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

Validation slider image for 9IZ1

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 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.

Macromolecule Content 

  • Total Structure Weight: 256.79 kDa 
  • Atom Count: 17,948 
  • Modeled Residue Count: 2,224 
  • Deposited Residue Count: 2,224 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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
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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