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1.  Interaction between NOD2 and CARD9 involves the NOD2 NACHT and the linker region between the NOD2 CARDs and NACHT domain 
Febs Letters  2014;588(17):2830-2836.
Highlights
•We have studied the interaction between NOD2 and CARD9.•The NACHT domain and CARD–NACHT linker of NOD2 are crucial for the interaction.•The CARD domains of NOD2 and CARD9 do not directly interact.
NOD2 activation by muramyl dipeptide causes a proinflammatory immune response in which the adaptor protein CARD9 works synergistically with NOD2 to drive p38 and c-Jun N-terminal kinase (JNK) signalling. To date the nature of the interaction between NOD2 and CARD9 remains undetermined. Here we show that this interaction is not mediated by the CARDs of NOD2 and CARD9 as previously suggested, but that NOD2 possesses two interaction sites for CARD9; one in the CARD–NACHT linker and one in the NACHT itself.
Structured summary of protein interactions
NOD2 physically interacts with CARD9 by anti tag coimmunoprecipitation (View interaction)
doi:10.1016/j.febslet.2014.06.035
PMCID: PMC4158416  PMID: 24960071
NOD, nucleotide oligomerisation domain; NLR, nucleotide-binding leucine-rich repeat containing receptor; NF-κB, nuclear factor kappa B; CARD, caspase activation and recruitment domain; RIP2, receptor interacting protein 2; SNP, single nucleotide polymorphism; MBP, maltose binding protein; Nucleotide-binding leucine-rich repeat containing receptor; Crohn’s Disease; Caspase activation and recruitment domain; Stress kinase pathway; Innate immunity; Signal transduction
2.  Structural basis for ligase-specific conjugation of linear ubiquitin chains by HOIP 
Nature  2013;503(7476):422-426.
Linear ubiquitin chains are important regulators of cellular signaling pathways that control innate immunity and inflammation through NF-κB activation and protection against TNFα-induced apoptosis1-5. They are synthesized by HOIP, which belongs to the RBR (RING-between-RING) family of E3 ligases and is the catalytic component of LUBAC (linear ubiquitin chain assembly complex), a multi-subunit E3 ligase6. RBR family members act as RING/HECT hybrids, employing RING1 to recognize ubiquitin-loaded E2 while a conserved cysteine in RING2 subsequently forms a thioester intermediate with the transferred or “donor” ubiquitin7. Here we report the crystal structure of the catalytic core of HOIP in its apo form and in complex with ubiquitin. The C-terminal portion of HOIP adopts a novel fold that, together with a zinc finger, forms an ubiquitin-binding platform which orients the acceptor ubiquitin and positions its α-amino group for nucleophilic attack on the E3~ubiquitin thioester. The carboxy-terminal tail of a second ubiquitin molecule is located in close proximity to the catalytic cysteine providing a unique snapshot of the ubiquitin transfer complex containing both donor and acceptor ubiquitin. These interactions are required for activation of the NF-kB pathway in vivo and explain the determinants of linear ubiquitin chain specificity by LUBAC.
doi:10.1038/nature12638
PMCID: PMC3838313  PMID: 24141947
E3 ubiquitin ligase; linear ubiquitin chains; structure; mechanism; ubiquitination
3.  Mechanism and function of Vav1 localisation in TCR signalling 
Journal of Cell Science  2012;125(22):5302-5314.
Summary
The antigen-specific binding of T cells to antigen presenting cells results in recruitment of signalling proteins to microclusters at the cell-cell interface known as the immunological synapse (IS). The Vav1 guanine nucleotide exchange factor plays a critical role in T cell antigen receptor (TCR) signalling, leading to the activation of multiple pathways. We now show that it is recruited to microclusters and to the IS in primary CD4+ and CD8+ T cells. Furthermore, we show that this recruitment depends on the SH2 and C-terminal SH3 (SH3B) domains of Vav1, and on phosphotyrosines 112 and 128 of the SLP76 adaptor protein. Biophysical measurements show that Vav1 binds directly to these residues on SLP76 and that efficient binding depends on the SH2 and SH3B domains of Vav1. Finally, we show that the same two domains are critical for the phosphorylation of Vav1 and its signalling function in TCR-induced calcium flux. We propose that Vav1 is recruited to the IS by binding to SLP76 and that this interaction is critical for the transduction of signals leading to calcium flux.
doi:10.1242/jcs.105148
PMCID: PMC3561853  PMID: 22956543
Immunological synapse; T cell; Signal transduction; SLP76; Vav1
4.  Function of the Nucleotide Exchange Activity of Vav1 in T cell Development and Activation* 
Science signaling  2009;2(101):ra83.
The guanine nucleotide exchange factor (GEF) Vav1 is essential for transducing T cell antigen receptor (TCR) signals and therefore plays a critical role in the development and activation of T cells. It has been presumed that the GEF activity of Vav1 is important for its function; however, there has been no direct demonstration of this. Here, we generated mice expressing enzymatically inactive, but normally folded, Vav1 protein. Analysis of these mice showed that the GEF activity of Vav1 was necessary for the selection of thymocytes and for the optimal activation of T cells, including signal transduction to Rac1, Akt, and integrins. In contrast, the GEF activity of Vav1 was not required for TCR-induced calcium flux, activation of extracellular signal–regulated kinase (ERK) and protein kinase D1 (PKD1), and cell polarization. Thus, in T cells, the GEF activity of Vav1 is essential for some, but not all, of its functions.
doi:10.1126/scisignal.2000420
PMCID: PMC3434450  PMID: 20009105
5.  LUBAC synthesizes linear ubiquitin chains via a thioester intermediate 
EMBO Reports  2012;13(9):840-846.
LUBAC synthesizes linear ubiquitin chains via a thioester intermediate
The N-terminus of the LUBAC catalytic subunit is shown to be autoinhibitory and counteracted by the other subunits of the complex. Linear ubiquitination proceeds through a thioesther intermediate, indicative of a RING/HECT hybrid mechanism.
The linear ubiquitin chain assembly complex (LUBAC) is a RING E3 ligase that regulates immune and inflammatory signalling pathways. Unlike classical RING E3 ligases, LUBAC determines the type of ubiquitin chain being formed, an activity normally associated with the E2 enzyme. We show that the RING-in-between-RING (RBR)-containing region of HOIP—the catalytic subunit of LUBAC—is sufficient to generate linear ubiquitin chains. However, this activity is inhibited by the N-terminal portion of the molecule, an inhibition that is released upon complex formation with HOIL-1L or SHARPIN. Furthermore, we demonstrate that HOIP transfers ubiquitin to the substrate through a thioester intermediate formed by a conserved cysteine in the RING2 domain, supporting the notion that RBR ligases act as RING/HECT hybrids.
doi:10.1038/embor.2012.105
PMCID: PMC3432797  PMID: 22791023
E3 ligase; mechanism; thioester; ubiquitination
6.  Crystallization of SHARPIN using an automated two-dimensional grid screen for optimization 
The expression, purification and crystallization of an N-terminal fragment of SHARPIN are reported. Diffraction-quality crystals were obtained using a two-dimensional grid-screen seeding technique.
An N-terminal fragment of human SHARPIN was recombinantly expressed in Escherichia coli, purified and crystallized. Crystals suitable for X-ray diffraction were obtained by a one-step optimization of seed dilution and protein concentration using a two-dimensional grid screen. The crystals belonged to the primitive tetragonal space group P43212, with unit-cell parameters a = b = 61.55, c = 222.81 Å. Complete data sets were collected from native and selenomethionine-substituted protein crystals at 100 K to 2.6 and 2.0 Å resolution, respectively.
doi:10.1107/S1744309112022208
PMCID: PMC3388930  PMID: 22750873
SHARPIN; seeding
7.  Structural Analysis of SHARPIN, a Subunit of a Large Multi-protein E3 Ubiquitin Ligase, Reveals a Novel Dimerization Function for the Pleckstrin Homology Superfold* 
The Journal of Biological Chemistry  2012;287(25):20823-20829.
Background: SHARPIN is a subunit of the E3 ligase complex LUBAC and the gene that is mutated in chronic proliferative dermatitis mice.
Results: The N-terminal portion of SHARPIN adopts the PH superfold and mediates homodimerization.
Conclusion: The PH superfold can be used as a protein dimerization module.
Significance: This study highlights the versatility of the PH superfold and its function as a protein interaction module.
SHARPIN (SHANK-associated RH domain interacting protein) is part of a large multi-protein E3 ubiquitin ligase complex called LUBAC (linear ubiquitin chain assembly complex), which catalyzes the formation of linear ubiquitin chains and regulates immune and apoptopic signaling pathways. The C-terminal half of SHARPIN contains ubiquitin-like domain and Npl4-zinc finger domains that mediate the interaction with the LUBAC subunit HOIP and ubiquitin, respectively. In contrast, the N-terminal region does not show any homology with known protein interaction domains but has been suggested to be responsible for self-association of SHARPIN, presumably via a coiled-coil region. We have determined the crystal structure of the N-terminal portion of SHARPIN, which adopts the highly conserved pleckstrin homology superfold that is often used as a scaffold to create protein interaction modules. We show that in SHARPIN, this domain does not appear to be used as a ligand recognition domain because it lacks many of the surface properties that are present in other pleckstrin homology fold-based interaction modules. Instead, it acts as a dimerization module extending the functional applications of this superfold.
doi:10.1074/jbc.M112.359547
PMCID: PMC3375506  PMID: 22549881
Protein Structure; Protein-Protein Interactions; Signal Transduction; Ubiquitin Ligase; Ubiquitination; X-ray Crystallography
8.  SHARPIN forms a linear ubiquitin ligase complex regulating NF-κB activity and apoptosis 
Nature  2011;471(7340):637-641.
SHARPIN is a ubiquitin-binding and ubiquitin-like domain-containing protein which, when mutated in mice, results in immune system disorders and multiorgan inflammation1,2. Here we report that SHARPIN functions as a novel component of the Linear Ubiquitin Chain Assembly Complex (LUBAC) and that the absence of SHARPIN causes disregulation of NF-κB and apoptotic signalling pathways, explaining the severe phenotypes displayed by chronic proliferative dermatitis in SHARPIN deficient mice. Upon binding to the LUBAC subunit HOIP, SHARPIN stimulates the formation of linear ubiquitin chains in vitro and in vivo. Co-expression of SHARPIN and HOIP promotes linear ubiquitylation of NEMO, an adaptor of the IκB kinases (IKKs) and subsequent activation of NF-κB signalling, while SHARPIN deficiency in mice causes an impaired activation of the IKK complex and NF-κB in B cells, macrophages, and mouse embryonic fibroblasts (MEFs). This effect is further enhanced upon concurrent downregulation of HOIL-1L, another HOIP-binding component of LUBAC. In addition, SHARPIN deficiency leads to rapid cell death upon TNFα stimulation via FADD- and Caspase-8-dependent pathways. SHARPIN thus activates NF-κB and inhibits apoptosis via distinct pathways in vivo.
doi:10.1038/nature09814
PMCID: PMC3085511  PMID: 21455181
9.  The Tandem CARDs of NOD2: Intramolecular Interactions and Recognition of RIP2 
PLoS ONE  2012;7(3):e34375.
Caspase recruitment domains (CARDs) are homotypic protein interaction modules that link the stimulus-dependent assembly of large signaling platforms such as inflammasomes to the activation of downstream effectors that often include caspases and kinases and thereby play an important role in the regulation of inflammatory and apoptotic signaling pathways. NOD2 belongs to the NOD-like (NLR) family of intracellular pattern recognition receptors (PRR) and induces activation of the NF-κB pathway in response to the recognition of bacterial components. This process requires the specific recognition of the CARD of the protein kinase RIP2 by the tandem CARDs of NOD2. Here we demonstrate that the tandem CARDs of NOD2 are engaged in an intramolecular interaction that is important for the structural stability of this region. Using a combination of ITC and pull-down experiments we identify distinct surface areas that are involved in the intramolecular tandem CARD interaction and the interaction with the downstream effector RIP2. Our findings indicate that while CARDa of NOD2 might be the primary binding partner of RIP2 the two CARDs of NOD2 do not act independently of one another but may cooperate to from a binding surface that is distinct from that of single CARDs.
doi:10.1371/journal.pone.0034375
PMCID: PMC3314614  PMID: 22470564
10.  Regulation of NOXO1 Activity through Reversible Interactions with p22phox and NOXA1 
PLoS ONE  2010;5(5):e10478.
Reactive oxygen species (ROS) have been known for a long time to play important roles in host defense against microbial infections. In addition, it has become apparent that they also perform regulatory roles in signal transduction and cell proliferation. The source of these chemicals are members of the NOX family of NADPH oxidases that are found in a variety of tissues. NOX1, an NADPH oxidase homologue that is most abundantly expressed in colon epithelial cells, requires the regulatory subunits NOXO1 (NOX organizing protein 1) and NOXA1 (NOX activating protein 1), as well as the flavocytochrome component p22phox for maximal activity. Unlike NOX2, the phagocytic NADPH oxidase whose activity is tightly repressed in the resting state, NOX1 produces superoxide constitutively at low levels. These levels can be further increased in a stimulus-dependent manner, yet the molecular details regulating this activity are not fully understood. Here we present the first quantitative characterization of the interactions made between the cytosolic regulators NOXO1 and NOXA1 and membrane-bound p22phox. Using isothermal titration calorimetry we show that the isolated tandem SH3 domains of NOXO1 bind to p22phox with high affinity, most likely adopting a superSH3 domain conformation. In contrast, complex formation is severely inhibited in the presence of the C-terminal tail of NOXO1, suggesting that this region competes for binding to p22phox and thereby contributes to the regulation of superoxide production. Furthermore, we provide data indicating that the molecular details of the interaction between NOXO1 and NOXA1 is significantly different from that between the homologous proteins of the phagocytic oxidase, suggesting that there are important functional differences between the two systems. Taken together, this study provides clear evidence that the assembly of the NOX1 oxidase complex can be regulated through reversible protein-protein interactions.
doi:10.1371/journal.pone.0010478
PMCID: PMC2864300  PMID: 20454568
11.  NEMO oligomerization and its ubiquitin-binding properties 
Biochemical Journal  2009;421(Pt 2):243-251.
The IKK [IκB (inhibitory κB) kinase] complex is a key regulatory component of NF-κB (nuclear factor κB) activation and is responsible for mediating the degradation of IκB, thereby allowing nuclear translocation of NF-κB and transcription of target genes. NEMO (NF-κB essential modulator), the regulatory subunit of the IKK complex, plays a pivotal role in this process by integrating upstream signals, in particular the recognition of polyubiquitin chains, and relaying these to the activation of IKKα and IKKβ, the catalytic subunits of the IKK complex. The oligomeric state of NEMO is controversial and the mechanism by which it regulates activation of the IKK complex is poorly understood. Using a combination of hydrodynamic techniques we now show that apo-NEMO is a highly elongated, dimeric protein that is in weak equilibrium with a tetrameric assembly. Interaction with peptides derived from IKKβ disrupts formation of the tetrameric NEMO complex, indicating that interaction with IKKα and IKKβ and tetramerization are mutually exclusive. Furthermore, we show that NEMO binds to linear di-ubiquitin with a stoichiometry of one molecule of di-ubiquitin per NEMO dimer. This stoichiometry is preserved in a construct comprising the second coiled-coil region and the leucine zipper and in one that essentially spans the full-length protein. However, our data show that at high di-ubiquitin concentrations a second weaker binding site becomes apparent, implying that two different NEMO–di-ubiquitin complexes are formed during the IKK activation process. We propose that the role of these two complexes is to provide a threshold for activation, thereby ensuring sufficient specificity during NF-κB signalling.
doi:10.1042/BJ20090427
PMCID: PMC2708934  PMID: 19422324
analytical ultracentrifugation (AUC); IKK (inhibitory κB kinase) complex; isothermal titration calorimetry (ITC); multi-angle light scattering (MALS); protein–protein interaction; ubiquitin; AUC, analytical ultracentrifugation; CoZi, C-terminal portion of NEMO encompassing the second coiled-coil region and the leucine zipper domain; IκB, inhibitory κB; IKK, IκB kinase; IKKNBD, IKKβ NEMO-binding domain; ITC, isothermal titration calorimetry; LZ, leucine zipper; MALS, multi-angle laser light scattering; NF-κB, nuclear factor κB; NEMO, NF-κB essential modulator; NEMO355, NEMO residues 1–355, with mutations C54S and K285N; SEC, size-exclusion chromatography; TCEP, tris-(2-carboxyethyl)phosphine; RI, refractive index; RIP1, receptor interaction protein kinase; vFLIP, viral FLICE [FADD (Fas-associated death domain)-like interleukin 1β-converting enzyme]-inhibitory protein; ZF, zinc finger
12.  Crucial structural role for the PH and C1 domains of the Vav1 exchange factor 
EMBO Reports  2008;9(7):655-661.
The Vav family of proteins are guanine nucleotide exchange factors (GEFs) for the Rho family of GTPases, which regulate various cellular functions, including T-cell activation. They contain a catalytic Dbl homology (DH) domain that is invariably followed by a pleckstrin homology (PH) domain, which is often required for catalytic activity. Vav proteins are the first GEFs for which an additional C1 domain is required for full biological activity. Here, we present the structure of a Vav1 fragment comprising the DH–PH–C1 domains bound to Rac1. This structure shows that the PH and C1 domains form a single structural unit that packs against the carboxy-terminal helix of the DH domain to stabilize its conformation and to promote nucleotide exchange. In contrast to previous reports, this structure shows that there are no direct contacts between the GTPase and C1 domain but instead suggests new mechanisms for the regulation of Vav1 activity.
doi:10.1038/embor.2008.80
PMCID: PMC2427238  PMID: 18511940
C1 domain; exchange factor; GTPase; Vav1; X-ray crystallography

Results 1-12 (12)