Crystal Structure of NOD2 (Maekawa, 2016).

Nucleotide oligomerization domain 2, or NOD2, is an intracellular receptor of the innate immune system and an apoptosis regulator. NOD2 recognizes lipopolysaccharides (LPS), include a part of the bacterial cell wall called muramyl dipeptide, and upon recognition, activates the NF-kβ and MAPK pathways, leading to an inflammatory response. NOD2 was first identified in 2001 (Ogura et al., 2001), and since then, both genetic and biochemical analyses have highlighted its role in Crohn’s disease. As was confirmed by genetic analysis, mutations in NOD2 make a host more susceptible to CD. Two Nature papers identified that mutations in the leucine-rich repeat region (LRR) of the protein increase susceptibility to CD (Hugot et al., 2001; Ogura et al., 2001). The LRR region binds bacterial lipopolysaccharides, and Crohn’s disease-associated variants of NOD2 have decreased responsiveness to LPS and thus limited NF-kβ activation.

In 2016, the crystal structure of rabbit NOD2 was solved! NOD2 contains a NOD domain, further divided into helical domains, and an LRR domain. The LRR domain has a hydrophobic pocket that could bind MDP, which is consistent with NOD2’s proposed function as an intracellular sensor of LPS. The researchers even mutated key residues in the pocket and observed that responsiveness to MDP decreased in the mutant proteins (Maekawa et al., 2016). This crystal structure can help inform future therapeutic avenues for Crohn’s disease.

After identification of NOD2 and CD-associated variants and characterization of the protein, research emerged providing more links to inflammatory diseases and NOD2. Keestra-Gounder, investigated the effects of NOD2 (and NOD1) in the unfolded protein response (UPR) and ER stress. The researchers demonstrate in mice that NOD1 and NOD2 are involved in initiating pro-inflammatory responses induced by ER stress.

Moreover, NOD2 has been shown to affect the microbiota composition in the gastrointestinal tract. Butera, conducted one such study that highlighted the defense against pathogenic bacteria NOD2 confers to mice. When NOD2-deficient mice were housed with Nod2+/+ mice, gut microbiota compositions in neighboring NOD2-deficient mice were affected and exacerbated colitis symptoms (Butera et al., 2018).

 Overall, NOD2 is the focus of many studies spanning a wide range of areas that will help further understanding of its role in Crohn’s disease.


Butera, A., Paola, M.D., Pavarini, L., Strati, F., Pindo, M., Sanchez, M., Cavalieri, D., Boirivant, M., Filippo, C.D., 2018. Nod2 Deficiency in mice is Associated with Microbiota Variation Favouring the Expansion of mucosal CD4+ LAP+ Regulatory Cells. Nature 8, 14241.

Hugot, J.-P., Chamaillard, M., Zouali, H., Lesage, S., Cézard, J.-P., Belaiche, J., Almer, S., Tysk, C., O’Morain, C.A., Gassull, M., Binder, V., Finkel, Y., Cortot, A., Modigliani, R., Laurent-Puig, P., Gower-Rousseau, C., Macry, J., Colombel, J.-F., Sahbatou, M., Thomas, G., 2001. Association of NOD2 leucine-rich repeat variants with susceptibility to Crohn’s disease. Nature 411, 599–603.

Maekawa, S., Ohto, U., Shibata, T., Miyake, K., Shimizu, T., 2016. Crystal structure of NOD2 and its implications in human disease. Nature Communications 7, 11813.

Ogura, Yasunori, Bonen, D.K., Inohara, N., Nicolae, D.L., Chen, F.F., Ramos, R., Britton, H., Moran, T., Karaliuskas, R., Duerr, R.H., Achkar, J.-P., Brant, S.R., Bayless, T.M., Kirschner, B.S., Hanauer, S.B., Nuñez, G., Cho, J.H., 2001. A frameshift mutation in NOD2 associated with susceptibility to Crohn’s disease. Nature 411, 603–606.

Ogura, Y., Inohara, N., Benito, A., Chen, F.F., Yamaoka, S., Nunez, G., 2001. Nod2, a Nod1/Apaf-1 family member that is restricted to monocytes and activates NF-kappaB. J. Biol. Chem. 276, 4812–4818.

3 thoughts on “NOD2”

  • Hi there – nice work! This project illustrates the connections between microbiome dynamics, protein biochemistry, and disease pathology – a very impressive feat! I found it interesting in the structural paper that they avoid making claims as to how ligand binding affects the structure of the protein. I also noticed that they mentioned some of the CD mutations affect membrane localization of the protein. Do you think that the interaction between NOD2 and the lipid membrane affect ligand binding? Or has any research since the structure was published filled in the holes about ligand binding and structure?

    Thank you!
    Zach Zimmerman (Biochem ’15)

    • So, NOD2 localization to the membrane has been shown to be important in initiating the NF-kB pathway, which is dysfunctional in NOD2 mutants, and NOD2 mutants show decreased responsiveness to MDP (one ligand). Regarding if NOD2-membrane association affects ligand binding, a 2017 paper by Grimes, suggests that it does! They say ” functional NOD2 exhibits a more stringent ligand
      binding specificity, only binding to compounds that are capable of activating a NOD2-dependent NF-κB response.” Functional NOD2 is NOD2 that can localize to the membrane. While Grimes, do show that membrane association is important for ligand biding, the specific mechanism behind that is still unclear. Although, I do think structural changes in NOD2 when membrane-bound is important. However, NOD2 is canonically known as an intracellular receptor, but this paper and others say membrane association is important for responding to MDP. I think more research needs to be done to fill in the mechanistic holes.

      • Cool! It will be interesting to see if any structures come out with that lipid interaction modeled in. Thank you!

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