7RTC

Crystal structure of the ARM domain from Drosophila SARM1 in complex with NaMN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.31 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.239 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Nicotinic acid mononucleotide is an allosteric SARM1 inhibitor promoting axonal protection.

Sasaki, Y.Zhu, J.Shi, Y.Gu, W.Kobe, B.Ve, T.DiAntonio, A.Milbrandt, J.

(2021) Exp Neurol 345: 113842-113842

  • DOI: https://doi.org/10.1016/j.expneurol.2021.113842
  • Primary Citation of Related Structures:  
    7RTC

  • PubMed Abstract: 

    SARM1 is an inducible NAD + hydrolase that is the central executioner of pathological axon loss. Recently, we elucidated the molecular mechanism of SARM1 activation, demonstrating that SARM1 is a metabolic sensor regulated by the levels of NAD + and its precursor, nicotinamide mononucleotide (NMN), via their competitive binding to an allosteric site within the SARM1 N-terminal ARM domain. In healthy neurons with abundant NAD + , binding of NAD + blocks access of NMN to this allosteric site. However, with injury or disease the levels of the NAD + biosynthetic enzyme NMNAT2 drop, increasing the NMN/ NAD + ratio and thereby promoting NMN binding to the SARM1 allosteric site, which in turn induces a conformational change activating the SARM1 NAD + hydrolase. Hence, NAD + metabolites both regulate the activation of SARM1 and, in turn, are regulated by the SARM1 NAD + hydrolase. This dual upstream and downstream role for NAD + metabolites in SARM1 function has hindered mechanistic understanding of axoprotective mechanisms that manipulate the NAD + metabolome. Here we reevaluate two methods that potently block axon degeneration via modulation of NAD + related metabolites, 1) the administration of the NMN biosynthesis inhibitor FK866 in conjunction with the NAD + precursor nicotinic acid riboside (NaR) and 2) the neuronal expression of the bacterial enzyme NMN deamidase. We find that these approaches not only lead to a decrease in the levels of the SARM1 activator NMN, but also an increase in the levels of the NAD + precursor nicotinic acid mononucleotide (NaMN). We show that NaMN inhibits SARM1 activation, and demonstrate that this NaMN-mediated inhibition is important for the long-term axon protection induced by these treatments. Analysis of the NaMN-ARM domain co-crystal structure shows that NaMN competes with NMN for binding to the SARM1 allosteric site and promotes the open, autoinhibited configuration of SARM1 ARM domain. Together, these results demonstrate that the SARM1 allosteric pocket can bind a diverse set of metabolites including NMN, NAD + , and NaMN to monitor cellular NAD + homeostasis and regulate SARM1 NAD + hydrolase activity. The relative promiscuity of the allosteric site may enable the development of potent pharmacological inhibitors of SARM1 activation for the treatment of neurodegenerative disorders.


  • Organizational Affiliation

    Washington University School of Medicine in Saint Louis, Department of Genetics, St. Louis, MO, USA; Needleman Center for Neurometabolism and Axonal Therapeutics, USA. Electronic address: sasaki@wustl.edu.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NAD(+) hydrolase sarm1
A, B, C
364Drosophila melanogasterMutation(s): 0 
Gene Names: SarmEct4CG43119
EC: 3.2.2.6
UniProt
Find proteins for Q6IDD9 (Drosophila melanogaster)
Explore Q6IDD9 
Go to UniProtKB:  Q6IDD9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6IDD9
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.31 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.239 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.122α = 90
b = 102.823β = 103.836
c = 100.198γ = 90
Software Package:
Software NamePurpose
autoPROCdata processing
PHASERphasing
PHENIXrefinement

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Health and Medical Research Council (NHMRC, Australia)Australia1107804
National Health and Medical Research Council (NHMRC, Australia)Australia1160570
National Health and Medical Research Council (NHMRC, Australia)Australia1071659
National Health and Medical Research Council (NHMRC, Australia)Australia1196590
Australian Research Council (ARC)AustraliaFL180100109
Australian Research Council (ARC)AustraliaFT200100572

Revision History  (Full details and data files)

  • Version 1.0: 2021-09-01
    Type: Initial release
  • Version 1.1: 2023-10-18
    Changes: Data collection, Refinement description