8UV4 | pdb_00008uv4

M. tuberculosis CTP synthase filament bound to substrates


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Evolutionarily divergent Mycobacterium tuberculosis CTP synthase filaments are under selective pressure.

Lynch, E.M.Lu, Y.Park, J.H.Shao, L.Kollman, J.M.Rego, E.H.

(2025) Nat Commun 16: 5993-5993

  • DOI: https://doi.org/10.1038/s41467-025-60847-6
  • Primary Citation of Related Structures:  
    8UV4, 8UV8, 8UV9, 8UVA

  • PubMed Abstract: 

    The final and rate-limiting enzyme in pyrimidine biosynthesis, cytidine triphosphate synthase (CTPS), is essential for the viability of Mycobacterium tuberculosis and other mycobacteria. Its product, cytidine triphosphate (CTP), is critical for RNA, DNA, lipid and cell wall synthesis, and is involved in chromosome segregation. In various organisms across the tree of life, CTPS assembles into higher-order filaments, leading us to hypothesize that M. tuberculosis CTPS (mtCTPS) also forms higher-order structures. Here, we show that mtCTPS does assemble into filaments but with an unusual architecture not seen in other organisms. Through a combination of structural, biochemical, and cellular techniques, we show that polymerization stabilizes the active conformation of the enzyme and resists product inhibition, potentially allowing for the highly localized production of CTP within the cell. Indeed, CTPS filaments localize near the CTP-dependent complex needed for chromosome segregation, and cells expressing mutant enzymes unable to polymerize are altered in their ability to robustly form this complex. Intriguingly, mutants that inhibit filament formation are under positive selection in clinical isolates of M. tuberculosis, pointing to a critical role needed to withstand pressures imposed by the host and/or antibiotics. Taken together, our data reveal an unexpected mechanism for the spatially organized production of a critical nucleotide in M. tuberculosis, which may represent a vulnerability of the pathogen that can be exploited with chemotherapy.


  • Organizational Affiliation
    • Department of Biochemistry, University of Washington, Seattle, WA, USA.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CTP synthase592Mycobacterium tuberculosisMutation(s): 0 
Gene Names: pyrG
EC: 6.3.4.2
UniProt
Find proteins for P9WHK7 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WHK7 
Go to UniProtKB:  P9WHK7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WHK7
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
5ZL (Subject of Investigation/LOI)
Query on 5ZL

Download Ideal Coordinates CCD File 
AA [auth b]
CB [auth H]
DA [auth A]
GB [auth L]
HA [auth E]
AA [auth b],
CB [auth H],
DA [auth A],
GB [auth L],
HA [auth E],
LA [auth G],
N [auth R],
PA [auth K],
S [auth V],
TA [auth B],
X,
XA [auth F]
[[(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
ADP (Subject of Investigation/LOI)
Query on ADP

Download Ideal Coordinates CCD File 
BB [auth H]
CA [auth A]
FB [auth L]
GA [auth E]
KA [auth G]
BB [auth H],
CA [auth A],
FB [auth L],
GA [auth E],
KA [auth G],
M [auth R],
OA [auth K],
R [auth V],
SA [auth B],
W [auth X],
WA [auth F],
Z [auth b]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
AB [auth H]
BA [auth b]
DB [auth H]
EA [auth A]
EB [auth L]
AB [auth H],
BA [auth b],
DB [auth H],
EA [auth A],
EB [auth L],
FA [auth A],
HB [auth L],
IA [auth E],
JA [auth E],
MA [auth G],
NA [auth G],
O [auth R],
P [auth R],
Q [auth R],
QA [auth K],
RA [auth K],
T [auth V],
U [auth V],
UA [auth B],
V,
VA [auth B],
Y [auth X],
YA [auth F],
ZA [auth F]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTISOLDE
MODEL REFINEMENTPHENIX

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)United StatesR35 GM149542

Revision History  (Full details and data files)

  • Version 1.0: 2025-07-02
    Type: Initial release
  • Version 1.1: 2026-01-14
    Changes: Data collection, Database references