrimidine nucleotide biosynthesis and has long served as a model for allosteric regulation. Despite decades of study, how nucleotide binding at distant regulatory sites controls cooperativity between active sites remained unresolved. Here we show that ATCase does not simply interconvert between two conformations, as traditionally depicted, but instead samples a continuum of conformations that tune enzyme cooperativity. Using complementary cryo-electron microscopy, small-angle X-ray scattering, and crystallography under conditions that ensure full assembly of the allosteric sites, we show that ATCase behaves like a flexible balloon whose global "breathing" motions directly regulate activity: compression enforces high cooperativity, inhibiting the enzyme, whereas expansion relieves this cooperativity and activates the enzyme. We further show that all four ribonucleoside triphosphates act in symmetric pairs to tune this motion, with the pyrimidines CTP and UTP compressing the enzyme to limit further pyrimidine production, and the purines ATP and GTP expanding it to balance pyrimidine and purine pools. Together, these findings uncover a dynamic breathing mechanism for long-range allosteric communication in ATCase.
#1: Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionNov 19, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 15, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Aspartate carbamoyltransferase
B: Aspartate carbamoyltransferase
C: Aspartate carbamoyltransferase
D: Aspartate carbamoyltransferase regulatory chain
E: Aspartate carbamoyltransferase regulatory chain
F: Aspartate carbamoyltransferase
G: Aspartate carbamoyltransferase
H: Aspartate carbamoyltransferase regulatory chain
I: Aspartate carbamoyltransferase regulatory chain
J: Aspartate carbamoyltransferase regulatory chain
K: Aspartate carbamoyltransferase
L: Aspartate carbamoyltransferase regulatory chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)317,06348
Polymers308,88412
Non-polymers8,17936
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)129.049, 148.793, 207.866
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 2 types, 12 molecules ABCFGKDEHIJL

#1: Protein
Aspartate carbamoyltransferase / Aspartate transcarbamylase / ATCase


Mass: 34337.105 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Gene: pyrB, A2J79_003077, ABE91_001635, ABT96_002053, ACN81_01160, ACW72_001368, ATM34_004868, AW118_07535, AWP47_22680, B6R15_003056, B6R31_000750, BANRA_02937, BE932_21750, BER14_11960, BG944_ ...Gene: pyrB, A2J79_003077, ABE91_001635, ABT96_002053, ACN81_01160, ACW72_001368, ATM34_004868, AW118_07535, AWP47_22680, B6R15_003056, B6R31_000750, BANRA_02937, BE932_21750, BER14_11960, BG944_000740, BGM66_001590, BGZ_01518, BGZ_05217, BJI68_10440, BK300_13470, BK383_13480, BKL28_003429, BRV02_003861, BTB68_002687, BTQ06_18960, BvCmsNSP007_04794, BVE17_001554, BXT93_08870, C0P57_000163, C1Q91_004309, C2M16_07715, C2R31_000937, C3F40_13755, C4M78_05240, C719_002693, C9114_01215, C9160_23140, C9Z68_08980, CF22_004479, CG704_05430, CIG67_22815, CLG78_001649, CQ842_08915, CQ842_12490, CR538_22700, CTR35_001468, CV628_004970, CV83915_01779, CWS33_03955, D3C88_12940, D3G36_17310, D4M65_07255, D4N09_04845, D9D43_13600, D9E49_11435, D9J61_12555, DAH27_26520, DIV22_16805, DNQ45_09630, DNX30_17140, DS732_03300, DTL43_02750, DU321_18175, E2865_05519, E5H86_07990, E6D34_03380, EAI46_26260, ECs5222, EF082_09955, EIA08_16955, EIZ93_20760, EN85_001335, EPS76_30055, EPS97_17825, EWK56_08300, ExPECSC038_04763, F7F11_04770, F7G01_01060, F7N46_16830, F9413_07035, F9B07_19120, FEH53_07480, FGAF1022_42670, FIJ20_18930, FJQ40_01260, FKO60_19415, FOI11_014380, FOI11_21300, FPI65_26085, FPS11_22335, FVB16_24685, FZU14_19575, G3V95_10555, G3W53_08345, G4A38_03455, G4A47_10535, G5603_09990, G6Z99_20225, GAI89_04005, GAJ12_10370, GKF66_08525, GNW61_17465, GNZ05_12485, GOP25_13765, GP965_09375, GP979_09965, GQE86_05410, GQM04_23140, GQM13_11160, GQM21_13835, GQN24_22415, GRC73_06815, GRW05_26905, GRW24_19535, GTP92_08545, GUC01_09445, HEP34_001710, HHH44_002259, HI055_001287, HI084_001705, HIA71_17170, HID72_003759, HIE29_003970, HJ488_000368, HJS37_003257, HKA49_000761, HLX92_11970, HLZ39_13930, HLZ50_15085, HND12_14900, HV209_29455, HVV39_15605, HVW04_12090, HVW43_13615, HVW90_11235, HVY77_22735, I6H00_15800, I6H02_17085, IFN33_000225, IG021_000549, IH772_04275, J0541_002249, J5U05_001302, J8F57_000038, KQO22_002766, NCTC10082_01748, NCTC10089_04451, NCTC10764_04395, NCTC10767_00303, NCTC10865_05523, NCTC10974_05016, NCTC11112_02870, NCTC11181_01680, NCTC11341_03161, NCTC13148_04788, NCTC7922_05337, NCTC7928_04108, NCTC8179_04755, NCTC8500_04950, NCTC8621_04481, NCTC8959_04205, NCTC8960_01943, NCTC8985_03619, NCTC9001_04952, NCTC9044_02747, NCTC9045_05133, NCTC9073_03832, NCTC9081_01672, NCTC9117_05502, NCTC9702_05190, NCTC9703_03794, OFN31_17640, OGM49_02125, P6223_000603, QDW62_23130, R8G00_26825, R8O40_003191, RZR61_03900, SAMEA3472044_01445, SAMEA3472112_04514, SAMEA3752557_01748, TUM18780_38870
Production host: Escherichia coli (E. coli) / References: UniProt: C3SF53, aspartate carbamoyltransferase
#2: Protein
Aspartate carbamoyltransferase regulatory chain


Mass: 17143.625 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Gene: pyrI, A2J79_003078, A5U30_000934, ABE91_001630, ABT96_002052, ACN81_01165, ACU57_15645, ACW72_001369, ATM34_004869, AWP47_22675, B6R15_003055, B6R31_000751, BANRA_00251, BANRA_02936, BCB93_ ...Gene: pyrI, A2J79_003078, A5U30_000934, ABE91_001630, ABT96_002052, ACN81_01165, ACU57_15645, ACW72_001369, ATM34_004869, AWP47_22675, B6R15_003055, B6R31_000751, BANRA_00251, BANRA_02936, BCB93_002761, BE932_21745, BG944_000741, BGM66_001591, BGZ_01519, BGZ_05216, BJI68_10435, BK300_13465, BK383_13475, BKL28_003430, BMT50_05825, BRV02_003862, BTB68_002686, BTQ06_18965, BvCmsKKP061_03433, BvCmsNSP007_04795, BVE17_001555, BXT93_08875, C0P57_000164, C1Q91_004308, C2M16_07710, C2R31_000938, C3F40_13760, C4M78_05245, C7B02_12530, C9160_23135, CF22_004478, CG704_05435, CIG67_22820, CLG78_001650, CQ842_08920, CQ842_12485, CR538_22705, CTR35_001469, CV628_004971, CV83915_01780, CWS33_03950, D3C88_12935, D3G36_17315, D4M65_07260, D4N09_04840, D9D43_13595, D9E49_11440, D9J61_12550, DAH27_26525, DD762_15800, DIV22_16800, DL738_14650, DL968_06885, DNQ45_09635, DNX30_17145, DS732_03295, DTL43_02745, DU321_18180, E0I52_01830, E2865_05518, E4K51_15130, E5H86_07995, E6D34_03385, EAI46_26265, ECs5221, EF082_09960, EIA08_16950, EN85_001336, EPS97_17820, EWK56_08305, ExPECSC038_04762, F7G01_01055, F7N46_16835, F9413_07040, F9461_17650, F9B07_19115, FGAF1022_42660, FGAF848_40920, FIJ20_18925, FJQ40_01265, FKO60_19420, FOI11_014385, FOI11_21295, FPI65_26080, FPS11_22330, FTV93_15585, FWK02_19125, FZU14_19580, G3V95_10560, G3W53_08350, G4A38_03450, G4A47_10540, G5603_09985, GAI89_04010, GAJ12_10375, GNW61_17470, GOP25_13770, GP711_18320, GP954_15650, GP965_09380, GP979_09970, GQA06_14590, GQE86_05415, GQM04_23145, GQM13_11155, GQN24_22420, GQN34_01855, GRC73_06810, GRW05_26910, GRW24_19530, GUC01_09440, H0O72_05310, HEP30_009870, HEP34_001711, HHH44_002260, HI084_001706, HIA71_17175, HID72_003760, HIE29_003971, HJ488_000369, HJQ60_002439, HJS37_003258, HKA49_000762, HLZ39_13925, HLZ50_15090, HMV95_06310, HV109_21095, HV209_29450, HVV39_15600, HVW43_13620, HVW90_11240, HVY77_22740, I6H00_15805, I6H02_17080, IFC14_000343, IG021_000550, J0541_002250, J8F57_000039, JNP96_03410, KTF03_003069, NCTC10082_01749, NCTC10089_04452, NCTC10418_06552, NCTC10429_04598, NCTC10764_04396, NCTC10767_00304, NCTC10865_05524, NCTC10974_05017, NCTC11112_02869, NCTC11126_02378, NCTC11181_01681, NCTC11341_03160, NCTC13148_04787, NCTC7922_05338, NCTC7927_04891, NCTC8009_07825, NCTC8179_04754, NCTC8621_04480, NCTC8622_02187, NCTC8959_04206, NCTC8960_01944, NCTC8985_03620, NCTC9045_05134, NCTC9073_03833, NCTC9077_05555, NCTC9081_01671, NCTC9117_05503, NCTC9702_05191, NCTC9703_03795, NCTC9706_01714, NCTC9962_01701, OFN31_17645, OGM49_02120, P6223_000604, PWL68_003651, QDW62_23135, R8G00_26830, R8O40_003192, RZR61_03905, SAMEA3472044_01446, SAMEA3472112_04513, SAMEA3752557_01747, TUM18780_38880
Production host: Escherichia coli (E. coli) / References: UniProt: C3SF57

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Non-polymers , 5 types, 36 molecules

#3: Chemical
ChemComp-CP / PHOSPHORIC ACID MONO(FORMAMIDE)ESTER


Mass: 141.020 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: CH4NO5P
#4: Chemical
ChemComp-SIN / SUCCINIC ACID


Mass: 118.088 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H6O4
#5: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#6: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#7: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg

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Details

Has ligand of interestN
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: 3.23 Å3/Da / Density % sol: 61.92 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Protein solution: 0.016 mM ATCase in 40 mM Tris pH 7.0, 20 mM CP, 20 mM succinate, 30 mM MgCl2, and 10 mM ATP Well solution: 0.1 M Bis-Tris pH 6.5 and 20-25% PEG 300 Drops: 0.001 mL each of ...Details: Protein solution: 0.016 mM ATCase in 40 mM Tris pH 7.0, 20 mM CP, 20 mM succinate, 30 mM MgCl2, and 10 mM ATP Well solution: 0.1 M Bis-Tris pH 6.5 and 20-25% PEG 300 Drops: 0.001 mL each of protein and well solution
Temp details: ambient temperature

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: cryogenic temperature / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 27, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3→103.9 Å / Num. obs: 80502 / % possible obs: 99.3 % / Redundancy: 5.8 % / Biso Wilson estimate: 62.34 Å2 / CC1/2: 0.966 / Rmerge(I) obs: 0.2676 / Rpim(I) all: 0.1213 / Net I/σ(I): 4.2
Reflection shellResolution: 3→3.11 Å / Rmerge(I) obs: 1.027 / Mean I/σ(I) obs: 0.7 / Num. unique obs: 7971 / CC1/2: 0.642 / Rpim(I) all: 0.454

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
DIALS3.18.0data reduction
DIALS3.18.0data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→103.9 Å / SU ML: 0.4512 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.9719
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2488 1992 2.49 %
Rwork0.2178 78143 -
obs0.2185 80135 99.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 71.23 Å2
Refinement stepCycle: LAST / Resolution: 3→103.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21457 0 480 0 21937
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.001722315
X-RAY DIFFRACTIONf_angle_d0.51830341
X-RAY DIFFRACTIONf_chiral_restr0.04253497
X-RAY DIFFRACTIONf_plane_restr0.00373887
X-RAY DIFFRACTIONf_dihedral_angle_d13.02458557
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.080.36091330.34275357X-RAY DIFFRACTION96.1
3.08-3.160.38661480.31975493X-RAY DIFFRACTION98.9
3.16-3.250.3521340.31085525X-RAY DIFFRACTION99.77
3.25-3.360.34741460.29365533X-RAY DIFFRACTION99.68
3.36-3.480.32541410.27785538X-RAY DIFFRACTION99.51
3.48-3.620.31411300.26055491X-RAY DIFFRACTION98.74
3.62-3.780.27461240.23195594X-RAY DIFFRACTION99.22
3.78-3.980.25511500.21735552X-RAY DIFFRACTION99.84
3.98-4.230.23371570.19335581X-RAY DIFFRACTION99.76
4.23-4.550.18471490.17685609X-RAY DIFFRACTION99.77
4.56-5.010.2071500.16845621X-RAY DIFFRACTION99.71
5.01-5.740.20171490.19545638X-RAY DIFFRACTION99.74
5.74-7.230.23311390.21275672X-RAY DIFFRACTION99.28
7.23-103.90.18511420.16645939X-RAY DIFFRACTION99.69

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