7DPT

Structural basis for ligand binding modes of CTP synthase


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.48 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Structural basis for ligand binding modes of CTP synthase.

Zhou, X.Guo, C.J.Chang, C.C.Zhong, J.Hu, H.H.Lu, G.M.Liu, J.L.

(2021) Proc Natl Acad Sci U S A 118

  • DOI: https://doi.org/10.1073/pnas.2026621118
  • Primary Citation of Related Structures:  
    7DPT, 7DPW, 7WIZ, 7WJ4

  • PubMed Abstract: 

    Cytidine triphosphate synthase (CTPS), which comprises an ammonia ligase domain and a glutamine amidotransferase domain, catalyzes the final step of de novo CTP biosynthesis. The activity of CTPS is regulated by the binding of four nucleotides and glutamine. While glutamine serves as an ammonia donor for the ATP-dependent conversion of UTP to CTP, the fourth nucleotide GTP acts as an allosteric activator. Models have been proposed to explain the mechanisms of action at the active site of the ammonia ligase domain and the conformational changes derived by GTP binding. However, actual GTP/ATP/UTP binding modes and relevant conformational changes have not been revealed fully. Here, we report the discovery of binding modes of four nucleotides and a glutamine analog 6-diazo-5-oxo-L-norleucine in Drosophila CTPS by cryo-electron microscopy with near-atomic resolution. Interactions between GTP and surrounding residues indicate that GTP acts to coordinate reactions at both domains by directly blocking ammonia leakage and stabilizing the ammonia tunnel. Additionally, we observe the ATP-dependent UTP phosphorylation intermediate and determine interacting residues at the ammonia ligase. A noncanonical CTP binding at the ATP binding site suggests another layer of feedback inhibition. Our findings not only delineate the structure of CTPS in the presence of all substrates but also complete our understanding of the underlying mechanisms of the allosteric regulation and CTP synthesis.


  • Organizational Affiliation

    School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CTP synthase
A, B, C, D
627Drosophila melanogasterMutation(s): 0 
Gene Names: CTPsynCG45070
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
5ZL (Subject of Investigation/LOI)
Query on 5ZL

Download Ideal Coordinates CCD File 
FA [auth D],
L [auth A],
R [auth B],
Z [auth C]
[[(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
C9 H17 N2 O18 P4
RYGLMDXZXSWNKW-XVFCMESISA-O
GTP (Subject of Investigation/LOI)
Query on GTP

Download Ideal Coordinates CCD File 
AA [auth D],
E [auth A],
M [auth B],
S [auth C]
GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
ADP (Subject of Investigation/LOI)
Query on ADP

Download Ideal Coordinates CCD File 
CA [auth D],
G [auth A],
O [auth B],
U [auth C]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
DON (Subject of Investigation/LOI)
Query on DON

Download Ideal Coordinates CCD File 
BA [auth D],
F [auth A],
N [auth B],
T [auth C]
6-DIAZENYL-5-OXO-L-NORLEUCINE
C6 H11 N3 O3
CKRLZVNSTCQAJW-YFKPBYRVSA-N
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
DA [auth D]
EA [auth D]
H [auth A]
I [auth A]
J [auth A]
DA [auth D],
EA [auth D],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
P [auth B],
Q [auth B],
V [auth C],
W [auth C],
X [auth C],
Y [auth C]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.48 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


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

Revision History  (Full details and data files)

  • Version 1.0: 2021-09-15
    Type: Initial release