Structure of the Semaphorin-3A Receptor Binding Module

Antipenko, Alexander; Himanen, Juha P.; Leyen, Klaus van; Nardi‐Dei, Vincenzo; Lesniak, Jacob; Barton, William A.; Rajashankar, Kanagalaghatta R.; Lu, Min; Hoemme, Claudia; Püschel, Andreas W.; Nikolov, Dimitar B.

doi:10.1016/s0896-6273(03)00502-6

Cited by 151 publications

(175 citation statements)

References 35 publications

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“…Second, we found that Sema3A triggered NRP1 oligomerization because NRP1 was redistributed in heavy fractions of the gradients upon ligand binding. Although calculated sedimentation constants are approximate because only partial crystal structure of the protein has been resolved (Antipenko et al, 2003), oligomerization is evident from our results and may possibly be underestimated. This further supports the conclusion that both MAM and TM domain interactions are necessary for the induction of neuropilin signaling, possibly in a concerted manner, because both types of interactions can be effectively antagonized.…”

Section: Discussionmentioning

confidence: 76%

“…We hypothesized that the biological function of Sema3A was abrogated when interfering with the TM domain because of the destabilization of the receptor complex required for signal transduction. Indeed, it has been proposed that Sema3A dimer (known to be important for binding and collapsing activity; Klostermann et al, 1998;Koppel and Raper, 1998) may undergo a dimer-to-monomer transition upon binding to monomeric NRP1 (Antipenko et al, 2003), a transition that would explain the persistence of binding after destabilization of NRP1 homodimerization. In the other hand, the interference of the TM domain dimerization may be sufficient to generate conformational changes altering optimal binding at the extracellular level.…”

Section: Discussionmentioning

confidence: 99%

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Transmembrane Domain Interactions Control Biological Functions of Neuropilin-1

Roth

Nasarre

Dirrig‐Grosch

et al. 2008

MBoC

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Neuropilin-1 (NRP1) is a transmembrane receptor playing a pivotal role in the control of semaphorins and VEGF signaling pathways. The exact mechanism controlling semaphorin receptor complex formation is unknown. A structural analysis and modeling of NRP1 revealed a putative dimerization GxxxG motif potentially important for NRP1 dimerization and oligomerization. Our data show that this motif mediates the dimerization of the transmembrane domain of NRP1 as demonstrated by a dimerization assay (ToxLuc assay) performed in natural membrane and FRET analysis. A synthetic peptide derived from the transmembrane segment of NRP1 abolished the inhibitory effect of Sema3A. This effect depends on the capacity of the peptide to interfere with NRP1 dimerization and the formation of oligomeric complexes. Mutation of the GxxxG dimerization motif in the transmembrane domain of NRP1 confirmed its biological importance for Sema3A signaling. Overall, our results shed light on an essential step required for semaphorin signaling and provide novel evidence for the crucial role of transmembrane domain of bitopic protein containing GxxxG motif in the formation of receptor complexes that are a prerequisite for cell signaling.

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Section: Discussionmentioning

confidence: 76%

Section: Discussionmentioning

confidence: 99%

Transmembrane Domain Interactions Control Biological Functions of Neuropilin-1

Roth

Nasarre

Dirrig‐Grosch

et al. 2008

MBoC

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“…Known molecular causes of DA are mutations in at least seven genes (TNNI2, TNNT3, TPM2, MYH2, MYH3, MYH8, and MYH13) that encode components of the contractile apparatus of fast-twitch myofibers [Sung et al, 2003a,b;Toydemir et al, 2006a,b]. Since it was shown that Sema3a-signaling controls the timing of motor axon in-growth to the limb and is involved in intramuscular motor reinnervation and restoration of muscle fiber contractile integrity [Antipenko et al, 2003] are shown in green. Residues involved in Plexin binding were deduced from the homologous Sema4D complex [Janssen et al, 2010] and are shown in cyan (stick presentation).…”

Section: Discussionmentioning

confidence: 99%

“…Bidirectional sequencing was performed with vector specific primers (Supplementary Table SIV) and sequencing primers binding within the insert. The crystal structure of murine Sema3a containing the full semaphorin domain (residues 26-520) was retrieved from the PDB databank (PDB code 1Q47) [Antipenko et al, 2003]. The structure of human SEMA3A, which Exhibits 97% sequence identity to murine Sema3a, was generated using SwissModel [Guex and Peitsch, 1997].…”

Section: Materials and Methods Clinical Reportmentioning

confidence: 99%

Biallelic SEMA3A defects cause a novel type of syndromic short stature

Hofmann

Zweier

Sticht

et al. 2013

American J of Med Genetics Pt A

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Chromosomal microarray testing is commonly used to identify disease causing de novo copy number variants in patients with developmental delay and multiple congenital anomalies. In such a patient we now observed an 150 kb deletion on chromosome 7q21.11 affecting the first exon of the axon guidance molecule gene SEMA3A (sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3A). This deletion was inherited from the healthy father, but considering the function of SEMA3A and phenotypic similarity to the knock‐out mice, we still assumed a pathogenic relevance and tested for a recessive second defect. Sequencing of SEMA3A in the patient indeed revealed the de novo in‐frame mutation p.Phe316_Lys317delinsThrSerSerAsnGlu. Cloning of the mutated allele in combination with two informative SNPs confirmed compound heterozygosity in the patient. While the altered protein structure was predicted to be benign, aberrant splicing resulting in a premature stop codon was proven by RT‐PCR to occur in about half of the transcripts from this allele. Expression profiling in human fetal and adult cDNA panels, confirmed a high expression of SEMA3A in all brain regions as well as in adult and fetal heart and fetal skeletal muscle. Normal intellectual development in the patient was surprising but may be explained by the remaining 20% of SEMA3A expression level demonstrated by quantitative RT‐PCR. We therefore report a novel autosomal recessive syndrome characterized by postnatal short stature with relative macrocephaly, camptodactyly, septal heart defect and several minor anomalies caused by biallelic mutations in SEMA3A. © 2013 Wiley Periodicals, Inc.

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“…Plexins act as the signal transducing receptors for semaphorins, a family of secreted and cell surface-attached proteins best characterized by their chemorepulsive role in axon guidance (1). The extracellular portions of semaphorins and plexins share a distinctive ␤-propeller fold termed the sema domain (2,3); the plexin cytosolic regions are of unknown structure. Molecules of the MICAL [molecule interacting with CasL (4)] family link signaling from the cytosolic regions of class A plexins to the cytoskeleton (5).…”

mentioning

confidence: 99%

High-resolution structure of the catalytic region of MICAL (molecule interacting with CasL), a multidomain flavoenzyme-signaling molecule

Siebold

Berrow

Walter

et al. 2005

Proc. Natl. Acad. Sci. U.S.A.

123

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MICALs are large (Ͼ1,000 aa), multidomain, cytosolic proteins expressed in specific neuronal and nonneuronal (thymus, lung, spleen, and testis) tissues both during development and in adulthood (4).From sequence analysis, it has been shown that MICALs contain two protein-protein interaction domains implicated in signal transduction and cytoskeletal organization, a calponin homology (CH) domain (7) and a LIM domain (8), plus a proline-rich region for Src homology 3 (SH3) domain recognition that mediates interaction with CasL, a multidomain docking protein localized at focal adhesions and stress fibers (4). Human MICAL-1 associates with the small GTPase Rab1 (6, 9) and with vimentin (4), a major component of intermediate filaments. In addition to the SH3 domainbinding motif, the C-terminal region (of Ϸ250 residues) contains coiled-coil motifs and binds the cytosolic domain of class A plexins (5). Thus, the MICALs are protein-binding scaffolds, but, uniquely, they combine this property with a highly conserved N-terminal region of some 500 residues, characterized by sequence analyses and functional studies as a putative flavoprotein monooxygenase (MO) required for semaphorin-plexin-mediated axon guidance (5).Flavoenzymes bind the cofactor FAD as an integral part of their structure. Despite Ͻ20% sequence identity between disparate members of this family, they share a similar fold and essentially identical FAD-binding sites (10). In contrast, the catalytic reactions carried out by the flavoenzymes are varied, and their active-site architectures differ accordingly. The structure of p-hydroxybenzoate hydroxylase (PHBH) provides the paradigm for the flavoprotein MO (hydroxylase) subset of flavoenzymes (11). Flavoprotein MOs act on a broad range of small molecules (e.g., phydroxybenzoate, steroids, and amino acids). The substrate(s), mode of action, and, indeed, function of the putative MO region in the MICALs are unknown.Our structural and biophysical analyses on the N-terminal portion of murine MICAL-1 confirm that this region has the architecture and characteristics of a flavoenzyme of the MO family, demonstrate the enzymatic activity to be NADPH-dependent, and reveal a mechanism for controlled substrate access to the active site, which is strongly indicative of large (potentially protein) substrates. MethodsProtein Expression and Purification. The mMICAL 489 expression construct (amino acids 1-489 of the mouse MICAL-1 gene plus C-terminal His-tag) was generated by ligation-independent cloning (Gateway Technology, Invitrogen), overexpressed in Escherichia coli (DE3)pLysS (Novagen), and purified with Ni affinity and size-exclusion chromatography; all stages used the high-throughput pipeline of the Oxford Protein Production Facility (see Supporting Text, which is published as supporting information on the PNAS

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Structure of the Semaphorin-3A Receptor Binding Module

Cited by 151 publications

References 35 publications

Transmembrane Domain Interactions Control Biological Functions of Neuropilin-1

Transmembrane Domain Interactions Control Biological Functions of Neuropilin-1

Biallelic SEMA3A defects cause a novel type of syndromic short stature

High-resolution structure of the catalytic region of MICAL (molecule interacting with CasL), a multidomain flavoenzyme-signaling molecule

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