7RNR

Yeast CTP Synthase (Ura8) Bundle Bound to Substrates at Low pH


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Cryo-EM structures of CTP synthase filaments reveal mechanism of pH-sensitive assembly during budding yeast starvation.

Hansen, J.M.Horowitz, A.Lynch, E.M.Farrell, D.P.Quispe, J.DiMaio, F.Kollman, J.M.

(2021) Elife 10

  • DOI: 10.7554/eLife.73368
  • Primary Citation of Related Structures:  
    7RKH, 7RL0, 7RL5, 7RMC, 7RMF, 7RMK, 7RMO, 7RMV, 7RNL, 7RNR

  • PubMed 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 development, cancer, and stress. Yeast undergo cytoplasmic acidification upon starvation, triggering the assembly of many metabolic enzymes into filaments ...

    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.


    Organizational Affiliation

    Department of Biochemistry, University of Washington, seattle, United States.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CTP synthase559Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: PACBIOSEQ_LOCUS3439SCNYR20_0009027000
EC: 6.3.4.2
UniProt
Find proteins for A0A6A5PYW3 (Saccharomyces cerevisiae)
Explore A0A6A5PYW3 
Go to UniProtKB:  A0A6A5PYW3
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP (Subject of Investigation/LOI)
Query on ATP

Download Ideal Coordinates CCD File 
AB [auth I] , DA [auth B] , EC [auth b] , FB [auth M] , GC [auth g] , IA [auth F] , JB [auth J] , KA [auth Q] , 
AB [auth I], DA [auth B], EC [auth b], FB [auth M], GC [auth g], IA [auth F], JB [auth J], KA [auth Q], LC [auth k], OB [auth N], PA [auth Y], PC [auth h], QB [auth R], TA [auth S], U [auth A], UC [auth l], VB [auth Z], YA [auth a], Z [auth E], ZB [auth T]
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
UTP (Subject of Investigation/LOI)
Query on UTP

Download Ideal Coordinates CCD File 
BA [auth E] , CA [auth B] , DC [auth b] , EB [auth I] , HA [auth F] , HB [auth M] , IB [auth J] , KC [auth g] , 
BA [auth E], CA [auth B], DC [auth b], EB [auth I], HA [auth F], HB [auth M], IB [auth J], KC [auth g], NB [auth N], NC [auth k], OA [auth Q], OC [auth h], RA [auth Y], SA [auth S], TC [auth l], UB [auth R], XA [auth a], XB [auth Z], Y [auth A], YB [auth T]
URIDINE 5'-TRIPHOSPHATE
C9 H15 N2 O15 P3
PGAVKCOVUIYSFO-XVFCMESISA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
AA [auth E] , AC [auth T] , BB [auth I] , BC [auth T] , CB [auth I] , CC [auth T] , DB [auth I] , EA [auth B] , 
AA [auth E], AC [auth T], BB [auth I], BC [auth T], CB [auth I], CC [auth T], DB [auth I], EA [auth B], FA [auth B], FC [auth b], GA [auth B], GB [auth M], HC [auth g], IC [auth g], JA [auth F], JC [auth g], KB [auth J], LA [auth Q], LB [auth J], MA [auth Q], MB [auth J], MC [auth k], NA [auth Q], PB [auth N], QA [auth Y], QC [auth h], RB [auth R], RC [auth h], SB [auth R], SC [auth h], TB [auth R], UA [auth S], V [auth A], VA [auth S], VC [auth l], W [auth A], WA [auth S], WB [auth Z], X [auth A], ZA [auth a]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM118396
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32 GM007270

Revision History  (Full details and data files)

  • Version 1.0: 2021-11-24
    Type: Initial release