6U9O

Human IMPDH2 treated with ATP, IMP, NAD+, and 2 mM GTP. Fully compressed filament segment reconstruction.


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.36 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Cryo-EM structures demonstrate human IMPDH2 filament assembly tunes allosteric regulation.

Johnson, M.C.Kollman, J.M.

(2020) Elife 9

  • DOI: 10.7554/eLife.53243
  • Primary Citation of Related Structures:  
    6U8R, 6U8S, 6U8N, 6U8E, 6U9O, 6UA2, 6UA5, 6UA4, 6UAJ, 6UC2

  • PubMed Abstract: 
  • Inosine monophosphate dehydrogenase (IMPDH) mediates the first committed step in guanine nucleotide biosynthesis and plays important roles in cellular proliferation and the immune response. IMPDH reversibly polymerizes in cells and tissues in response to changes in metabolic demand ...

    Inosine monophosphate dehydrogenase (IMPDH) mediates the first committed step in guanine nucleotide biosynthesis and plays important roles in cellular proliferation and the immune response. IMPDH reversibly polymerizes in cells and tissues in response to changes in metabolic demand. Self-assembly of metabolic enzymes is increasingly recognized as a general mechanism for regulating activity, typically by stabilizing specific conformations of an enzyme, but the regulatory role of IMPDH filaments has remained unclear. Here, we report a series of human IMPDH2 cryo-EM structures in both active and inactive conformations. The structures define the mechanism of filament assembly, and reveal how filament-dependent allosteric regulation of IMPDH2 makes the enzyme less sensitive to feedback inhibition, explaining why assembly occurs under physiological conditions that require expansion of guanine nucleotide pools. Tuning sensitivity to an allosteric inhibitor distinguishes IMPDH from other metabolic filaments, and highlights the diversity of regulatory outcomes that can emerge from self-assembly.


    Organizational Affiliation

    Department of Biochemistry, University of Washington, Seattle, United States.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Inosine-5'-monophosphate dehydrogenase 2519Homo sapiensMutation(s): 0 
Gene Names: IMPDH2IMPD2
EC: 1.1.1.205
UniProt & NIH Common Fund Data Resources
Find proteins for P12268 (Homo sapiens)
Explore P12268 
Go to UniProtKB:  P12268
PHAROS:  P12268
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAD
Query on NAD

Download Ideal Coordinates CCD File 
DB [auth H], EA [auth C], JA [auth D], OA [auth E], TA [auth F], U [auth A], YA [auth G], Z [auth B]NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
 Ligand Interaction
GTP
Query on GTP

Download Ideal Coordinates CCD File 
AA [auth C] , AB [auth H] , BA [auth C] , FA [auth D] , GA [auth D] , KA [auth E] , LA [auth E] , PA [auth F] , 
AA [auth C],  AB [auth H],  BA [auth C],  FA [auth D],  GA [auth D],  KA [auth E],  LA [auth E],  PA [auth F],  Q [auth A],  QA [auth F],  R [auth A],  UA [auth G],  V [auth B],  VA [auth G],  W [auth B],  ZA [auth H]
GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
 Ligand Interaction
ATP
Query on ATP

Download Ideal Coordinates CCD File 
BB [auth H], CA [auth C], HA [auth D], MA [auth E], RA [auth F], S [auth A], WA [auth G], X [auth B]ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
IMP
Query on IMP

Download Ideal Coordinates CCD File 
CB [auth H], DA [auth C], IA [auth D], NA [auth E], SA [auth F], T [auth A], XA [auth G], Y [auth B]INOSINIC ACID
C10 H13 N4 O8 P
GRSZFWQUAKGDAV-KQYNXXCUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.36 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: SINGLE PARTICLE 

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 States5R01GM118396-04

Revision History  (Full details and data files)

  • Version 1.0: 2020-03-25
    Type: Initial release