Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Ligand Interaction

Global Symmetry: Dihedral - D4  (3D View)
Global Stoichiometry: Homo 8-mer - A8 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

 3D View: Structure | 1D-3D View | Electron Density | Ligand Interaction

Global Symmetry: Dihedral - D4  (3D View)
Global Stoichiometry: Homo 8-mer - A8 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 863.63 kDa 
• Atom Count: 52946 
• Modelled Residue Count: 6842 
• Deposited Residue Count: 8064 
• Unique protein chains: 1

7PMZ

Crystal structure of Streptomyces coelicolor guaB (IMP dehydrogenase) bound to ATP and ppGpp at 2.0 A resolution

• PDB DOI: 10.2210/pdb7PMZ/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Streptomyces coelicolor A3(2)
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2021-09-04 Released: 2022-05-11 
• Deposition Author(s): Fernandez-Justel, D., Revuelta, J.L., Buey, R.M.
• Funding Organization(s): Spanish Ministry of Science, Innovation, and Universities

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.03 Å
• R-Value Free: 0.212 
• R-Value Work: 0.180 
• R-Value Observed: 0.181 

wwPDB Validation 

Currently 7PMZ does not have a validation slider image.

Literature

Diversity of mechanisms to control bacterial GTP homeostasis by the mutually exclusive binding of adenine and guanine nucleotides to IMP dehydrogenase.

Fernandez-Justel, D., Marcos-Alcalde, I., Abascal, F., Vidana, N., Gomez-Puertas, P., Jimenez, A., Revuelta, J.L., Buey, R.M.

(2022) Protein Sci 31: e4314-e4314

• PubMed: 35481629 
• DOI: 10.1002/pro.4314
• Primary Citation of Related Structures:  
  7PMZ


• PubMed Abstract: 
  

IMP dehydrogenase(IMPDH) is an essential enzyme that catalyzes the rate-limiting step in the guanine nucleotide pathway. In eukaryotic cells, GTP binding to the regulatory domain allosterically controls the activity of IMPDH by a mechanism that is fine-tuned by post-translational modifications and enzyme polymerization. Nonetheless, the mechanisms of regulation of IMPDH in bacterial cells remain unclear. Using biochemical, structural, and evolutionary analyses, we demonstrate that, in most bacterial phyla, (p)ppGpp compete with ATP to allosterically modulate IMPDH activity by binding to a, previously unrecognized, conserved high affinity pocket within the regulatory domain. This pocket was lost during the evolution of Proteobacteria, making their IMPDHs insensitive to these alarmones. Instead, most proteobacterial IMPDHs evolved to be directly modulated by the balance between ATP and GTP that compete for the same allosteric binding site. Altogether, we demonstrate that the activity of bacterial IMPDHs is allosterically modulated by a universally conserved nucleotide-controlled conformational switch that has divergently evolved to adapt to the specific particularities of each organism. These results reconcile the reported data on the crosstalk between (p)ppGpp signaling and the guanine nucleotide biosynthetic pathway and reinforce the essential role of IMPDH allosteric regulation on bacterial GTP homeostasis.

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Organizational Affiliation: 

Metabolic Engineering Group, Department of Microbiology and Genetics, Universidad de Salamanca, Salamanca, Spain.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Inosine-5'-monophosphate dehydrogenase	A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	504	Streptomyces coelicolor A3(2)	Mutation(s): 0  Gene Names: guaB, SCO4770 EC: 1.1.1.205
UniProt
Find proteins for Q9L0I7 (Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145)) Explore Q9L0I7  Go to UniProtKB:  Q9L0I7

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
G4P (Subject of Investigation/LOI)	BB [auth J], DA [auth D], FB [auth K], HA [auth E], JB [auth L], LA [auth F], NB [auth M], PA [auth G], R [auth A], RB [auth N], TA [auth H], V [auth B], VB [auth O], XA [auth I], Z [auth C], ZB [auth P]	GUANOSINE-5',3'-TETRAPHOSPHATE C10 H17 N5 O17 P4 BUFLLCUFNHESEH-UUOKFMHZSA-N
ATP (Subject of Investigation/LOI)	AB [auth J], CA [auth D], EB [auth K], GA [auth E], IB [auth L], KA [auth F], MB [auth M], OA [auth G], Q [auth A], QB [auth N], SA [auth H], U [auth B], UB [auth O], WA [auth I], Y [auth C], YB [auth P]	ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N
MG (Subject of Investigation/LOI)	AA [auth C], AC [auth P], BA [auth C], BC [auth P], CB [auth J], DB [auth J], EA [auth D], FA [auth D], GB [auth K], HB [auth K], IA [auth E], JA [auth E], KB [auth L], LB [auth L], MA [auth F], NA [auth F], OB [auth M], PB [auth M], QA [auth G], RA [auth G], S [auth A], SB [auth N], T [auth A], TB [auth N], UA [auth H], VA [auth H], W [auth B], WB [auth O], X [auth B], XB [auth O], YA [auth I], ZA [auth I]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.03 Å
• R-Value Free: 0.212 
• R-Value Work: 0.180 
• R-Value Observed: 0.181 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 119.294	α = 90
b = 300.896	β = 90.28
c = 123.093	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
autoPROC	data reduction
autoPROC	data scaling
PHASER	phasing

Structure Validation

Currently 7PMZ does not have a validation slider image.

Entry History & Funding Information

Deposition Data

• Deposited Date: 2021-09-04 
• Released Date: 2022-05-11 
Deposition Author(s): Fernandez-Justel, D., Revuelta, J.L., Buey, R.M.

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Funding Organization	Location	Grant Number
Spanish Ministry of Science, Innovation, and Universities	Spain	PID2019-109671GB-I00

Revision History  

• Version 1.0: 2022-05-11
  Type: Initial release