8QQP

Mycobacterium smegmatis inosine monophosphate dehydrogenase (IMPDH) ATP+GTP-bound form, super-compressed


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.35 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Deciphering the allosteric regulation of mycobacterial inosine-5'-monophosphate dehydrogenase.

Bulvas, O.Knejzlik, Z.Sys, J.Filimonenko, A.Cizkova, M.Clarova, K.Rejman, D.Kouba, T.Pichova, I.

(2024) Nat Commun 15: 6673-6673

  • DOI: https://doi.org/10.1038/s41467-024-50933-6
  • Primary Citation of Related Structures:  
    8PW3, 8Q65, 8QQP, 8QQQ, 8QQR, 8QQT, 8QQV, 8QQW, 8QQX

  • PubMed Abstract: 

    Allosteric regulation of inosine 5'-monophosphate dehydrogenase (IMPDH), an essential enzyme of purine metabolism, contributes to the homeostasis of adenine and guanine nucleotides. However, the precise molecular mechanism of IMPDH regulation in bacteria remains unclear. Using biochemical and cryo-EM approaches, we reveal the intricate molecular mechanism of the IMPDH allosteric regulation in mycobacteria. The enzyme is inhibited by both GTP and (p)ppGpp, which bind to the regulatory CBS domains and, via interactions with basic residues in hinge regions, lock the catalytic core domains in a compressed conformation. This results in occlusion of inosine monophosphate (IMP) substrate binding to the active site and, ultimately, inhibition of the enzyme. The GTP and (p)ppGpp allosteric effectors bind to their dedicated sites but stabilize the compressed octamer by a common mechanism. Inhibition is relieved by the competitive displacement of GTP or (p)ppGpp by ATP allowing IMP-induced enzyme expansion. The structural knowledge and mechanistic understanding presented here open up new possibilities for the development of allosteric inhibitors with antibacterial potential.


  • Organizational Affiliation

    Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Inosine-5'-monophosphate dehydrogenase
A, B, C, D, E
A, B, C, D, E, F, G, H
513Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: guaBMSMEG_1602
EC: 1.1.1.205
UniProt
Find proteins for A0QSU3 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Explore A0QSU3 
Go to UniProtKB:  A0QSU3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0QSU3
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GTP (Subject of Investigation/LOI)
Query on GTP

Download Ideal Coordinates CCD File 
DA [auth F]
HA [auth G]
J [auth A]
LA [auth H]
N [auth B]
DA [auth F],
HA [auth G],
J [auth A],
LA [auth H],
N [auth B],
R [auth C],
V [auth D],
Z [auth E]
GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
ATP (Subject of Investigation/LOI)
Query on ATP

Download Ideal Coordinates CCD File 
CA [auth F]
GA [auth G]
I [auth A]
KA [auth H]
M [auth B]
CA [auth F],
GA [auth G],
I [auth A],
KA [auth H],
M [auth B],
Q [auth C],
U [auth D],
Y [auth E]
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
AA [auth E]
BA [auth E]
EA [auth F]
FA [auth F]
IA [auth G]
AA [auth E],
BA [auth E],
EA [auth F],
FA [auth F],
IA [auth G],
JA [auth G],
K [auth A],
L [auth A],
MA [auth H],
NA [auth H],
O [auth B],
P [auth B],
S [auth C],
T [auth C],
W [auth D],
X [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.35 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1
MODEL REFINEMENTCoot0.9.8 EL
MODEL REFINEMENTISOLDE1.4

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Union (EU)European UnionLX22NPO5103

Revision History  (Full details and data files)

  • Version 1.0: 2024-08-14
    Type: Initial release
  • Version 1.1: 2024-08-21
    Changes: Data collection, Database references