7PMZ

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


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.


This is version 1.0 of the entry. See complete history


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

  • 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 ...

    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.


    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Inosine-5'-monophosphate dehydrogenase
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
504Streptomyces coelicolor A3(2)Mutation(s): 0 
Gene Names: guaBSCO4770
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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9L0I7
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
G4P (Subject of Investigation/LOI)
Query on G4P

Download Ideal Coordinates CCD File 
BB [auth J],
DA [auth D],
FB [auth K],
HA [auth E],
JB [auth L],
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
 Ligand Interaction
ATP (Subject of Investigation/LOI)
Query on ATP

Download Ideal Coordinates CCD File 
AB [auth J],
CA [auth D],
EB [auth K],
GA [auth E],
IB [auth L],
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
 Ligand Interaction
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
AA [auth C],
AC [auth P],
BA [auth C],
BC [auth P],
CB [auth J],
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
 Ligand Interaction
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 = 119.294α = 90
b = 300.896β = 90.28
c = 123.093γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing

Structure Validation

Currently 7PMZ does not have a validation slider image.




Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Spanish Ministry of Science, Innovation, and UniversitiesSpainPID2019-109671GB-I00

Revision History  (Full details and data files)

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