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PMC4774019
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The immunity-related GTPase Irga6 dimerizes in a parallel head-to-head fashion.
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The following structures are shown in cylinder representations, in similar orientations of their GTPase domains: a the GMPPNP-bound Irga6 dimer, b the GDP-AlF4 -bound dynamin 1 GTPase-minimal BSE construct [pdb 2X2E], c the GDP-bound atlastin 1 dimer [pdb 3Q5E], d the GDP-AlF3- bound GBP1 GTPase domain dimer [pdb 2B92], e the BDLP dimer bound to GDP [pdb 2J68] and f the GTP-bound GIMAP2 dimer [pdb 2XTN].
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PMC4774019
|
The immunity-related GTPase Irga6 dimerizes in a parallel head-to-head fashion.
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The GTPase domains of the left molecules are shown in orange, helical domains or extensions in blue.
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PMC4774019
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The immunity-related GTPase Irga6 dimerizes in a parallel head-to-head fashion.
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Nucleotide, Mg (green) and AlF4 are shown in sphere representation, the buried interface sizes per molecule are indicated on the right.
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PMC4774019
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The immunity-related GTPase Irga6 dimerizes in a parallel head-to-head fashion.
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Irga6 immunity-related GTPase 6, GMPPNP 5'-guanylyl imidodiphosphate, GTP guanosine-triphosphate, BDLP bacterial dynamin like protein, GIMAP2, GTPase of immunity associated protein 2 A conserved dimerization mode via the G interface in dynamin and septin GTPases.
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PMC4774019
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The immunity-related GTPase Irga6 dimerizes in a parallel head-to-head fashion.
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The overall architecture of the parallel GTPase domain dimer of Irga6 is related to that of other dynamin and septin superfamily proteins.
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PMC4774019
|
The immunity-related GTPase Irga6 dimerizes in a parallel head-to-head fashion.
|
The following structures are shown in cylinder representations, in similar orientations of their GTPase domains: a the GMPPNP-bound Irga6 dimer, b the GDP-AlF4 -bound dynamin 1 GTPase-minimal BSE construct [pdb 2X2E], c the GDP-bound atlastin 1 dimer [pdb 3Q5E], d the GDP-AlF3- bound GBP1 GTPase domain dimer [pdb 2B92], e the BDLP dimer bound to GDP [pdb 2J68] and f the GTP-bound GIMAP2 dimer [pdb 2XTN].
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PMC4774019
|
The immunity-related GTPase Irga6 dimerizes in a parallel head-to-head fashion.
|
The GTPase domains of the left molecules are shown in orange, helical domains or extensions in blue.
|
PMC4774019
|
The immunity-related GTPase Irga6 dimerizes in a parallel head-to-head fashion.
|
Nucleotide, Mg (green) and AlF4 are shown in sphere representation, the buried interface sizes per molecule are indicated on the right.
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PMC4774019
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The immunity-related GTPase Irga6 dimerizes in a parallel head-to-head fashion.
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Irga6 immunity-related GTPase 6, GMPPNP 5'-guanylyl imidodiphosphate, GTP guanosine-triphosphate, BDLP bacterial dynamin like protein, GIMAP2, GTPase of immunity associated protein 2 IRG proteins are crucial mediators of the innate immune response in mice against a specific subset of intracellular pathogens, all of which enter the cell to form a membrane-bounded vacuole without engagement of the phagocytic machinery.
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PMC4774019
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The immunity-related GTPase Irga6 dimerizes in a parallel head-to-head fashion.
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As members of the dynamin superfamily, IRGs oligomerize at cellular membranes in response to GTP binding.
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PMC4774019
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The immunity-related GTPase Irga6 dimerizes in a parallel head-to-head fashion.
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Oligomerization and oligomerization-induced GTP hydrolysis are thought to induce membrane remodeling events ultimately leading to disruption of the PVM.
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PMC4774019
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The immunity-related GTPase Irga6 dimerizes in a parallel head-to-head fashion.
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Recent structural and mechanistic analyses have begun to unravel the molecular basis for the membrane-remodeling activity and mechano-chemical function of some members (reviewed in ).
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PMC4774019
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The immunity-related GTPase Irga6 dimerizes in a parallel head-to-head fashion.
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For example, for dynamin and atlastin, it was shown that GTP binding and/or hydrolysis leads to dimerization of the GTPase domains and to the reorientation of the adjacent helical domains.
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PMC4774019
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The immunity-related GTPase Irga6 dimerizes in a parallel head-to-head fashion.
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The resulting domain movement was suggested to act as a “power stroke” during membrane remodeling events .
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PMC4774019
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The immunity-related GTPase Irga6 dimerizes in a parallel head-to-head fashion.
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However, for other dynamin superfamily members such as IRGs, the molecular basis for GTP hydrolysis and the exact role of the mechano-chemical function are still unclear.
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PMC4774019
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The immunity-related GTPase Irga6 dimerizes in a parallel head-to-head fashion.
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Our structural analysis of an oligomerization- and GTPase-defective Irga6 mutant indicates that Irga6 dimerizes via the G interface in a parallel orientation.
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PMC4774019
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The immunity-related GTPase Irga6 dimerizes in a parallel head-to-head fashion.
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Only one of the seven Irga6 molecules in the asymmetric unit formed this contact pointing to a low affinity interaction via the G interface, which is in agreement with its small size.
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PMC4774019
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The immunity-related GTPase Irga6 dimerizes in a parallel head-to-head fashion.
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In the crystals, dimerization via the G interface is promoted by the high protein concentrations which may mimic a situation when Irga6 oligomerizes on a membrane surface.
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PMC4774019
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The immunity-related GTPase Irga6 dimerizes in a parallel head-to-head fashion.
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Such a low affinity interaction mode may allow reversibility of oligomerization following GTP hydrolysis.
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PMC4774019
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The immunity-related GTPase Irga6 dimerizes in a parallel head-to-head fashion.
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Similar low affinity G interface interactions were reported for dynamin and MxA .
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PMC4774019
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The immunity-related GTPase Irga6 dimerizes in a parallel head-to-head fashion.
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The dimerization mode is strikingly different from the previously proposed anti-parallel model that was based on the crystal structure of the signal recognition particle GTPase, SRP54 and its homologous receptor .
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PMC4774019
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The immunity-related GTPase Irga6 dimerizes in a parallel head-to-head fashion.
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However, the G dimer interface is reminiscent of the GTPase domain dimers observed for several other dynamin superfamily members, such as dynamin, GBP1, atlastin, and BDLP.
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PMC4774019
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The immunity-related GTPase Irga6 dimerizes in a parallel head-to-head fashion.
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It was recently shown that septin and septin-related GTPases, such as the Tocs GTPases or GTPases of immunity related proteins (GIMAPs) , also employ a GTP-dependent parallel dimerization mode.
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PMC4774019
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The immunity-related GTPase Irga6 dimerizes in a parallel head-to-head fashion.
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Based on phylogenetic and structural analysis, these observations suggest that dynamin and septin superfamilies are derived from a common ancestral membrane-associated GTPase that featured a GTP-dependent parallel dimerization mode .
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PMC4774019
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The immunity-related GTPase Irga6 dimerizes in a parallel head-to-head fashion.
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Importantly, our analysis indicates that IRGs are not outliers, but bona-fide representatives of the dynamin superfamily.
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PMC4774019
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The immunity-related GTPase Irga6 dimerizes in a parallel head-to-head fashion.
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Whereas the overall dimerization mode is similar in septin and dynamin GTPases, family-specific differences in the G interface and the oligomerization interfaces exist.
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PMC4774019
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The immunity-related GTPase Irga6 dimerizes in a parallel head-to-head fashion.
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For example, the involvement of the 2’ and 3’-OH groups of the ribose in the dimerization interface of Irga6 has not been observed for other dynamin and septin superfamily members.
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PMC4774019
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The immunity-related GTPase Irga6 dimerizes in a parallel head-to-head fashion.
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The surface-exposed location of the ribose in the Irga6 structure, with a wide-open nucleotide-binding pocket, facilitates its engagement in the dimerization interface.
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PMC4774019
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The immunity-related GTPase Irga6 dimerizes in a parallel head-to-head fashion.
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This contact, in turn, appears to activate GTP hydrolysis by inducing rearrangements in switch I and the positioning of the catalytic E106.
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PMC4774019
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The immunity-related GTPase Irga6 dimerizes in a parallel head-to-head fashion.
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During dimerization of GBP1, an arginine finger from the P loop reorients towards the nucleotide in cis to trigger GTP hydrolysis .
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PMC4774019
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The immunity-related GTPase Irga6 dimerizes in a parallel head-to-head fashion.
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In dynamin, the corresponding serine residue coordinates a sodium ion that is crucial for GTP hydrolysis .
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PMC4774019
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The immunity-related GTPase Irga6 dimerizes in a parallel head-to-head fashion.
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Irga6 bears Gly79 at this position, which in the dimerizing molecule A appears to approach the bridging imido group of GMPPNP via a main chain hydrogen bond.
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PMC4774019
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The immunity-related GTPase Irga6 dimerizes in a parallel head-to-head fashion.
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Higher resolution structures of the Irga6 dimer in the presence of a transition state analogue are required to show whether Gly79 directly participates in GTP hydrolysis or whether it may also position a catalytic cation.
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PMC4774019
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The immunity-related GTPase Irga6 dimerizes in a parallel head-to-head fashion.
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In dynamin, further assembly sites are provided by the helical domains which assemble in a criss-cross fashion to form a helical filament.
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PMC4774019
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The immunity-related GTPase Irga6 dimerizes in a parallel head-to-head fashion.
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In dynamin-related Eps15 homology domain containing proteins (EHDs), a second assembly interface is present in the GTPase domain .
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PMC4774019
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The immunity-related GTPase Irga6 dimerizes in a parallel head-to-head fashion.
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For Irga6, additional interfaces in the helical domain are presumably involved in oligomerization, such as the secondary patch residues whose mutation prevented oligomerization in the crystallized mutant.
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PMC4774019
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The immunity-related GTPase Irga6 dimerizes in a parallel head-to-head fashion.
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Further structural studies, especially electron microscopy analysis of the Irga6 oligomers, are required to clarify the assembly mode via the helical domains and to show how these interfaces cooperate with the G interface to mediate the regulated assembly on a membrane surface.
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PMC4774019
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The immunity-related GTPase Irga6 dimerizes in a parallel head-to-head fashion.
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Notably, we did not observe major rearrangements of the helical domain versus the GTPase domain in the Irga6 molecules that dimerized via the G interface.
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PMC4774019
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The immunity-related GTPase Irga6 dimerizes in a parallel head-to-head fashion.
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In a manner similar to BDLP , such large-scale conformational changes may be induced by membrane binding.
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PMC4774019
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The immunity-related GTPase Irga6 dimerizes in a parallel head-to-head fashion.
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Our structural analysis and the identification of the G-interface paves the way for determining the specific assembly of Irga6 into a membrane-associated scaffold as the prerequisite to understand its action as an anti-parasitic machine.
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PMC4774019
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The immunity-related GTPase Irga6 dimerizes in a parallel head-to-head fashion.
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Selenomethionine-substituted Mus musculus Irga6 was expressed as a GST-fusion from the vector pGEX-4T-2 in BL21 Rosetta2(DE3) cells according to reference .
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PMC4774019
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The immunity-related GTPase Irga6 dimerizes in a parallel head-to-head fashion.
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Protein was purified as previously described and the protein stored in small aliquots at a concentration of 118 mg/mL in 50 mM Tris-HCl, pH 7.4, 5 mM MgCl2, 2 mM DTT.
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PMC4774019
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The immunity-related GTPase Irga6 dimerizes in a parallel head-to-head fashion.
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Oligomerization and GTPase assays for the Irga6 mutant were carried out as described in .
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PMC4774019
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The immunity-related GTPase Irga6 dimerizes in a parallel head-to-head fashion.
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The protein was gently thawed on ice and diluted to a final concentration of 10 mg/mL with buffer containing 20 mM Tris-HCl, pH 7.5, 8 mM MgCl2, 3 mM DTT.
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PMC4774019
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The immunity-related GTPase Irga6 dimerizes in a parallel head-to-head fashion.
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GMPPNP was added to a final concentration of 2 mM. Crystallization was carried out in a 96 well format using the sitting drop vapor diffusion method.
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PMC4774019
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The immunity-related GTPase Irga6 dimerizes in a parallel head-to-head fashion.
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The reservoir contained 100 mM HEPES-NaOH pH 7.0, 9 % PEG4000, 6 % isopropanol.
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PMC4774019
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The immunity-related GTPase Irga6 dimerizes in a parallel head-to-head fashion.
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The sitting drop was set up using an Art Robbins Gryphon system and consisted of 200 nL protein solution and 200 nL reservoir solution.
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PMC4774019
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The immunity-related GTPase Irga6 dimerizes in a parallel head-to-head fashion.
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For cryo-protection, crystals were transferred into a cryo solution containing 33 % PEG4000, 3 % isopropanol, 50 mM HEPES pH 7.0, 4 mM MgCl2, 2 mM DTT, and 2 mM GMPPNP at 4 °C for at least 5 sec. Crystals were screened for diffraction at beamline BL 14.1 at BESSY II, Berlin, Germany.
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PMC4774019
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The immunity-related GTPase Irga6 dimerizes in a parallel head-to-head fashion.
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All data were recorded at beamline P11 at PETRA III, DESY Hamburg, Germany using a PILATUS 6 M detector.
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PMC4774019
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The immunity-related GTPase Irga6 dimerizes in a parallel head-to-head fashion.
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To achieve spot separation along the long cell axis, three data sets were collected with a φ increment of 0.05/0.1° at a temperature of 100 K using detector distances between 1300 and 598.5 mm (Additional file 1: Table S1).
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PMC4774019
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The immunity-related GTPase Irga6 dimerizes in a parallel head-to-head fashion.
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The wavelength was 0.972/0.979 Å. Calculation of an optimal data collection strategy was done with the Mosflm software .
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PMC4774019
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The immunity-related GTPase Irga6 dimerizes in a parallel head-to-head fashion.
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The high- and low-resolution datasets were processed and merged using the XDS program suite .
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PMC4774019
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The immunity-related GTPase Irga6 dimerizes in a parallel head-to-head fashion.
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Structure solution was done by molecular replacement with Phaser employing the structure of Irga6 without nucleotide [PDB: 1TQ2] as search model .
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PMC4774019
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The immunity-related GTPase Irga6 dimerizes in a parallel head-to-head fashion.
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Atomic model building was done by Coot .
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PMC4774019
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The immunity-related GTPase Irga6 dimerizes in a parallel head-to-head fashion.
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Iterative refinement was done using Phenix at a maximum resolution of 3.2 Å .
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PMC4774019
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The immunity-related GTPase Irga6 dimerizes in a parallel head-to-head fashion.
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For the refinement strategy, a seven-fold non-crystallographic symmetry as well as one molecule of Irga6 [PDB: 1TQ4] as high resolution reference structure was chosen.
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PMC4774019
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The immunity-related GTPase Irga6 dimerizes in a parallel head-to-head fashion.
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Five percent of the measured X-ray intensities were set aside from the refinement as cross-validation .
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PMC4774019
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The immunity-related GTPase Irga6 dimerizes in a parallel head-to-head fashion.
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Methionine sites in the protein were confirmed by the anomalous signal of the selenium atoms.
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PMC4774019
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The immunity-related GTPase Irga6 dimerizes in a parallel head-to-head fashion.
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Protein superposition was done with lsqkab and the PyMol Molecular Graphics System, Version 1.3 Schrödinger, LLC.
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PMC4774019
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The immunity-related GTPase Irga6 dimerizes in a parallel head-to-head fashion.
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Figures were prepared using the PyMOL Molecular Graphics System, Version 1.7.4 Schrödinger, LLC.
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PMC4774019
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The immunity-related GTPase Irga6 dimerizes in a parallel head-to-head fashion.
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Evaluation of atom contacts and geometry of the atomic model was done by the Molprobity server .
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PMC4774019
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The immunity-related GTPase Irga6 dimerizes in a parallel head-to-head fashion.
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Interface sizes were calculated by the PISA server .
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PMC4774019
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The immunity-related GTPase Irga6 dimerizes in a parallel head-to-head fashion.
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The Irga6 coordinates were submitted to the Protein Data Bank (pdb) database with accession code 5fph.
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PMC4774019
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The immunity-related GTPase Irga6 dimerizes in a parallel head-to-head fashion.
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http://www.rcsb.org/pdb/explore/explore.do?structureId=5fph.
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PMC4774019
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The immunity-related GTPase Irga6 dimerizes in a parallel head-to-head fashion.
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Our study indicates that Irg proteins dimerize via the G interface in a parallel head-to-head fashion thereby facilitating GTPase activation.
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PMC4774019
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The immunity-related GTPase Irga6 dimerizes in a parallel head-to-head fashion.
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These findings contribute to a molecular understanding of the anti-parasitic action of the Irg protein family and suggest that Irgs are bona-fide members of the dynamin superfamily.
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PMC4852598
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Structural basis for Mep2 ammonium transceptor activation by phosphorylation.
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Mep2 proteins are fungal transceptors that play an important role as ammonium sensors in fungal development.
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PMC4852598
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Structural basis for Mep2 ammonium transceptor activation by phosphorylation.
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Mep2 activity is tightly regulated by phosphorylation, but how this is achieved at the molecular level is not clear.
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PMC4852598
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Structural basis for Mep2 ammonium transceptor activation by phosphorylation.
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Here we report X-ray crystal structures of the Mep2 orthologues from Saccharomyces cerevisiae and Candida albicans and show that under nitrogen-sufficient conditions the transporters are not phosphorylated and present in closed, inactive conformations.
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PMC4852598
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Structural basis for Mep2 ammonium transceptor activation by phosphorylation.
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Relative to the open bacterial ammonium transporters, non-phosphorylated Mep2 exhibits shifts in cytoplasmic loops and the C-terminal region (CTR) to occlude the cytoplasmic exit of the channel and to interact with His2 of the twin-His motif.
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PMC4852598
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Structural basis for Mep2 ammonium transceptor activation by phosphorylation.
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The phosphorylation site in the CTR is solvent accessible and located in a negatively charged pocket ∼30 Å away from the channel exit.
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PMC4852598
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Structural basis for Mep2 ammonium transceptor activation by phosphorylation.
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The crystal structure of phosphorylation-mimicking Mep2 variants from C. albicans show large conformational changes in a conserved and functionally important region of the CTR.
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PMC4852598
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Structural basis for Mep2 ammonium transceptor activation by phosphorylation.
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The results allow us to propose a model for regulation of eukaryotic ammonium transport by phosphorylation.
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PMC4852598
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Structural basis for Mep2 ammonium transceptor activation by phosphorylation.
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Transceptors are membrane proteins that function not only as transporters but also as receptors/sensors during nutrient sensing to activate downstream signalling pathways1.
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PMC4852598
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Structural basis for Mep2 ammonium transceptor activation by phosphorylation.
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A common feature of transceptors is that they are induced when cells are starved for their substrate.
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PMC4852598
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Structural basis for Mep2 ammonium transceptor activation by phosphorylation.
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While most studies have focused on the Saccharomyces cerevisiae transceptors for phosphate (Pho84), amino acids (Gap1) and ammonium (Mep2), transceptors are found in higher eukaryotes as well (for example, the mammalian SNAT2 amino-acid transporter and the GLUT2 glucose transporter)2.
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PMC4852598
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Structural basis for Mep2 ammonium transceptor activation by phosphorylation.
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One of the most important unresolved questions in the field is how the transceptors couple to downstream signalling pathways.
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PMC4852598
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Structural basis for Mep2 ammonium transceptor activation by phosphorylation.
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One hypothesis is that downstream signalling is dependent on a specific conformation of the transporter2.
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PMC4852598
|
Structural basis for Mep2 ammonium transceptor activation by phosphorylation.
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Mep2 (methylammonium (MA) permease) proteins are ammonium transceptors that are ubiquitous in fungi.
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PMC4852598
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Structural basis for Mep2 ammonium transceptor activation by phosphorylation.
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They belong to the Amt/Mep/Rh family of transporters that are present in all kingdoms of life and they take up ammonium from the extracellular environment3.
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PMC4852598
|
Structural basis for Mep2 ammonium transceptor activation by phosphorylation.
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Fungi typically have more than one Mep paralogue, for example, Mep1-3 in S. cerevisiae4.
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PMC4852598
|
Structural basis for Mep2 ammonium transceptor activation by phosphorylation.
|
Of these, only Mep2 proteins function as ammonium receptors/sensors in fungal development5.
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PMC4852598
|
Structural basis for Mep2 ammonium transceptor activation by phosphorylation.
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Under conditions of nitrogen limitation, Mep2 initiates a signalling cascade that results in a switch from the yeast form to filamentous (pseudohyphal) growth6 that may be required for fungal pathogenicity7.
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PMC4852598
|
Structural basis for Mep2 ammonium transceptor activation by phosphorylation.
|
As is the case for other transceptors, it is not clear how Mep2 interacts with downstream signalling partners, but the protein kinase A and mitogen-activated protein kinase pathways have been proposed as downstream effectors of Mep2 (refs 6, 8, 9).
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PMC4852598
|
Structural basis for Mep2 ammonium transceptor activation by phosphorylation.
|
Compared with Mep1 and Mep3, Mep2 is highly expressed and functions as a low-capacity, high-affinity transporter in the uptake of MA10.
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PMC4852598
|
Structural basis for Mep2 ammonium transceptor activation by phosphorylation.
|
In addition, Mep2 is also important for uptake of ammonium produced by growth on other nitrogen sources11.
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PMC4852598
|
Structural basis for Mep2 ammonium transceptor activation by phosphorylation.
|
With the exception of the human RhCG structure12, no structural information is available for eukaryotic ammonium transporters.
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PMC4852598
|
Structural basis for Mep2 ammonium transceptor activation by phosphorylation.
|
By contrast, several bacterial Amt orthologues have been characterized in detail via high-resolution crystal structures and a number of molecular dynamics (MD) studies13141516171819.
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PMC4852598
|
Structural basis for Mep2 ammonium transceptor activation by phosphorylation.
|
All the solved structures including that of RhCG are very similar, establishing the basic architecture of ammonium transporters.
|
PMC4852598
|
Structural basis for Mep2 ammonium transceptor activation by phosphorylation.
|
The proteins form stable trimers, with each monomer having 11 transmembrane (TM) helices and a central channel for the transport of ammonium.
|
PMC4852598
|
Structural basis for Mep2 ammonium transceptor activation by phosphorylation.
|
All structures show the transporters in open conformations.
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PMC4852598
|
Structural basis for Mep2 ammonium transceptor activation by phosphorylation.
|
Intriguingly, fundamental questions such as the nature of the transported substrate and the transport mechanism are still controversial.
|
PMC4852598
|
Structural basis for Mep2 ammonium transceptor activation by phosphorylation.
|
Where earlier studies favoured the transport of ammonia gas1320, recent data and theoretical considerations suggest that Amt/Mep proteins are instead active, electrogenic transporters of either NH4 (uniport) or NH3/H (symport)151721222324.
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PMC4852598
|
Structural basis for Mep2 ammonium transceptor activation by phosphorylation.
|
A highly conserved pair of channel-lining histidine residues dubbed the twin-His motif may serve as a proton relay system while NH3 moves through the channel during NH3/H symport16.
|
PMC4852598
|
Structural basis for Mep2 ammonium transceptor activation by phosphorylation.
|
Ammonium transport is tightly regulated.
|
PMC4852598
|
Structural basis for Mep2 ammonium transceptor activation by phosphorylation.
|
In animals, this is due to toxicity of elevated intracellular ammonium levels25, whereas for microorganisms ammonium is a preferred nitrogen source.
|
PMC4852598
|
Structural basis for Mep2 ammonium transceptor activation by phosphorylation.
|
In bacteria, amt genes are present in an operon with glnK, encoding a PII-like signal transduction class protein26.
|
PMC4852598
|
Structural basis for Mep2 ammonium transceptor activation by phosphorylation.
|
By binding tightly to Amt proteins without inducing a conformational change in the transporter27, GlnK sterically blocks ammonium conductance when nitrogen levels are sufficient.
|
PMC4852598
|
Structural basis for Mep2 ammonium transceptor activation by phosphorylation.
|
Under conditions of nitrogen limitation, GlnK becomes uridylated, blocking its ability to bind and inhibit Amt proteins28.
|
PMC4852598
|
Structural basis for Mep2 ammonium transceptor activation by phosphorylation.
|
Importantly, eukaryotes do not have GlnK orthologues and have a different mechanism for regulation of ammonium transport activity.
|
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