7RFH

HUMAN RETINAL VARIANT IMPDH1(595) TREATED WITH ATP, OCTAMER-CENTERED

  • Classification: OXIDOREDUCTASE
  • Organism(s): Homo sapiens
  • Expression System: Escherichia coli BL21(DE3)
  • Mutation(s): No 

  • Deposited: 2021-07-14 Released: 2022-01-12 
  • Deposition Author(s): Burrell, A.L., Kollman, J.M.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Eye Institute (NIH/NEI)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 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

IMPDH1 retinal variants control filament architecture to tune allosteric regulation.

Burrell, A.L.Nie, C.Said, M.Simonet, J.C.Fernandez-Justel, D.Johnson, M.C.Quispe, J.Buey, R.M.Peterson, J.R.Kollman, J.M.

(2022) Nat Struct Mol Biol 

  • DOI: 10.1038/s41594-021-00706-2
  • Primary Citation of Related Structures:  
    7RER, 7RES, 7RFE, 7RFF, 7RFG, 7RFH, 7RFI, 7RGD, 7RGI, 7RGL, 7RGM, 7RGQ

  • PubMed Abstract: 
  • Inosine-5'-monophosphate dehydrogenase (IMPDH), a key regulatory enzyme in purine nucleotide biosynthesis, dynamically assembles filaments in response to changes in metabolic demand. Humans have two isoforms: IMPDH2 filaments reduce sensitivity to feedback inhibition, while IMPDH1 assembly remains uncharacterized ...

    Inosine-5'-monophosphate dehydrogenase (IMPDH), a key regulatory enzyme in purine nucleotide biosynthesis, dynamically assembles filaments in response to changes in metabolic demand. Humans have two isoforms: IMPDH2 filaments reduce sensitivity to feedback inhibition, while IMPDH1 assembly remains uncharacterized. IMPDH1 plays a unique role in retinal metabolism, and point mutants cause blindness. Here, in a series of cryogenic-electron microscopy structures we show that human IMPDH1 assembles polymorphic filaments with different assembly interfaces in extended and compressed states. Retina-specific splice variants introduce structural elements that reduce sensitivity to GTP inhibition, including stabilization of the extended filament form. Finally, we show that IMPDH1 disease mutations fall into two classes: one disrupts GTP regulation and the other has no effect on GTP regulation or filament assembly. These findings provide a foundation for understanding the role of IMPDH1 in retinal function and disease and demonstrate the diverse mechanisms by which metabolic enzyme filaments are allosterically regulated.


    Organizational Affiliation

    Department of Biochemistry, University of Washington, Seattle, WA, USA. jkoll@uw.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Isoform 5 of Inosine-5'-monophosphate dehydrogenase 1A, B, C, D, E, F, G, H595Homo sapiensMutation(s): 0 
Gene Names: IMPDH1IMPD1
EC: 1.1.1.205
UniProt & NIH Common Fund Data Resources
Find proteins for P20839 (Homo sapiens)
Explore P20839 
Go to UniProtKB:  P20839
PHAROS:  P20839
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP (Subject of Investigation/LOI)
Query on ATP

Download Ideal Coordinates CCD File 
I [auth A] , J [auth A] , K [auth B] , L [auth B] , M [auth C] , N [auth C] , O [auth D] , P [auth D] , 
I [auth A], J [auth A], K [auth B], L [auth B], M [auth C], N [auth C], O [auth D], P [auth D], Q [auth E], R [auth E], S [auth F], T [auth F], U [auth G], V [auth G], W [auth H], X [auth H]
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 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 StatesR01GM118396
National Institutes of Health/National Eye Institute (NIH/NEI)United StatesEY030732
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM008268

Revision History  (Full details and data files)

  • Version 1.0: 2022-01-12
    Type: Initial release
  • Version 1.1: 2022-01-26
    Changes: Database references