Structural basis for activation and non-canonical catalysis of the Rap GTPase activating protein domain of plexin

Wang, Yuxiao; Pascoe, Heath G.; Brautigam, Chad A.; He, Huawei; Zhang, Xuewu

doi:10.7554/elife.01279

Cited by 69 publications

(119 citation statements)

References 73 publications

(139 reference statements)

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“…S1). The structure of PlexinB2 cyto , except for the disordered JM-segment, is similar to reported structures of other plexins (2,3,(8)(9)(10). The PDZ domain here is similar to the NMR structure of the PDZ domain of LARG (Fig.…”

Section: Resultssupporting

confidence: 80%

“…Before activation, plexin exists as an inactive monomer or inhibitory dimer (3,9,36). Semaphorin binding induces the formation of the active dimer of plexin (2,(4)(5)(6)(7). PDZ-RhoGEF and LARG also form dimers or oligomers through their C-terminal coiled-coil region (37).…”

Section: Discussionmentioning

confidence: 99%

“…Binding of semaphorin to the extracellular region of plexin induces formation of the active dimer of the cytoplasmic region, which transduces signal to downstream pathways (2)(3)(4)(5)(6)(7). The plexin cytoplasmic region contains a juxtamembrane segment (JM-segment), a RhoGTPase binding domain (RBD), and a GTPase activating protein (GAP) domain (8)(9)(10).…”

mentioning

confidence: 99%

“…The plexin cytoplasmic region contains a juxtamembrane segment (JM-segment), a RhoGTPase binding domain (RBD), and a GTPase activating protein (GAP) domain (8)(9)(10). The GAP domain, activated by the dimerization, transduces signal through converting its substrate GTPase Rap from the GTP-bound active to the GDP-bound inactive state (2,3). The RBD regulates plexin activity in response to binding of Rho family GTPases, such as Rac1 (reviewed in ref.…”

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confidence: 99%

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Secondary PDZ domain-binding site on class B plexins enhances the affinity for PDZ–RhoGEF

Pascoe

Gutowski

Chen

et al. 2015

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

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PDZ domains are abundant protein interaction modules and typically recognize a short motif at the C terminus of their ligands, with a few residues in the motif endowing the binding specificity. The sequence-based rules, however, cannot fully account for the specificity between the vast number of PDZ domains and ligands in the cell. Plexins are transmembrane receptors that regulate processes such as axon guidance and angiogenesis. Two related guanine nucleotide exchange factors (GEFs), PDZ-RhoGEF and leukemiaassociated RhoGEF (LARG), use their PDZ domains to bind class B plexins and play critical roles in signaling. Here, we present the crystal structure of the full-length cytoplasmic region of PlexinB2 in complex with the PDZ domain of PDZ-RhoGEF. The structure reveals that, in addition to the canonical C-terminal motif/PDZ interaction, the 3D domain of PlexinB2 forms a secondary interface with the PDZ domain. Our biophysical and cell-based assays show that the secondary interface contributes to the specific interaction between plexin and PDZ-RhoGEF and to signaling by plexin in the cell. Formation of secondary interfaces may be a general mechanism for increasing affinity and specificity of modular domain-mediated interactions.PDZ | plexin | signaling | protein interaction module | specificity P lexins are cell surface receptors for semaphorins, extracellular cues that control essential processes such as neuronal axon guidance and vasculature development (1). Binding of semaphorin to the extracellular region of plexin induces formation of the active dimer of the cytoplasmic region, which transduces signal to downstream pathways (2-7). The plexin cytoplasmic region contains a juxtamembrane segment (JM-segment), a RhoGTPase binding domain (RBD), and a GTPase activating protein (GAP) domain (8-10). The GAP domain, activated by the dimerization, transduces signal through converting its substrate GTPase Rap from the GTP-bound active to the GDP-bound inactive state (2, 3). The RBD regulates plexin activity in response to binding of Rho family GTPases, such as Rac1 (reviewed in ref. 11).In addition to the common signaling pathways through the domains shared by all plexins, class B plexins (B1, B2, and B3) mediate a pathway through their unique C terminus. The conserved "VTDL" motif at the C terminus of these plexins binds to the N-terminal PDZ (PSD-95/Discs-large/ZO-1) domains of two related guanine nucleotide exchange factors (GEFs), PDZ-RhoGEF, and leukemia-associated RhoGEF (LARG) (12)(13)(14)(15)(16)(17). This interaction recruits PDZ-RhoGEF and LARG to the plasma membrane, where they promote the exchange of GDP for GTP on RhoA. GTP-bound RhoA binds its downstream effectors and contributes to plexin signaling (13)(14)(15)18). A recent study has shown that deletion of the C terminus of PlexinB2 causes defects in the development of the liver vasculature in mice, highlighting the critical role of the PDZ-RhoGEF/LARG-RhoA pathway in plexin function in vivo (19).More than 250 PDZ domains exist in the human proteome, con...

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Section: Resultssupporting

confidence: 80%

Section: Discussionmentioning

confidence: 99%

mentioning

confidence: 99%

mentioning

confidence: 99%

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Secondary PDZ domain-binding site on class B plexins enhances the affinity for PDZ–RhoGEF

Pascoe

Gutowski

Chen

et al. 2015

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

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“…The RBD/RhoGTPase interaction plays a regulatory role in plexin signaling. In addition to the GAP domain and the RBD, the crystal structures also revealed a juxtamembrane segment at the N-terminus of the plexin cytoplasmic region (Figure 1), which is an essential regulatory element (He et al, 2009; Wang et al, 2013). …”

Section: Overall Architecture and Signaling Mechanisms Of The Plexmentioning

confidence: 99%

Structural mechanisms of plexin signaling

Pascoe

Wang

Zhang

2015

Progress in Biophysics and Molecular Biology

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Signaling through plexin, the major cell surface receptor for semaphorin, plays critical roles in regulating processes such as neuronal axon guidance, angiogenesis and immune response. Plexin is normally kept inactive in the absence of semaphorin. Upon binding of semaphorin to the extracellular region, plexin is activated and transduces signal to the inside of the cell through its cytoplasmic region. The GTPase Activating Protein (GAP) domain in the plexin cytoplasmic region mediates the major intracellular signaling pathway. The substrate specificity and regulation mechanisms of the GAP domain have only been revealed recently. Many intracellular proteins serve as either upstream regulators or downstream transducers by directly interacting with plexin. The mechanisms of action for some of these proteins also start to emerge from recent studies. We review here these advances in the mechanistic understanding of plexin intracellular signaling from a structural perspective.

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Dual‐Specificity R as/ R ap GTPase Activating Proteins

Sot

2018

Encyclopedia of Life Sciences

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The small GTP‐binding proteins Ras and Rap regulate important cellular events switching between an activated GTP‐bound form and an inactivated GDP‐bound state. Guanine exchange factors (GEFs) control the GDP to GTP‐bound cycle, while the conversion, through hydrolysis, of GTP to GDP is catalysed by GTPase‐activating proteins (GAPs). The GAPs complete Ras and Rap catalytic site for efficient GTP hydrolysis. Although Ras and Rap are highly homologous, they possess different residues in the catalytic site. In consequence, Ras and Rap GTPase‐activating proteins (RasGAPs and RapGAPs) are structurally unrelated and use different mechanisms. Surprisingly, there are several RasGAPs with dual Ras/Rap specificity: SynGAP; GAP1 family members GAP1 IP4BP , Rasal and Capri; and Plexins. This characteristic was an intriguing issue for years, but today structural and biochemical studies have enlightened the overall general mechanism of these dual GAPs. Key Concepts Small GTP‐binding proteins Rap and Ras control different cellular signalling switching between inactive GDP and active GTP‐bound states. Ras and Rap GTPase‐activating proteins (RasGAPs and RapGAPs) inactivate their downstream signalling catalysing the GTP hydrolysis, using RasGAP and RapGAP domains. RasGAPs–Ras‐GTP interaction positions Ras Gln61, situated in switch II loop, for nucleophilic attack, while the GAP contributes an Arg (arginine finger) to neutralise unfavourable negative charges of the reaction intermediate. Rap has a Thr in position 61, and RapGAPs catalyse GTP hydrolysis, contributing an Asn (Asn thumb) for nucleophilic attack. There are five RasGAPs with dual Rap/Ras specificity: SynGAP, Rasal, GAP1 IP4BP , Capri and Plexin. Dual GAPs need extra‐GAP domains to act as RapGAPs. Dual GAPs promote a specific orientation of Rap switch II, locating Gln63 as the catalytic residue. Plexin‐Rap X‐ray structure showed that residues of GAP domain and an extra‐GAP motif (juxtamembrane segment) are responsible for Gln63 correct orientation. SynGAP, Rasal, GAP1 IP4BP , Plexin and Capri do not share the same residues, and thus they still need to be found.

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Structural basis for activation and non-canonical catalysis of the Rap GTPase activating protein domain of plexin

Cited by 69 publications

References 73 publications

Secondary PDZ domain-binding site on class B plexins enhances the affinity for PDZ–RhoGEF

Secondary PDZ domain-binding site on class B plexins enhances the affinity for PDZ–RhoGEF

Structural mechanisms of plexin signaling

Dual‐Specificity R as/ R ap GTPase Activating Proteins

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