|Entry||Database: PDB / ID: 7rnr|
|Title||Yeast CTP Synthase (Ura8) Bundle Bound to Substrates at Low pH|
|Components||CTP synthaseCTP synthetase|
|Keywords||PROTEIN FIBRIL / glutaminase and amido-ligase|
|Function / homology|
Function and homology information
CTP synthase (glutamine hydrolysing) / CTP synthase activity / 'de novo' CTP biosynthetic process / glutamine metabolic process / ATP binding
Similarity search - Function
CTP synthase / CTP synthase, N-terminal / CTP synthase GATase domain / CTP synthase N-terminus / Glutamine amidotransferase class-I / Glutamine amidotransferase / Class I glutamine amidotransferase-like / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / URIDINE 5'-TRIPHOSPHATE / CTP synthase
Similarity search - Component
|Biological species||Saccharomyces cerevisiae (baker's yeast)|
|Method||ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å|
|Model details||cryo-EM D2 reconstruction|
|Authors||Hansen, J.M. / Lynch, E.M. / Farrell, D.P. / DiMaio, F. / Quispe, J. / Kollman, J.M.|
|Funding support||2items |
|Citation||Journal: Elife / Year: 2021|
Title: Cryo-EM structures of CTP synthase filaments reveal mechanism of pH-sensitive assembly during budding yeast starvation.
Authors: Jesse M Hansen / Avital Horowitz / Eric M Lynch / Daniel P Farrell / Joel Quispe / Frank DiMaio / Justin M Kollman /
Abstract: Many metabolic enzymes self-assemble into micron-scale filaments to organize and regulate metabolism. The appearance of these assemblies often coincides with large metabolic changes as in ...Many metabolic enzymes self-assemble into micron-scale filaments to organize and regulate metabolism. The appearance of these assemblies often coincides with large metabolic changes as in development, cancer, and stress. Yeast undergo cytoplasmic acidification upon starvation, triggering the assembly of many metabolic enzymes into filaments. However, it is unclear how these filaments assemble at the molecular level and what their role is in the yeast starvation response. CTP Synthase (CTPS) assembles into metabolic filaments across many species. Here, we characterize in vitro polymerization and investigate in vivo consequences of CTPS assembly in yeast. Cryo-EM structures reveal a pH-sensitive assembly mechanism and highly ordered filament bundles that stabilize an inactive state of the enzyme, features unique to yeast CTPS. Disruption of filaments in cells with non-assembly or pH-insensitive mutations decreases growth rate, reflecting the importance of regulated CTPS filament assembly in homeotstasis.
|Structure viewer||Molecule: |
Downloads & links
A: CTP synthase
E: CTP synthase
B: CTP synthase
F: CTP synthase
Q: CTP synthase
Y: CTP synthase
S: CTP synthase
a: CTP synthase
I: CTP synthase
M: CTP synthase
J: CTP synthase
N: CTP synthase
R: CTP synthase
Z: CTP synthase
T: CTP synthase
b: CTP synthase
g: CTP synthase
k: CTP synthase
h: CTP synthase
l: CTP synthase
Mass: 62439.168 Da / Num. of mol.: 20
Source method: isolated from a genetically manipulated source
Details: 6XHIS c-ter
Source: (gene. exp.) Saccharomyces cerevisiae (baker's yeast)
Gene: PACBIOSEQ_LOCUS3439, SCNYR20_0009027000 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus (DE3)-RIL
References: UniProt: A0A6A5PYW3, CTP synthase (glutamine hydrolysing)
Mass: 507.181 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
Mass: 484.141 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C9H15N2O15P3 / Comment: UTP*YM
|Has ligand of interest||N|
|Experiment||Method: ELECTRON MICROSCOPY|
|EM experiment||Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction|
|Component||Name: CTP Synthase Bundle assembled with Substrates / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT|
|Source (natural)||Organism: Saccharomyces cerevisiae (baker's yeast)|
|Source (recombinant)||Organism: Escherichia coli (E. coli)|
|Buffer solution||pH: 6|
|Specimen||Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES|
|Vitrification||Cryogen name: ETHANE|
-Electron microscopy imaging
Model: Titan Krios / Image courtesy: FEI Company
|Microscopy||Model: FEI TITAN KRIOS|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM|
|Electron lens||Mode: BRIGHT FIELDBright-field microscopy|
|Image recording||Electron dose: 90 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)|
|CTF correction||Type: PHASE FLIPPING AND AMPLITUDE CORRECTION|
|Symmetry||Point symmetry: C2 (2 fold cyclic)|
|3D reconstruction||Resolution: 3.3 Å / Resolution method: OTHER / Num. of particles: 21220 / Details: FSCref0.5 (Phenix Density Modification) / Symmetry type: POINT|
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