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- PDB-9iz1: dmCTPS tetramer with dATP dUTP dGTP and DON -

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Basic information

Entry
Database: PDB / ID: 9iz1
TitledmCTPS tetramer with dATP dUTP dGTP and DON
ComponentsCTP synthase
KeywordsLIGASE / filament / CTPS
Function / homology
Function and homology information


Interconversion of nucleotide di- and triphosphates / larval lymph gland hemopoiesis / cytoophidium / CTP synthase (glutamine hydrolysing) / CTP synthase activity / 'de novo' CTP biosynthetic process / pyrimidine nucleobase biosynthetic process / CTP biosynthetic process / glutamine metabolic process / ATP binding ...Interconversion of nucleotide di- and triphosphates / larval lymph gland hemopoiesis / cytoophidium / CTP synthase (glutamine hydrolysing) / CTP synthase activity / 'de novo' CTP biosynthetic process / pyrimidine nucleobase biosynthetic process / CTP biosynthetic process / glutamine metabolic process / ATP binding / identical protein binding / cytosol / cytoplasm
Similarity search - Function
CTP synthase / CTP synthase, N-terminal / CTP synthase GATase domain / CTP synthase N-terminus / Glutamine amidotransferase / Glutamine amidotransferase class-I / Glutamine amidotransferase type 1 domain profile. / Class I glutamine amidotransferase-like / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Chem-5ZL / 2'-DEOXYADENOSINE-5'-DIPHOSPHATE / 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE / 6-DIAZENYL-5-OXO-L-NORLEUCINE / CTP synthase
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.73 Å
AuthorsGuo, C.J. / Liu, J.L.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: J Mol Biol / Year: 2024
Title: Structural Basis of Bifunctional CTP/dCTP Synthase.
Authors: Chen-Jun Guo / Zherong Zhang / Jia-Li Lu / Jiale Zhong / Yu-Fen Wu / Shu-Ying Guo / Ji-Long Liu /
Abstract: The final step in the de novo synthesis of cytidine 5'-triphosphate (CTP) is catalyzed by CTP synthase (CTPS), which can form cytoophidia in all three domains of life. Recently, we have discovered ...The final step in the de novo synthesis of cytidine 5'-triphosphate (CTP) is catalyzed by CTP synthase (CTPS), which can form cytoophidia in all three domains of life. Recently, we have discovered that CTPS binds to ribonucleotides (NTPs) to form filaments, and have successfully resolved the structures of Drosophila melanogaster CTPS bound with NTPs. Previous biochemical studies have shown that CTPS can bind to deoxyribonucleotides (dNTPs) to produce 2'-deoxycytidine-5'-triphosphate (dCTP). However, the structural basis of CTPS binding to dNTPs is still unclear. In this study, we find that Drosophila CTPS can also form filaments with dNTPs. Using cryo-electron microscopy, we are able to resolve the structure of Drosophila melanogaster CTPS bound to dNTPs with a resolution of up to 2.7 Å. By combining these structural findings with biochemical analysis, we compare the binding and reaction characteristics of NTPs and dNTPs with CTPS. Our results indicate that the same enzyme can act bifunctionally as CTP/dCTP synthase in vitro, and provide a structural basis for these activities.
History
DepositionJul 31, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 27, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CTP synthase
B: CTP synthase
C: CTP synthase
D: CTP synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)256,79036
Polymers249,7754
Non-polymers7,01632
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
CTP synthase / CTP synthetase / UTP--ammonia ligase


Mass: 62443.656 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: CTPsyn, CG45070
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q9VUL1, CTP synthase (glutamine hydrolysing)

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Non-polymers , 5 types, 32 molecules

#2: Chemical
ChemComp-DON / 6-DIAZENYL-5-OXO-L-NORLEUCINE / (S)-2-AMINO-6-DIAZENYL-5-OXOHEXANOIC ACID


Type: L-peptide linking / Mass: 173.170 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H11N3O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-DAT / 2'-DEOXYADENOSINE-5'-DIPHOSPHATE / DADP


Mass: 411.202 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O9P2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-DGT / 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-5ZL / [[(2~{R},3~{S},4~{R},5~{R})-3,4-bis(oxidanyl)-5-(2-oxidanyl-4-phosphonooxy-pyrimidin-1-yl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate


Mass: 565.129 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H17N2O18P4 / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: dmCTPS with dATP dUTP dGTP and DON / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Source (recombinant)Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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: FLOOD BEAM
Electron lensMode: DARK FIELD / Nominal defocus max: 20000 nm / Nominal defocus min: 5000 nm
Image recordingElectron dose: 59.5 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.73 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 639301 / Symmetry type: POINT
RefinementCross valid method: NONE

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