Skip to main content

 9V2G | pdb_00009v2g

CTP synthase dDON-condition state 6


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.96 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 9V2G

This is version 1.0 of the entry. See complete history. 

Literature

GTP orchestrates CTP synthase via an allosteric effector-cycling mechanism.

Guo, C.J., Wu, Y.F., Guo, S.Y., Lu, J.L., Xu, L., Fu, Y., Zhou, X., Zhong, J., Zhang, Z., Liu, J.L.

(2026) Proc Natl Acad Sci U S A 123: e2620272123-e2620272123

  • DOI: https://doi.org/10.1073/pnas.2620272123

  • PubMed Abstract: 

    Cytidine triphosphate (CTP), a fundamental building block of RNA, plays vital roles in diverse biological processes. CTP synthase (CTPS) is the only known enzyme for de novo synthesis of CTP. Efficient CTPS catalysis requires guanosine triphosphate (GTP) in a dose-dependent, nonconsumptive manner; however, the precise mechanism by which GTP drives CTP formation remains unclear. Here, we integrate a series of cryo-EM structures of Drosophila melanogaster CTPS captured from actively catalyzing samples with biochemical and mutagenesis analyses, yielding 34 distinct CTPS states at resolutions up to 2.0 Å. We find that GTP binds to and dissociates from CTPS once per catalytic cycle, thereby enabling the production of a single CTP molecule. Initial GTP engagement requires formation of 4-phosphoryl-UTP in the AL domain, whereas full stabilization of GTP binding is promoted by occupancy of the GAT active site. Together, these two checkpoints couple GTP recruitment and stabilization to catalytic progress in the two domains, enabling the coordinated synthesis of one CTP molecule per GTP binding-dissociation cycle. Moreover, the GTP-recognition site is highly conserved across the three domains of life. These findings establish a comprehensive mechanistic framework for efficient CTPS catalysis and define "effector-cycling"-in which GTP undergoes obligatory binding and dissociation during each catalytic cycle to regulate an intermediate step in a multistep catalytic process-as a distinct mode of allosteric regulation.


  • Organizational Affiliation: 
    • School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China.

Macromolecule Content 

  • Total Structure Weight: 189.06 kDa 
  • Atom Count: 5,230 
  • Modeled Residue Count: 649 
  • Deposited Residue Count: 1,668 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
CTP synthaseA [auth B],
B [auth C],
C [auth A]
556Drosophila melanogasterMutation(s): 0 
Gene Names: Ctps, CTPsyn, CG45070
EC: 6.3.4.2
UniProt
Find proteins for Q9VUL1 (Drosophila melanogaster)
Explore Q9VUL1 
Go to UniProtKB:  Q9VUL1
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9VUL1
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1FGS
(Subject of Investigation/LOI)

Query on A1FGS



Download:Ideal Coordinates CCD File
F [auth A][(2~{R},3~{S},5~{R})-3-oxidanyl-5-(2-oxidanylidene-4-phosphonooxy-pyrimidin-1-yl)oxolan-2-yl]methyl [oxidanyl(phosphonooxy)phosphoryl] hydrogen phosphate
C9 H16 N2 O17 P4
VYDHROQYKNLDCY-SHYZEUOFSA-N
DGT
(Subject of Investigation/LOI)

Query on DGT



Download:Ideal Coordinates CCD File
G [auth A]2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
HAAZLUGHYHWQIW-KVQBGUIXSA-N
DAT
(Subject of Investigation/LOI)

Query on DAT



Download:Ideal Coordinates CCD File
E [auth A]2'-DEOXYADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O9 P2
DAEAPNUQQAICNR-RRKCRQDMSA-N
8WY
(Subject of Investigation/LOI)

Query on 8WY



Download:Ideal Coordinates CCD File
K [auth A]5,5-dihydroxy-L-norleucine
C6 H13 N O4
CRZSOCVDEBRAJD-BYPYZUCNSA-N
MG
(Subject of Investigation/LOI)

Query on MG



Download:Ideal Coordinates CCD File
D [auth C],
H [auth A],
I [auth A],
J [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.96 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1_4487:

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data

  • Released Date: 2026-11-04 
  • Deposition Author(s): Guo, C.J.

Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China--

Revision History  (Full details and data files)

  • Version 1.0: 2026-11-04
    Type: Initial release