9IZ1 | pdb_00009iz1

dmCTPS tetramer with dATP dUTP dGTP and DON


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.73 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 of Bifunctional CTP/dCTP Synthase.

Guo, C.J.Zhang, Z.Lu, J.L.Zhong, J.Wu, Y.F.Guo, S.Y.Liu, J.L.

(2024) J Mol Biology 436: 168750-168750

  • DOI: https://doi.org/10.1016/j.jmb.2024.168750
  • Primary Citation of Related Structures:  
    9IZ1, 9IZ2

  • PubMed 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 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.


  • 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
556Drosophila 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 
BA [auth C],
JA [auth D],
K [auth A],
T [auth B]
[[(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
DGT (Subject of Investigation/LOI)
Query on DGT

Download Ideal Coordinates CCD File 
AA [auth C],
IA [auth D],
J [auth A],
S [auth B]
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 
HA [auth D],
I [auth A],
R [auth B],
Z [auth C]
2'-DEOXYADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O9 P2
DAEAPNUQQAICNR-RRKCRQDMSA-N
DON (Subject of Investigation/LOI)
Query on DON

Download Ideal Coordinates CCD File 
DA [auth D],
E [auth A],
N [auth B],
U [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 
CA [auth C]
EA [auth D]
F [auth A]
FA [auth D]
G [auth A]
CA [auth C],
EA [auth D],
F [auth A],
FA [auth D],
G [auth A],
GA [auth D],
H [auth A],
L [auth A],
M [auth B],
O [auth B],
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: 2.73 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: 2024-11-27
    Type: Initial release