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+<collection><source>PMC</source><date>20201215</date><key>pmc.key</key><document><id>4832331</id><infon key="license">CC BY</infon><passage><infon key="article-id_doi">10.1038/srep24601</infon><infon key="article-id_pii">srep24601</infon><infon key="article-id_pmc">4832331</infon><infon key="article-id_pmid">27080013</infon><infon key="elocation-id">24601</infon><infon key="license">This work is licensed under a Creative Commons Attribution 4.0
+International License. The images or other third party material in this article are
+included in the article’s Creative Commons license, unless indicated
+otherwise in the credit line; if the material is not included under the Creative
+Commons license, users will need to obtain permission from the license holder to
+reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/</infon><infon key="name_0">surname:Kandiah;given-names:Eaazhisai</infon><infon key="name_1">surname:Carriel;given-names:Diego</infon><infon key="name_10">surname:Gutsche;given-names:Irina</infon><infon key="name_2">surname:Perard;given-names:Julien</infon><infon key="name_3">surname:Malet;given-names:Hélène</infon><infon key="name_4">surname:Bacia;given-names:Maria</infon><infon key="name_5">surname:Liu;given-names:Kaiyin</infon><infon key="name_6">surname:Chan;given-names:Sze W. S.</infon><infon key="name_7">surname:Houry;given-names:Walid A.</infon><infon key="name_8">surname:Ollagnier de Choudens;given-names:Sandrine</infon><infon key="name_9">surname:Elsen;given-names:Sylvie</infon><infon key="section_type">TITLE</infon><infon key="type">front</infon><infon key="volume">6</infon><infon key="year">2016</infon><offset>0</offset><text>Structural insights into the Escherichia coli lysine decarboxylases and molecular determinants of interaction with the AAA+ ATPase RavA</text></passage><passage><infon key="section_type">ABSTRACT</infon><infon key="type">abstract</infon><offset>136</offset><text>The inducible lysine decarboxylase LdcI is an important enterobacterial acid stress response enzyme whereas LdcC is its close paralogue thought to play mainly a metabolic role. A unique macromolecular cage formed by two decamers of the Escherichia coli LdcI and five hexamers of the AAA+ ATPase RavA was shown to counteract acid stress under starvation. Previously, we proposed a pseudoatomic model of the LdcI-RavA cage based on its cryo-electron microscopy map and crystal structures of an inactive LdcI decamer and a RavA monomer. We now present cryo-electron microscopy 3D reconstructions of the E. coli LdcI and LdcC, and an improved map of the LdcI bound to the LARA domain of RavA, at pH optimal for their enzymatic activity. Comparison with each other and with available structures uncovers differences between LdcI and LdcC explaining why only the acid stress response enzyme is capable of binding RavA. We identify interdomain movements associated with the pH-dependent enzyme activation and with the RavA binding. Multiple sequence alignment coupled to a phylogenetic analysis reveals that certain enterobacteria exert evolutionary pressure on the lysine decarboxylase towards the cage-like assembly with RavA, implying that this complex may have an important function under particular stress conditions.</text></passage><passage><infon key="section_type">INTRO</infon><infon key="type">paragraph</infon><offset>1452</offset><text>Enterobacterial inducible decarboxylases of basic amino acids lysine, arginine and ornithine have a common evolutionary origin and belong to the α-family of pyridoxal-5′-phosphate (PLP)-dependent enzymes. They counteract acid stress experienced by the bacterium in the host digestive and urinary tract, and in particular in the extremely acidic stomach. Each decarboxylase is induced by an excess of the target amino acid and a specific range of extracellular pH, and works in conjunction with a cognate inner membrane antiporter. Decarboxylation of the amino acid into a polyamine is catalysed by a PLP cofactor in a multistep reaction that consumes a cytoplasmic proton and produces a CO2 molecule passively diffusing out of the cell, while the polyamine is excreted by the antiporter in exchange for a new amino acid substrate. Consequently, these enzymes buffer both the bacterial cytoplasm and the local extracellular environment. These amino acid decarboxylases are therefore called acid stress inducible or biodegradative to distinguish them from their biosynthetic lysine and ornithine decarboxylase paralogs catalysing the same reaction but responsible for the polyamine production at neutral pH.</text></passage><passage><infon key="section_type">INTRO</infon><infon key="type">paragraph</infon><offset>2662</offset><text>Inducible enterobacterial amino acid decarboxylases have been intensively studied since the early 1940 because the ability of bacteria to withstand acid stress can be linked to their pathogenicity in humans. In particular, the inducible lysine decarboxylase LdcI (or CadA) attracts attention due to its broad pH range of activity and its capacity to promote survival and growth of pathogenic enterobacteria such as Salmonella enterica serovar Typhimurium, Vibrio cholerae and Vibrio vulnificus under acidic conditions. Furthermore, both LdcI and the biosynthetic lysine decarboxylase LdcC of uropathogenic Escherichia coli (UPEC) appear to play an important role in increased resistance of this pathogen to nitrosative stress produced by nitric oxide and other damaging reactive nitrogen intermediates accumulating during the course of urinary tract infections (UTI). This effect is attributed to cadaverine, the diamine produced by decarboxylation of lysine by LdcI and LdcC, that was shown to enhance UPEC colonisation of the bladder. In addition, the biosynthetic E. coli lysine decarboxylase LdcC, long thought to be constitutively expressed in low amounts, was demonstrated to be strongly upregulated by fluoroquinolones via their induction of RpoS. A direct correlation between the level of cadaverine and the resistance of E. coli to these antibiotics commonly used as a first-line treatment of UTI could be established. Both acid pH and cadaverine induce closure of outer membrane porins thereby contributing to bacterial protection from acid stress, but also from certain antibiotics, by reduction in membrane permeability.</text></passage><passage><infon key="section_type">INTRO</infon><infon key="type">paragraph</infon><offset>4295</offset><text>The crystal structure of the E. coli LdcI as well as its low resolution characterisation by electron microscopy (EM) showed that it is a decamer made of two pentameric rings. Each monomer is composed of three domains – an N-terminal wing domain (residues 1–129), a PLP-binding core domain (residues 130–563), and a C-terminal domain (CTD, residues 564–715). Monomers tightly associate via their core domains into 2-fold symmetrical dimers with two complete active sites, and further build a toroidal D5-symmetrical structure held by the wing and core domain interactions around the central pore, with the CTDs at the periphery.</text></passage><passage><infon key="section_type">INTRO</infon><infon key="type">paragraph</infon><offset>4931</offset><text>Ten years ago we showed that the E. coli AAA+ ATPase RavA, involved in multiple stress response pathways, tightly interacted with LdcI but was not capable of binding to LdcC. We described how two double pentameric rings of the LdcI tightly associate with five hexameric rings of RavA to form a unique cage-like architecture that enables the bacterium to withstand acid stress even under conditions of nutrient deprivation eliciting stringent response. Furthermore, we recently solved the structure of the E. coli LdcI-RavA complex by cryo-electron microscopy (cryoEM) and combined it with the crystal structures of the individual proteins. This allowed us to make a pseudoatomic model of the whole assembly, underpinned by a cryoEM map of the LdcI-LARA complex (with LARA standing for LdcI associating domain of RavA), and to identify conformational rearrangements and specific elements essential for complex formation. The main determinants of the LdcI-RavA cage assembly appeared to be the N-terminal loop of the LARA domain of RavA and the C-terminal β-sheet of LdcI.</text></passage><passage><infon key="section_type">INTRO</infon><infon key="type">paragraph</infon><offset>6005</offset><text>In spite of this wealth of structural information, the fact that LdcC does not interact with RavA, although the two lysine decarboxylases are 69% identical and 84% similar, and the physiological significance of the absence of this interaction remained unexplored. To solve this discrepancy, in the present work we provided a three-dimensional (3D) cryoEM reconstruction of LdcC and compared it with the available LdcI and LdcI-RavA structures. Given that the LdcI crystal structures were obtained at high pH where the enzyme is inactive (LdcIi, pH 8.5), whereas the cryoEM reconstructions of LdcI-RavA and LdcI-LARA were done at acidic pH optimal for the enzymatic activity, for a meaningful comparison, we also produced a 3D reconstruction of the LdcI at active pH (LdcIa, pH 6.2). This comparison pinpointed differences between the biodegradative and the biosynthetic lysine decarboxylases and brought to light interdomain movements associated to pH-dependent enzyme activation and RavA binding, notably at the predicted RavA binding site at the level of the C-terminal β-sheet of LdcI. Consequently, we tested the capacity of cage formation by LdcI-LdcC chimeras where we interchanged the C-terminal β-sheets in question. Finally, we performed multiple sequence alignment of 22 lysine decarboxylases from Enterobacteriaceae containing the ravA-viaA operon in their genome. Remarkably, this analysis revealed that several specific residues in the above-mentioned β-sheet, independently of the rest of the protein sequence, are sufficient to define if a particular lysine decarboxylase should be classified as an “LdcC-like” or an “LdcI-like”. Moreover, this classification perfectly agrees with the genetic environment of the lysine decarboxylase genes. This fascinating parallelism between the propensity for RavA binding and the genetic environment of an enterobacterial lysine decarboxylase, as well as the high degree of conservation of this small structural motif, emphasize the functional importance of the interaction between biodegradative enterobacterial lysine decarboxylases and the AAA+ ATPase RavA.</text></passage><passage><infon key="section_type">RESULTS</infon><infon key="type">title_1</infon><offset>8130</offset><text>Results and Discussion</text></passage><passage><infon key="section_type">RESULTS</infon><infon key="type">title_2</infon><offset>8153</offset><text>CryoEM 3D reconstructions of LdcC, LdcIa and LdcI-LARA</text></passage><passage><infon key="section_type">RESULTS</infon><infon key="type">paragraph</infon><offset>8208</offset><text>In the frame of this work, we produced two novel subnanometer resolution cryoEM reconstructions of the E. coli lysine decarboxylases at pH optimal for their enzymatic activity – a 5.5 Å resolution cryoEM map of the LdcC (pH 7.5) for which no 3D structural information has been previously available (Figs 1A,B and S1), and a 6.1 Å resolution cryoEM map of the LdcIa, (pH 6.2) (Figs 1C,D and S2). In addition, we improved our earlier cryoEM map of the LdcI-LARA complex from 7.5 Å to 6.2 Å resolution (Figs 1E,F and S3). Based on these reconstructions, reliable pseudoatomic models of the three assemblies were obtained by flexible fitting of either the crystal structure of LdcIi or a derived structural homology model of LdcC (Table S1). Significant differences between these pseudoatomic models can be interpreted as movements between specific biological states of the proteins as described below.</text></passage><passage><infon key="section_type">RESULTS</infon><infon key="type">title_2</infon><offset>9121</offset><text>The wing domains as a stable anchor at the center of the double-ring</text></passage><passage><infon key="section_type">RESULTS</infon><infon key="type">paragraph</infon><offset>9190</offset><text>As a first step of a comparative analysis, we superimposed the three cryoEM reconstructions (LdcIa, LdcI-LARA and LdcC) and the crystal structure of the LdcIi decamer (Fig. 2 and Movie S1). This superposition reveals that the densities lining the central hole of the toroid are roughly at the same location, while the rest of the structure exhibits noticeable changes. Specifically, at the center of the double-ring the wing domains of the subunits provide the conserved basis for the assembly with the lowest root mean square deviation (RMSD) (between 1.4 and 2 Å for the Cα atoms only), whereas the peripheral CTDs containing the RavA binding interface manifest the highest RMSD (up to 4.2 Å) (Table S2). In addition, the wing domains of all structures are very similar, with the RMSD after optimal rigid body alignment (RMSDmin) less than 1.1 Å. Thus, taking the limited resolution of the cryoEM maps into account, we consider that the wing domains of all the four structures are essentially identical and that in the present study the RMSD of less than 2 Å can serve as a baseline below which differences may be assumed as insignificant. This preservation of the central part of the double-ring assembly may help the enzymes to maintain their decameric state upon activation and incorporation into the LdcI-RavA cage.</text></passage><passage><infon key="section_type">RESULTS</infon><infon key="type">title_2</infon><offset>10525</offset><text>The core domain and the active site rearrangements upon pH-dependent enzyme activation and LARA binding</text></passage><passage><infon key="section_type">RESULTS</infon><infon key="type">paragraph</infon><offset>10629</offset><text>Both visual inspection (Fig. 2) and RMSD calculations (Table S2) show that globally the three structures at active pH (LdcIa, LdcI-LARA and LdcC) are more similar to each other than to the structure determined at high pH conditions (LdcIi). The decameric enzyme is built of five dimers associating into a 5-fold symmetrical double-ring (two monomers making a dimer are delineated in Fig. 1). As common for the α family of the PLP-dependent decarboxylases, dimerization is required for the enzymatic activity because the active site is buried in the dimer interface (Fig. 3A,B). This interface is formed essentially by the core domains with some contribution of the CTDs. The core domain is built by the PLP-binding subdomain (PLP-SD, residues 184–417) flanked by two smaller subdomains rich in partly disordered loops – the linker region (residues 130–183) and the subdomain 4 (residues 418–563). Zooming in the variations in the PLP-SD shows that most of the structural changes concern displacements in the active site (Fig. 3C–F). The most conspicuous differences between the PLP-SDs can be linked to the pH-dependent activation of the enzymes. The resolution of the cryoEM maps does not allow modeling the position of the PLP moiety and calls for caution in detailed mechanistic interpretations in terms of individual amino acids. Therefore we restrict our analysis to secondary structure elements. In particular, transition from LdcIi to LdcI-LARA involves ~3.5 Å and ~4.5 Å shifts away from the 5-fold axis in the active site α-helices spanning residues 218–232 and 246–254 respectively (Fig. 3C–E). Between these two extremes, the PLP-SDs of LdcIa and LdcC are similar both in the context of the decamer (Fig. 3F) and in terms of RMSDmin = 0.9 Å, which probably reflects the fact that, at the optimal pH, these lysine decarboxylases have a similar enzymatic activity. In addition, our earlier biochemical observation that the enzymatic activity of LdcIa is unaffected by RavA binding is consistent with the relatively small changes undergone by the active site upon transition from LdcIa to LdcI-LARA. Worthy of note, our previous comparison of the crystal structure of LdcIi with that of the inducible arginine decarboxylase AdiA revealed high conservation of the PLP-coordinating residues and identified a patch of negatively charged residues lining the active site channel as a potential binding site for the target amino acid substrate (Figs S3 and S4 in ref.).</text></passage><passage><infon key="section_type">RESULTS</infon><infon key="type">title_2</infon><offset>13132</offset><text>Rearrangements of the ppGpp binding pocket upon pH-dependent enzyme activation and LARA binding</text></passage><passage><infon key="section_type">RESULTS</infon><infon key="type">paragraph</infon><offset>13228</offset><text>An inhibitor of the LdcI and LdcC activity, the stringent response alarmone ppGpp, is known to bind at the interface between neighboring monomers within each ring (Fig. S4). The ppGpp binding pocket is made up by residues from all domains and is located approximately 30 Å away from the PLP moiety. Whereas the crystal structure of the ppGpp-LdcIi was solved to 2 Å resolution, only a 4.1 Å resolution structure of the ppGpp-free LdcIi could be obtained. At this resolution, the apo-LdcIi and ppGpp-LdcIi structures (both solved at pH 8.5) appeared indistinguishable except for the presence of ppGpp (Fig. S11 in ref. ). Thus, we speculated that inhibition of LdcI by ppGpp would be accompanied by a transduction of subtle structural changes at the level of individual amino acid side chains between the ppGpp binding pocket and the active site of the enzyme. All our current cryoEM reconstructions of the lysine decarboxylases were obtained in the absence of ppGpp in order to be closer to the active state of the enzymes under study. While differences in the ppGpp binding site could indeed be visualized (Fig. S4), the level of resolution warns against speculations about their significance. The fact that interaction with RavA reduces the ppGpp affinity for LdcI despite the long distance of ~30 Å between the LARA domain binding site and the closest ppGpp binding pocket (Fig. S5) seems to favor an allosteric regulation mechanism. Interestingly, although a number of ppGpp binding residues are strictly conserved between LdcI and AdiA that also forms decamers at low pH optimal for its arginine decarboxylase activity, no ppGpp regulation of AdiA could be demonstrated.</text></passage><passage><infon key="section_type">RESULTS</infon><infon key="type">title_2</infon><offset>14916</offset><text>Swinging and stretching of the CTDs upon pH-dependent LdcI activation and LARA binding</text></passage><passage><infon key="section_type">RESULTS</infon><infon key="type">paragraph</infon><offset>15003</offset><text>Inspection of the superimposed decameric structures (Figs 2 and S6) suggests a depiction of the wing domains as an anchor around which the peripheral CTDs swing. This swinging movement seems to be mediated by the core domains and is accompanied by a stretching of the whole LdcI subunits attracted by the RavA magnets. Indeed, all CTDs have very similar structures (RMSDmin &lt;1 Å). Yet the superposition of the decamers lays bare a progressive movement of the CTD as a whole upon enzyme activation by pH and the binding of LARA. The LdcIi monomer is the most compact, whereas LdcIa and especially LdcI-LARA gradually extend their CTDs towards the LARA domain of RavA (Figs 2 and 4). These small but noticeable swinging and stretching (up to ~4 Å) may be related to the incorporation of the LdcI decamer into the LdcI-RavA cage.</text></passage><passage><infon key="section_type">RESULTS</infon><infon key="type">title_2</infon><offset>15836</offset><text>The C-terminal β-sheet of a lysine decarboxylase as a major determinant of the interaction with RavA</text></passage><passage><infon key="section_type">RESULTS</infon><infon key="type">paragraph</infon><offset>15940</offset><text>In our previous contribution, based on the fit of the LdcIi and the LARA crystal structures into the LdcI-LARA cryoEM density, we predicted that the LdcI-RavA interaction should involve the C-terminal two-stranded β-sheet of the LdcI. Our present cryoEM maps and pseudoatomic models provide first structure-based insights into the differences between the inducible and the constitutive lysine decarboxylases. However, at the level of this structural element the two proteins are actually surpisingly similar. Therefore, we wanted to check the influence of the primary sequence of the two proteins in this region on their ability to interact with RavA. To this end, we swapped the relevant β-sheets of the two proteins and produced their chimeras, namely LdcIC (i.e. LdcI with the C-terminal β-sheet of LdcC) and LdcCI (i.e. LdcC with the C-terminal β-sheet of LdcI) (Fig. 5A–C). Both constructs could be purified and could form decamers visually indistinguishable from the wild-type proteins. As expected, binding of LdcI to RavA was completely abolished by this procedure and no LdcIC-RavA complex could be detected. On the contrary, introduction of the C-terminal β-sheet of LdcI into LdcC led to an assembly of the LdcCI-RavA complex. On the negative stain EM grid, the chimeric cages appeared less rigid than the native LdcI-RavA, which probably means that the environment of the β-sheet contributes to the efficiency of the interaction and the stability of the entire architecture (Fig. 5D–F).</text></passage><passage><infon key="section_type">RESULTS</infon><infon key="type">title_2</infon><offset>17457</offset><text>The C-terminal β-sheet of a lysine decarboxylase is a highly conserved signature allowing to distinguish between LdcI and LdcC</text></passage><passage><infon key="section_type">RESULTS</infon><infon key="type">paragraph</infon><offset>17587</offset><text>Alignment of the primary sequences of the E. coli LdcI and LdcC shows that some amino acid residues of the C-terminal β-sheet are the same in the two proteins, whereas others are notably different in chemical nature. Importantly, most of the amino acid differences between the two enzymes are located in this very region. Thus, to advance beyond our experimental confirmation of the C-terminal β-sheet as a major determinant of the capacity of a particular lysine decarboxylase to form a cage with RavA, we set out to investigate whether certain residues in this β-sheet are conserved in lysine decarboxylases of different enterobacteria that have the ravA-viaA operon in their genome. We inspected the genetic environment of lysine decarboxylases from 22 enterobacterial species referenced in the NCBI database, corrected the gene annotation where necessary (Tables S3 and S4), and performed multiple sequence alignment coupled to a phylogenetic analysis (see Methods). This procedure yielded several unexpected and exciting results. First of all, consensus sequence for the entire lysine decarboxylase family was derived. Second, the phylogenetic analysis clearly split the lysine decarboxylases into two groups (Fig. 6A). All lysine decarboxylases predicted to be “LdcI-like” or biodegradable based on their genetic environment, as for example their organization in an operon with a gene encoding the CadB antiporter (see Methods), were found in one group, whereas all enzymes predicted as “LdcC-like” or biosynthetic partitioned into another group. Thus, consensus sequences could also be determined for each of the two groups (Figs 6B,C and S7). Inspection of these consensus sequences revealed important differences between the groups regarding charge, size and hydrophobicity of several residues precisely at the level of the C-terminal β-sheet that is responsible for the interaction with RavA (Fig. 6B–D). For example, in our previous study, site-directed mutations identified Y697 as critically required for the RavA binding. Our current analysis shows that Y697 is strictly conserved in the “LdcI-like” group whereas the “LdcC-like” enzymes always have a lysine in this position; it also uncovers several other residues potentially essential for the interaction with RavA which can now be addressed by site-directed mutagenesis. The third and most remarkable finding was that exactly the same separation into “LdcI-like” and “LdcC”-like groups can be obtained based on a comparison of the C-terminal β-sheets only, without taking the rest of the primary sequence into account. Therefore the C-terminal β-sheet emerges as being a highly conserved signature sequence, sufficient to unambiguously discriminate between the “LdcI-like” and “LdcC-like” enterobacterial lysine decarboxylases independently of any other information (Figs 6 and S7). Our structures show that this motif is not involved in the enzymatic activity or the oligomeric state of the proteins. Thus, enterobacteria identified here (Fig. 6, Table S4) appear to exert evolutionary pressure on the biodegradative lysine decarboxylase towards the RavA binding. One of the elucidated roles of the LdcI-RavA cage is to maintain LdcI activity under conditions of enterobacterial starvation by preventing LdcI inhibition by the stringent response alarmone ppGpp. Furthermore, the recently documented interaction of both LdcI and RavA with specific subunits of the respiratory complex I, together with the unanticipated link between RavA and maturation of numerous iron-sulfur proteins, tend to suggest an additional intriguing function for this 3.5 MDa assembly. The conformational rearrangements of LdcI upon enzyme activation and RavA binding revealed in this work, and our amazing finding that the molecular determinant of the LdcI-RavA interaction is the one that straightforwardly determines if a particular enterobacterial lysine decarboxylase belongs to “LdcI-like” or “LdcC-like” proteins, should give a new impetus to functional studies of the unique LdcI-RavA cage. Besides, the structures and the pseudoatomic models of the active ppGpp-free states of both the biodegradative and the biosynthetic E. coli lysine decarboxylases offer an additional tool for analysis of their role in UPEC infectivity. Together with the apo-LdcI and ppGpp-LdcIi crystal structures, our cryoEM reconstructions provide a structural framework for future studies of structure-function relationships of lysine decarboxylases from other enterobacteria and even of their homologues outside Enterobacteriaceae. For example, the lysine decarboxylase of Eikenella corrodens is thought to play a major role in the periodontal disease and its inhibitors were shown to retard gingivitis development. Finally, cadaverine being an important platform chemical for the production of industrial polymers such as nylon, structural information is valuable for optimisation of bacterial lysine decarboxylases used for its production in biotechnology.</text></passage><passage><infon key="section_type">METHODS</infon><infon key="type">title_1</infon><offset>22628</offset><text>Methods</text></passage><passage><infon key="section_type">METHODS</infon><infon key="type">title_2</infon><offset>22636</offset><text>Protein expression and purification</text></passage><passage><infon key="section_type">METHODS</infon><infon key="type">paragraph</infon><offset>22672</offset><text>LdcI and LdcC were expressed and purified as described from an E. coli strain that cannot produce ppGpp (MG1655 ΔrelA ΔspoT strain). LdcI was stored in 20 mM Tris-HCl, 100 mM NaCl, 1 mM DTT, 0.1 mM PLP, pH 6.8 (buffer A) and LdcC in 20 mM Tris-HCl, 100 mM NaCl, 1 mM DTT, 0.1 mM PLP, pH 7.5 (buffer B).</text></passage><passage><infon key="section_type">METHODS</infon><infon key="type">paragraph</infon><offset>22993</offset><text>Chimeric LdcIC and LdcCI were constructed, expressed and purified as follows. The chimeras were designed by exchange, between LdcI and LdcC, of residues from 631 to 640 and from 697 to the C-terminus, corresponding to the regions around the two strands of the C-terminal β-sheet (Fig. 5B,C), while leaving the rest of the sequence unaltered. The synthetic ldcIC and ldcCI genes (2148 bp and 2154 bp respectively), provided within a pUC57 vector (GenScript) were subcloned into pET-TEV vector based on pET-28a (Invitrogen) containing an N-terminal TEV-cleavable 6x-His-Tag. Proteins were expressed in Rosetta 2 (DE3) cells (Novagen) in LB medium supplemented with kanamycin and chloramphenicol at 37 °C, upon induction with 0.5 mM IPTG at 18 °C. Cells were harvested by centrifugation, the pellet resuspended in a 50 mM Tris-HCl, 150 mM NaCl, pH 8 buffer supplemented with Complete EDTA free (Roche) and 0.1 mM PMSF (Sigma), and disrupted by sonication at 4 °C. After centrifugation at 75000 g at 4 °C for 20 min, the supernatant was loaded on a Ni-NTA column. The eluted protein-containing fractions were pooled and the His-Tag removed by incubation with the TEV protease at 1/100 ratio and an extensive dialysis in a 50 mM Tris-HCl, 150 mM NaCl, 1 mM DTT, 5 mM EDTA, pH 8 buffer. After a second dialysis in a 50 mM Tris-HCl, 150 mM NaCl, pH 8 buffer supplemented with 10 mM imidazole, the sample was loaded on a Ni-NTA column in the same buffer, which allowed to separate the TEV protease and LdcCI/LdcIC. Finally, the pure proteins were obtained by size exclusion chromatography on a Superdex-S200 column in buffer A.</text></passage><passage><infon key="section_type">METHODS</infon><infon key="type">title_2</infon><offset>24652</offset><text>LdcIa -cryoEM data collection and 3D reconstruction</text></passage><passage><infon key="section_type">METHODS</infon><infon key="type">paragraph</infon><offset>24704</offset><text>LdcI was prepared at 2 mg/ml in a buffer containing 25 mM MES, 100 mM NaCl, 0.2 mM PLP, 1 mM DTT, pH 6.2. 3 μl of sample were applied to glow-discharged quantifoil grids 300 mesh 2/1 (Quantifoil Micro Tools GmbH, Germany), excess solution was blotted during 2.5 s with a Vitrobot (FEI) and the grid frozen in liquid ethane. Data collection was performed on a FEI Polara microscope operated at 300 kV under low dose conditions. Micrographs were recorded on Kodak SO-163 film at 59,000 magnification, with defocus ranging from 0.6 to 4.9 μm. Films were digitized on a Zeiss scanner (Photoscan) at a step size of 7 μm giving a pixel size of 1.186 Å. The contrast transfer function (CTF) for each micrograph was determined with CTFFIND3.</text></passage><passage><infon key="section_type">METHODS</infon><infon key="type">paragraph</infon><offset>25462</offset><text>Initially ~2500 particles of 256 × 256 pixels were extracted manually, binned 4 times and subjected to one round of multivariate statistical analysis and classification using IMAGIC. Representative class averages corresponding to projections in different orientations were used as input for an ab-initio 3D reconstruction by RICOserver (rico.ibs.fr/). The resulting 3D reconstruction was refined using RELION, which yielded an 18 Å resolution map. Using projections of this model as a template, particles of size 256 × 256 pixels were semi-automatically selected from all the micrographs using the Fast Projection Matching (FPM) algorithm. The resulting dataset of ~46000 particles was processed in RELION with the previous map as an initial model and with a full CTF correction after the first peak. The final map comprised 44207 particles with a resolution of 7.4 Å as per the gold-standard FSC = 0.143 criterion. It was sharpened with EMBfactor using calculated B-factor of −350 Å2 and masked with a soft mask to obtain a final map with a resolution of 6.1 Å (Fig. S3, Table S1).</text></passage><passage><infon key="section_type">METHODS</infon><infon key="type">title_2</infon><offset>26571</offset><text>LdcC - cryoEM data collection and 3D reconstruction</text></passage><passage><infon key="section_type">METHODS</infon><infon key="type">paragraph</infon><offset>26623</offset><text>LdcC was prepared at 2 mg/ml in a buffer containing 25 mM HEPES, 100 mM NaCl, 0.2 mM PLP, 1 mM DTT, pH 7.2. Grids were prepared and sample imaged as LdcIa. Data were processed essentially as LdcIa described above. Briefly, an initial ~20 Å resolution model was generated by angular reconstitution after manual picking of circa 3000 particles from the first micrographs, filtered to 60 Å resolution, refined with RELION and used for a semi-automatic selection with FPM. The dataset was processed in RELION with a full CTF correction to yield a final reconstruction comprising 61000 particles. The map was sharpened with Relion postprocessing, using a soft mask and automated B-factor estimation (−690 Å2), yielding a map at 5.5 Å resolution (Fig. S1, Table S1).</text></passage><passage><infon key="section_type">METHODS</infon><infon key="type">title_2</infon><offset>27400</offset><text>LdcI-LARA - 3D reconstruction</text></passage><passage><infon key="section_type">METHODS</infon><infon key="type">paragraph</infon><offset>27430</offset><text>In our first study, the dataset was processed in SPIDER and the CTF correction involved a simple phase-flipping. Therefore, for consistency with the present work, we revisited the dataset and processed it in RELION with a full CTF correction after the first peak. It was sharpened with EMBfactor using calculated B-factor of −350 Å2 and masked with a soft mask to obtain a final map with a resolution of 6.2 Å (Fig. S2). This reconstruction is of a slightly better quality in terms of the continuity of the internal density. Therefore we used this improved map for fitting of the atomic model and further analysis (Fig. S2, Table S1).</text></passage><passage><infon key="section_type">METHODS</infon><infon key="type">title_2</infon><offset>28073</offset><text>Additional image processing</text></passage><passage><infon key="section_type">METHODS</infon><infon key="type">paragraph</infon><offset>28101</offset><text>As a crosscheck, each data set was also refined either from other initial models: a “featureless donut” with approximate dimensions of the decamer, and low pass-filtered reconstructions from the two other data sets (i.e. the LdcC reconstruction was used as a model for the LdcIa and LdcI-LARA data sets, etc). All refinements converged to the same solutions independently of the starting model. Local resolution of all maps was determined with ResMap.</text></passage><passage><infon key="section_type">METHODS</infon><infon key="type">title_2</infon><offset>28557</offset><text>LdcCI and LdcIC chimeras —negative stain EM and 2D image analysis</text></passage><passage><infon key="section_type">METHODS</infon><infon key="type">paragraph</infon><offset>28625</offset><text>0.4 mg/ml of RavA (in a 20 mM Tris-HCl, 500 mM NaCl, 10 mM MgCl2, 1 mM DTT, 5% glycerol, pH 6.8 buffer) was mixed with 0.3 mg/ml of either LdcI, LdcC, LdcCI or LdcIC in the presence of 2 mM ADP and 10 mM MgCl2 in a buffer containing 20 mM Hepes and 150 mM NaCl at pH 7.4. After 10 minutes incubation at room temperature, 3 μl of mixture were applied to the clear side of the carbon on a carbon-mica interface and negatively stained with 2% uranyl acetate. Images were recorded with a JEOL 1200 EX II microscope at 100 kV at a nominal magnification of 15000 on a CCD camera yielding a pixel size of 4.667 Å. No complexes between RavA and LdcC or LdcIC could be observed, whereas the LdcCI-RavA preparation manifested cage-like particles similar to the previously published LdcI-RavA, but also unbound RavA and LdcCI, which implies that the affinity of RavA to the LdcCI chimera is lower than its affinity to the native LdcI. 1260 particles of 96 × 96 pixels were extracted interactively from several micrographs. 2D centering, multivariate statistical analysis and classification were performed using IMAGIC. Class-averages similar to the cage-like LdcI-RavA complex were used as references for multi-reference alignment followed by multivariate statistical analysis and classification.</text></passage><passage><infon key="section_type">METHODS</infon><infon key="type">title_2</infon><offset>29946</offset><text>Fitting of atomic models into cryoEM maps</text></passage><passage><infon key="section_type">METHODS</infon><infon key="type">paragraph</infon><offset>29988</offset><text>A homology model of LdcC was obtained using the atomic coordinates of the LdcI monomer (3N75) as the template in SWISS-MODEL server. The RMSD between the template and the resulting model was 0.26 Å. The LdcC model was then fitted as a rigid body into the LdcC cryoEM map using the fit-in-map module of UCSF Chimera. This rigid fit indicated movements of several parts of the protein. Therefore, the density corresponding to one LdcC monomer was extracted and flexible fitting was performed using IMODFIT at 8 Å resolution. This monomeric model was then docked into the decameric cryoEM map with URO and its graphical version VEDA that use symmetry information for fitting in Fourier space. The Cα RMSDmin between the initial model of the LdcC monomer and the final IMODFIT LdcC model is 1.2 Å. In the case of LdcIa, the density corresponding to an individual monomer was extracted and the fit performed similarly to the one described above, with the final model of the decameric particle obtained with URO and VEDA. The Cα RMSDmin between the LdcIi monomer and the final IMODFIT model is 1.4 Å. For LdcI-LARA, the density accounting for one LdcI monomer bound to a LARA domain was extracted and further separated into individual densities corresponding to LdcI and to LARA. The fit of LdcI was performed as for LdcC and LdcIa, while the crystal structure of LARA was docked into the monomeric LdcI-LARA map as a rigid body using SITUS. The resulting pseudoatomic models were used to create the final model of the LdcI-LARA decamer with URO and VEDA. The Cα RMSDmin between the LdcIi monomer and the final IMODFIT model is 1.4 Å. A brief summary of relevant parameters is provided in Table S1.</text></passage><passage><infon key="section_type">METHODS</infon><infon key="type">title_2</infon><offset>31699</offset><text>Sequence analysis</text></passage><passage><infon key="section_type">METHODS</infon><infon key="type">paragraph</infon><offset>31717</offset><text>Out of a non-exhaustive list of 50 species of Enterobacteriaceae (Table S3), 22 were found to contain genes annotated as ldcI or ldcC and containing the ravA-viaA operon (Table S4). An analysis using MUSCLE with default parameters showed that these genes share more than 65% identity. To verify annotation of these genes, we compared their genetic environment with that of E. coli ldcI and ldcC. Indeed, in E. coli the ldcI gene is in operon with the cadB gene encoding a lysine-cadaverine antiporter, whereas the ldcC gene is present between the accA gene (encoding an acetyl-CoA carboxylase alpha subunit carboxyltransferase) and the yaeR gene (coding for an unknown protein belonging to the family of Glyoxalase/Dioxygenase/Bleomycin resistance proteins). Compared with this genetic environment, the annotation of several ldcI and ldcC genes in enterobacteria was found to be inconsistent (Table S4). For example, several strains contain genes annotated as ldcC in the genetic background of ldcI and vice versa, as in the case of Salmonella enterica and Trabulsiella guamensi. Furthermore, the gene with an “ldcC-like” environment was found to be annotated as cadA in particular strains of Citrobacter freundii, Cronobacter sakazakii, Enterobacter cloacae subsp. Cloaca, Erwinia amylovora, Pantoea agglomerans, Rahnella aquatilis, Shigella dysenteriae, and Yersinia enterocolitica subsp. enterocolitica, whereas in Hafnia alvei, Kluyvera ascorbata, and Serratia marcescens subsp. marcescens, the gene with an “ldcI-like” environment was found to be annotated as ldcC. In addition, as far as the genetic environment is concerned, Plesiomonas appears to have two ldc genes with the organization of the E. coli ldcI (operon cadA-cadB). Consequently, we corrected for gene annotation consistent with the genetic environment and made multiple sequence alignments using version 8.0.1 of the CLC Genomics Workbench software. A phylogenetic tree was generated based on Maximum Likelihood and following the Neighbor-Joining method with the WAG protein substitution model. The reliability of the generated phylogenetic tree was assessed by bootstrap analysis. The presented unrooted phylogenetic tree shows the nodes that are reliable over 95% (Fig. 6A). Remarkably, the multiple sequence alignment and the resulting phylogenetic tree clearly grouped together all sequences annotated as ldcI on the one side, and all sequences annotated as ldcC on the other side. Thus, we conclude that all modifications in gene annotations that we introduced for the sake of consistency with the genetic environment are perfectly corroborated by the multiple sequence alignment and the phylogenetic analysis. Since the regulation of the lysine decarboxylase gene (i.e. inducible or constitutive) cannot be assessed by this analysis, we call the resulting groups “ldcI-like” and “ldcC-like” as referred to the E. coli enzymes, and make a parallel between the membership in a given group and the ability of the protein to form a cage complex with RavA.</text></passage><passage><infon key="section_type">METHODS</infon><infon key="type">title_1</infon><offset>34762</offset><text>Additional Information</text></passage><passage><infon key="section_type">METHODS</infon><infon key="type">paragraph</infon><offset>34785</offset><text>Accession codes: CryoEM maps and corresponding fitted atomic structures (main chain atoms) have been deposited in the Electron Microscopy Data Bank and Protein Data Bank, respectively, with accession codes EMD-3205 and 5FKZ for LdcC, EMD-3204 and 5FKX for LdcIa and EMD-3206 and 5FL2 for LdcI-LARA.</text></passage><passage><infon key="section_type">METHODS</infon><infon key="type">paragraph</infon><offset>35084</offset><text>How to cite this article: Kandiah, E. et al. Structural insights into the Escherichia coli lysine decarboxylases and molecular determinants of interaction with the AAA+ ATPase RavA. Sci. Rep. 6, 24601; doi: 10.1038/srep24601 (2016).</text></passage><passage><infon key="section_type">SUPPL</infon><infon key="type">title_1</infon><offset>35317</offset><text>Supplementary Material</text></passage><passage><infon key="fpage">436</infon><infon key="lpage">447</infon><infon key="name_0">surname:Christen;given-names:P.</infon><infon key="name_1">surname:Mehta;given-names:P. K.</infon><infon key="section_type">REF</infon><infon key="source">Chem. Rec.
+N. Y. N</infon><infon key="type">ref</infon><infon key="volume">1</infon><infon key="year">2001</infon><offset>35340</offset><text>From cofactor to enzymes. The molecular evolution of pyridoxal-5′-phosphate-dependent enzymes</text></passage><passage><infon key="fpage">383</infon><infon key="lpage">415</infon><infon key="name_0">surname:Eliot;given-names:A. C.</infon><infon key="name_1">surname:Kirsch;given-names:J. F.</infon><infon key="pub-id_pmid">15189147</infon><infon key="section_type">REF</infon><infon key="source">Annu. Rev. Biochem.</infon><infon key="type">ref</infon><infon key="volume">73</infon><infon key="year">2004</infon><offset>35436</offset><text>Pyridoxal phosphate enzymes: mechanistic, structural, and evolutionary considerations</text></passage><passage><infon key="fpage">301</infon><infon key="lpage">314</infon><infon key="name_0">surname:Zhao;given-names:B.</infon><infon key="name_1">surname:Houry;given-names:W. A.</infon><infon key="section_type">REF</infon><infon key="source">Biochem. Cell Biol. Biochim. Biol. Cell.</infon><infon key="type">ref</infon><infon key="volume">88</infon><infon key="year">2010</infon><offset>35522</offset><text>Acid stress response in enteropathogenic gammaproteobacteria: an aptitude for survival</text></passage><passage><infon key="fpage">65</infon><infon key="lpage">81</infon><infon key="name_0">surname:Kanjee;given-names:U.</infon><infon key="name_1">surname:Houry;given-names:W. A.</infon><infon key="pub-id_pmid">23701194</infon><infon key="section_type">REF</infon><infon key="source">Annu. Rev.
+Microbiol.</infon><infon key="type">ref</infon><infon key="volume">67</infon><infon key="year">2013</infon><offset>35609</offset><text>Mechanisms of acid resistance in Escherichia coli</text></passage><passage><infon key="fpage">e22397</infon><infon key="name_0">surname:Viala;given-names:J. P. M.</infon><infon key="pub-id_pmid">21799843</infon><infon key="section_type">REF</infon><infon key="source">PloS One</infon><infon key="type">ref</infon><infon key="volume">6</infon><infon key="year">2011</infon><offset>35659</offset><text>Sensing and adaptation to low pH mediated by inducible amino acid decarboxylases in Salmonella</text></passage><passage><infon key="fpage">600</infon><infon key="lpage">618</infon><infon key="name_0">surname:Gale;given-names:E. F.</infon><infon key="name_1">surname:Epps;given-names:H. M.</infon><infon key="pub-id_pmid">16747564</infon><infon key="section_type">REF</infon><infon key="source">Biochem.
+J.</infon><infon key="type">ref</infon><infon key="volume">36</infon><infon key="year">1942</infon><offset>35754</offset><text>The effect of the pH of the medium during growth on the enzymic activities of bacteria (Escherichia coli and Micrococcus lysodeikticus) and the biological significance of the changes produced</text></passage><passage><infon key="fpage">232</infon><infon key="lpage">242</infon><infon key="name_0">surname:Gale;given-names:E. F.</infon><infon key="name_1">surname:Epps;given-names:H. M.</infon><infon key="pub-id_pmid">16747785</infon><infon key="section_type">REF</infon><infon key="source">Biochem. J.</infon><infon key="type">ref</infon><infon key="volume">38</infon><infon key="year">1944</infon><offset>35946</offset><text>Studies on bacterial amino-acid decarboxylases: 1. l(+)-lysine decarboxylase</text></passage><passage><infon key="fpage">836</infon><infon key="lpage">849</infon><infon key="name_0">surname:Merrell;given-names:D. S.</infon><infon key="name_1">surname:Camilli;given-names:A.</infon><infon key="pub-id_pmid">10564522</infon><infon key="section_type">REF</infon><infon key="source">Mol. Microbiol.</infon><infon key="type">ref</infon><infon key="volume">34</infon><infon key="year">1999</infon><offset>36023</offset><text>The cadA gene of Vibrio cholerae is induced during infection and plays a role in acid tolerance</text></passage><passage><infon key="fpage">8586</infon><infon key="lpage">8592</infon><infon key="name_0">surname:Kim;given-names:J.-S.</infon><infon key="name_1">surname:Choi;given-names:S. H.</infon><infon key="name_2">surname:Lee;given-names:J.
+K.</infon><infon key="pub-id_pmid">17012399</infon><infon key="section_type">REF</infon><infon key="source">J. Bacteriol.</infon><infon key="type">ref</infon><infon key="volume">188</infon><infon key="year">2006</infon><offset>36119</offset><text>Lysine decarboxylase expression by Vibrio vulnificus is induced by SoxR in response to superoxide stress</text></passage><passage><infon key="fpage">928</infon><infon key="lpage">933</infon><infon key="name_0">surname:Bower;given-names:J. M.</infon><infon key="name_1">surname:Mulvey;given-names:M. A.</infon><infon key="pub-id_pmid">16428396</infon><infon key="section_type">REF</infon><infon key="source">J. Bacteriol.</infon><infon key="type">ref</infon><infon key="volume">188</infon><infon key="year">2006</infon><offset>36224</offset><text>Polyamine-mediated resistance of uropathogenic Escherichia coli to nitrosative stress</text></passage><passage><infon key="fpage">2104</infon><infon key="lpage">2112</infon><infon key="name_0">surname:Bower;given-names:J. M.</infon><infon key="name_1">surname:Gordon-Raagas;given-names:H. B.</infon><infon key="name_2">surname:Mulvey;given-names:M. A.</infon><infon key="pub-id_pmid">19255192</infon><infon key="section_type">REF</infon><infon key="source">Infect. Immun.</infon><infon key="type">ref</infon><infon key="volume">77</infon><infon key="year">2009</infon><offset>36310</offset><text>Conditioning of uropathogenic Escherichia coli for enhanced colonization of host</text></passage><passage><infon key="fpage">575</infon><infon key="lpage">579</infon><infon key="name_0">surname:Akhova;given-names:A. V.</infon><infon key="name_1">surname:Tkachenko;given-names:A. G.</infon><infon key="section_type">REF</infon><infon key="source">Microbiology</infon><infon key="type">ref</infon><infon key="volume">78</infon><infon key="year">2009</infon><offset>36391</offset><text>Lysine Decarboxylase Activity as a Factor of Fluoroquinolone Resistance in Escherichia coli</text></passage><passage><infon key="fpage">1267</infon><infon key="lpage">1270</infon><infon key="name_0">surname:Kikuchi;given-names:Y.</infon><infon key="name_1">surname:Kurahashi;given-names:O.</infon><infon key="name_2">surname:Nagano;given-names:T.</infon><infon key="name_3">surname:Kamio;given-names:Y.</infon><infon key="pub-id_pmid">9692215</infon><infon key="section_type">REF</infon><infon key="source">Biosci. Biotechnol. Biochem.</infon><infon key="type">ref</infon><infon key="volume">62</infon><infon key="year">1998</infon><offset>36483</offset><text>RpoS-dependent expression of the second lysine decarboxylase gene in Escherichia coli</text></passage><passage><infon key="fpage">13</infon><infon key="lpage">19</infon><infon key="name_0">surname:Samartzidou;given-names:H.</infon><infon key="name_1">surname:Mehrazin;given-names:M.</infon><infon key="name_2">surname:Xu;given-names:Z.</infon><infon key="name_3">surname:Benedik;given-names:M.
+J.</infon><infon key="name_4">surname:Delcour;given-names:A.
+H.</infon><infon key="pub-id_pmid">12486035</infon><infon key="section_type">REF</infon><infon key="source">J. Bacteriol.</infon><infon key="type">ref</infon><infon key="volume">185</infon><infon key="year">2003</infon><offset>36569</offset><text>Cadaverine inhibition of porin plays a role in cell survival at acidic pH</text></passage><passage><infon key="fpage">330</infon><infon key="lpage">334</infon><infon key="name_0">surname:Bekhit;given-names:A.</infon><infon key="name_1">surname:Fukamachi;given-names:T.</infon><infon key="name_2">surname:Saito;given-names:H.</infon><infon key="name_3">surname:Kobayashi;given-names:H.</infon><infon key="pub-id_pmid">21372380</infon><infon key="section_type">REF</infon><infon key="source">Biol. Pharm. Bull.</infon><infon key="type">ref</infon><infon key="volume">34</infon><infon key="year">2011</infon><offset>36643</offset><text>The role of OmpC and OmpF in acidic resistance in Escherichia coli</text></passage><passage><infon key="fpage">1042</infon><infon key="lpage">1049</infon><infon key="name_0">surname:Tkachenko;given-names:A. G.</infon><infon key="name_1">surname:Pozhidaeva;given-names:O. N.</infon><infon key="name_2">surname:Shumkov;given-names:M. S.</infon><infon key="section_type">REF</infon><infon key="source">Biochem.
+Biokhimiia</infon><infon key="type">ref</infon><infon key="volume">71</infon><infon key="year">2006</infon><offset>36710</offset><text>Role of polyamines in formation of multiple antibiotic resistance of Escherichia coli under stress conditions</text></passage><passage><infon key="fpage">931</infon><infon key="lpage">944</infon><infon key="name_0">surname:Kanjee;given-names:U.</infon><infon key="pub-id_pmid">21278708</infon><infon key="section_type">REF</infon><infon key="source">EMBO J.</infon><infon key="type">ref</infon><infon key="volume">30</infon><infon key="year">2011</infon><offset>36820</offset><text>Linkage between the bacterial acid stress and stringent responses: the structure of the inducible lysine decarboxylase</text></passage><passage><infon key="fpage">662</infon><infon key="lpage">670</infon><infon key="name_0">surname:Sabo;given-names:D. L.</infon><infon key="name_1">surname:Boeker;given-names:E. A.</infon><infon key="name_2">surname:Byers;given-names:B.</infon><infon key="name_3">surname:Waron;given-names:H.</infon><infon key="name_4">surname:Fischer;given-names:E. H.</infon><infon key="section_type">REF</infon><infon key="source">Biochemistry (Mosc.)</infon><infon key="type">ref</infon><infon key="volume">13</infon><infon key="year">1974</infon><offset>36939</offset><text>Purification and physical properties of inducible Escherichia coli lysine decarboxylase</text></passage><passage><infon key="fpage">1532</infon><infon key="lpage">1546</infon><infon key="name_0">surname:Snider;given-names:J.</infon><infon key="pub-id_pmid">16301313</infon><infon key="section_type">REF</infon><infon key="source">J. Biol. Chem.</infon><infon key="type">ref</infon><infon key="volume">281</infon><infon key="year">2006</infon><offset>37027</offset><text>Formation of a distinctive complex between the inducible bacterial lysine decarboxylase and a novel AAA+ ATPase</text></passage><passage><infon key="fpage">211</infon><infon key="lpage">221</infon><infon key="name_0">surname:Wong;given-names:K. S.</infon><infon key="name_1">surname:Houry;given-names:W. A.</infon><infon key="pub-id_pmid">22491058</infon><infon key="section_type">REF</infon><infon key="source">J. Struct. Biol.</infon><infon key="type">ref</infon><infon key="volume">179</infon><infon key="year">2012</infon><offset>37139</offset><text>Novel structural and functional insights into the MoxR family of AAA+ ATPases</text></passage><passage><infon key="fpage">22499</infon><infon key="lpage">22504</infon><infon key="name_0">surname:El Bakkouri;given-names:M.</infon><infon key="pub-id_pmid">21148420</infon><infon key="section_type">REF</infon><infon key="source">Proc. Natl. Acad. Sci. USA</infon><infon key="type">ref</infon><infon key="volume">107</infon><infon key="year">2010</infon><offset>37217</offset><text>Structure of RavA MoxR AAA+ protein reveals the design principles of a molecular cage modulating the inducible lysine decarboxylase activity</text></passage><passage><infon key="fpage">e85529</infon><infon key="name_0">surname:Wong;given-names:K. S.</infon><infon key="pub-id_pmid">24454883</infon><infon key="section_type">REF</infon><infon key="source">PloS
+One</infon><infon key="type">ref</infon><infon key="volume">9</infon><infon key="year">2014</infon><offset>37358</offset><text>The MoxR ATPase RavA and its cofactor ViaA interact with the NADH:ubiquinone oxidoreductase I in Escherichia coli</text></passage><passage><infon key="fpage">e03653</infon><infon key="name_0">surname:Malet;given-names:H.</infon><infon key="pub-id_pmid">25097238</infon><infon key="section_type">REF</infon><infon key="source">eLife</infon><infon key="type">ref</infon><infon key="volume">3</infon><infon key="year">2014</infon><offset>37472</offset><text>Assembly principles of a unique cage formed by hexameric and decameric E. coli proteins</text></passage><passage><infon key="fpage">167</infon><infon key="lpage">172</infon><infon key="name_0">surname:Yamamoto;given-names:Y.</infon><infon key="name_1">surname:Miwa;given-names:Y.</infon><infon key="name_2">surname:Miyoshi;given-names:K.</infon><infon key="name_3">surname:Furuyama;given-names:J.</infon><infon key="name_4">surname:Ohmori;given-names:H.</infon><infon key="pub-id_pmid">9339543</infon><infon key="section_type">REF</infon><infon key="source">Genes Genet. Syst.</infon><infon key="type">ref</infon><infon key="volume">72</infon><infon key="year">1997</infon><offset>37560</offset><text>The Escherichia coli ldcC gene encodes another lysine decarboxylase, probably a constitutive enzyme</text></passage><passage><infon key="fpage">857</infon><infon key="lpage">876</infon><infon key="name_0">surname:Käck;given-names:H.</infon><infon key="name_1">surname:Sandmark;given-names:J.</infon><infon key="name_2">surname:Gibson;given-names:K.</infon><infon key="name_3">surname:Schneider;given-names:G.</infon><infon key="name_4">surname:Lindqvist;given-names:Y.</infon><infon key="pub-id_pmid">10452893</infon><infon key="section_type">REF</infon><infon key="source">J. Mol. Biol.</infon><infon key="type">ref</infon><infon key="volume">291</infon><infon key="year">1999</infon><offset>37660</offset><text>Crystal structure of diaminopelargonic acid synthase: evolutionary relationships between pyridoxal-5′-phosphate-dependent enzymes</text></passage><passage><infon key="fpage">9388</infon><infon key="lpage">9398</infon><infon key="name_0">surname:Kanjee;given-names:U.</infon><infon key="name_1">surname:Gutsche;given-names:I.</infon><infon key="name_2">surname:Ramachandran;given-names:S.</infon><infon key="name_3">surname:Houry;given-names:W.
+A.</infon><infon key="section_type">REF</infon><infon key="source">Biochemistry
+(Mosc.)</infon><infon key="type">ref</infon><infon key="volume">50</infon><infon key="year">2011</infon><offset>37792</offset><text>The enzymatic activities of the Escherichia coli basic aliphatic amino acid decarboxylases exhibit a pH zone of inhibition</text></passage><passage><infon key="fpage">863</infon><infon key="lpage">871</infon><infon key="name_0">surname:Erhardt;given-names:H.</infon><infon key="pub-id_pmid">22063474</infon><infon key="section_type">REF</infon><infon key="source">Biochim. Biophys. Acta</infon><infon key="type">ref</infon><infon key="volume">1817</infon><infon key="year">2012</infon><offset>37915</offset><text>Disruption of individual nuo-genes leads to the formation of partially assembled NADH:ubiquinone oxidoreductase (complex I) in Escherichia coli</text></passage><passage><infon key="fpage">1176</infon><infon key="lpage">1184</infon><infon key="name_0">surname:Lohinai;given-names:Z.</infon><infon key="pub-id_pmid">26110450</infon><infon key="section_type">REF</infon><infon key="source">J. Periodontol.</infon><infon key="type">ref</infon><infon key="volume">86</infon><infon key="year">2015</infon><offset>38059</offset><text>Biofilm Lysine Decarboxylase, a New Therapeutic Target for Periodontal Inflammation</text></passage><passage><infon key="fpage">6706</infon><infon key="lpage">6712</infon><infon key="name_0">surname:Peters;given-names:J. L.</infon><infon key="pub-id_pmid">22975025</infon><infon key="section_type">REF</infon><infon key="source">Vaccine</infon><infon key="type">ref</infon><infon key="volume">30</infon><infon key="year">2012</infon><offset>38143</offset><text>Effects of immunization with natural and recombinant lysine decarboxylase on canine gingivitis development</text></passage><passage><infon key="fpage">1048</infon><infon key="lpage">1056</infon><infon key="name_0">surname:Lohinai;given-names:Z.</infon><infon key="pub-id_pmid">22141361</infon><infon key="section_type">REF</infon><infon key="source">J. Periodontol.</infon><infon key="type">ref</infon><infon key="volume">83</infon><infon key="year">2012</infon><offset>38250</offset><text>Bacterial lysine decarboxylase influences human dental biofilm lysine content, biofilm accumulation, and subclinical gingival inflammation</text></passage><passage><infon key="fpage">1108</infon><infon key="lpage">1113</infon><infon key="name_0">surname:Kim;given-names:H. J.</infon><infon key="pub-id_pmid">25674800</infon><infon key="section_type">REF</infon><infon key="source">J. Microbiol. Biotechnol</infon><infon key="type">ref</infon><infon key="volume">25</infon><infon key="year">2015</infon><offset>38389</offset><text>Optimization of Direct Lysine Decarboxylase Biotransformation for Cadaverine Production with Whole-Cell Biocatalysts at High Lysine Concentration</text></passage><passage><infon key="fpage">799</infon><infon key="lpage">806</infon><infon key="name_0">surname:Ma;given-names:W.</infon><infon key="pub-id_pmid">25515797</infon><infon key="section_type">REF</infon><infon key="source">Biotechnol. Lett.</infon><infon key="type">ref</infon><infon key="volume">37</infon><infon key="year">2015</infon><offset>38535</offset><text>Enhanced cadaverine production from L-lysine using recombinant Escherichia coli co-overexpressing CadA and CadB</text></passage><passage><infon key="fpage">965</infon><infon key="lpage">972</infon><infon key="name_0">surname:Li;given-names:N.</infon><infon key="name_1">surname:Chou;given-names:H.</infon><infon key="name_2">surname:Yu;given-names:L.</infon><infon key="name_3">surname:Xu;given-names:Y.</infon><infon key="section_type">REF</infon><infon key="source">Biotechnol. Bioprocess Eng.</infon><infon key="type">ref</infon><infon key="volume">19</infon><infon key="year">2014</infon><offset>38647</offset><text>Cadaverine production by heterologous expression of Klebsiella oxytoca lysine decarboxylase</text></passage><passage><infon key="fpage">129</infon><infon key="lpage">228</infon><infon key="name_0">surname:Dubochet;given-names:J.</infon><infon key="pub-id_pmid">3043536</infon><infon key="section_type">REF</infon><infon key="source">Q. Rev.
+Biophys.</infon><infon key="type">ref</infon><infon key="volume">21</infon><infon key="year">1988</infon><offset>38739</offset><text>Cryo-electron microscopy of vitrified specimens</text></passage><passage><infon key="fpage">334</infon><infon key="lpage">347</infon><infon key="name_0">surname:Mindell;given-names:J. A.</infon><infon key="name_1">surname:Grigorieff;given-names:N.</infon><infon key="pub-id_pmid">12781660</infon><infon key="section_type">REF</infon><infon key="source">J. Struct. Biol.</infon><infon key="type">ref</infon><infon key="volume">142</infon><infon key="year">2003</infon><offset>38787</offset><text>Accurate determination of local defocus and specimen tilt in electron microscopy</text></passage><passage><infon key="fpage">17</infon><infon key="lpage">24</infon><infon key="name_0">surname:van Heel;given-names:M.</infon><infon key="name_1">surname:Harauz;given-names:G.</infon><infon key="name_2">surname:Orlova;given-names:E.
+V.</infon><infon key="name_3">surname:Schmidt;given-names:R.</infon><infon key="name_4">surname:Schatz;given-names:M.</infon><infon key="pub-id_pmid">8742718</infon><infon key="section_type">REF</infon><infon key="source">J.
+Struct. Biol.</infon><infon key="type">ref</infon><infon key="volume">116</infon><infon key="year">1996</infon><offset>38868</offset><text>A new generation of the IMAGIC image processing system</text></passage><passage><infon key="fpage">13</infon><infon key="lpage">23</infon><infon key="name_0">surname:Navaza;given-names:J.</infon><infon key="pub-id_pmid">14643206</infon><infon key="section_type">REF</infon><infon key="source">J. Struct. Biol.</infon><infon key="type">ref</infon><infon key="volume">144</infon><infon key="year">2003</infon><offset>38923</offset><text>On the three-dimensional reconstruction of icosahedral particles</text></passage><passage><infon key="fpage">519</infon><infon key="lpage">530</infon><infon key="name_0">surname:Scheres;given-names:S. H. W.</infon><infon key="pub-id_pmid">23000701</infon><infon key="section_type">REF</infon><infon key="source">J. Struct. Biol.</infon><infon key="type">ref</infon><infon key="volume">180</infon><infon key="year">2012</infon><offset>38988</offset><text>RELION: implementation of a Bayesian approach to cryo-EM structure determination</text></passage><passage><infon key="fpage">253</infon><infon key="lpage">260</infon><infon key="name_0">surname:Estrozi;given-names:L. F.</infon><infon key="name_1">surname:Navaza;given-names:J.</infon><infon key="pub-id_pmid">20599509</infon><infon key="section_type">REF</infon><infon key="source">J. Struct. Biol.</infon><infon key="type">ref</infon><infon key="volume">172</infon><infon key="year">2010</infon><offset>39069</offset><text>Ab initio high-resolution single-particle 3D reconstructions: the symmetry adapted functions way</text></passage><passage><infon key="fpage">853</infon><infon key="lpage">854</infon><infon key="name_0">surname:Scheres;given-names:S. H. W.</infon><infon key="name_1">surname:Chen;given-names:S.</infon><infon key="pub-id_pmid">22842542</infon><infon key="section_type">REF</infon><infon key="source">Nat. Methods</infon><infon key="type">ref</infon><infon key="volume">9</infon><infon key="year">2012</infon><offset>39166</offset><text>Prevention of overfitting in cryo-EM structure determination</text></passage><passage><infon key="fpage">170</infon><infon key="lpage">175</infon><infon key="name_0">surname:Fernández;given-names:J. J.</infon><infon key="name_1">surname:Luque;given-names:D.</infon><infon key="name_2">surname:Castón;given-names:J. R.</infon><infon key="name_3">surname:Carrascosa;given-names:J. L.</infon><infon key="pub-id_pmid">18614378</infon><infon key="section_type">REF</infon><infon key="source">J. Struct. Biol.</infon><infon key="type">ref</infon><infon key="volume">164</infon><infon key="year">2008</infon><offset>39227</offset><text>Sharpening high resolution information in single particle electron cryomicroscopy</text></passage><passage><infon key="fpage">63</infon><infon key="lpage">65</infon><infon key="name_0">surname:Kucukelbir;given-names:A.</infon><infon key="name_1">surname:Sigworth;given-names:F. J.</infon><infon key="name_2">surname:Tagare;given-names:H. D.</infon><infon key="pub-id_pmid">24213166</infon><infon key="section_type">REF</infon><infon key="source">Nat.
+Methods</infon><infon key="type">ref</infon><infon key="volume">11</infon><infon key="year">2014</infon><offset>39309</offset><text>Quantifying the local resolution of cryo-EM density maps</text></passage><passage><infon key="fpage">3381</infon><infon key="lpage">3385</infon><infon key="name_0">surname:Schwede;given-names:T.</infon><infon key="name_1">surname:Kopp;given-names:J.</infon><infon key="name_2">surname:Guex;given-names:N.</infon><infon key="name_3">surname:Peitsch;given-names:M. C.</infon><infon key="pub-id_pmid">12824332</infon><infon key="section_type">REF</infon><infon key="source">Nucleic Acids Res.</infon><infon key="type">ref</infon><infon key="volume">31</infon><infon key="year">2003</infon><offset>39366</offset><text>SWISS-MODEL: An automated protein homology-modeling server</text></passage><passage><infon key="fpage">1605</infon><infon key="lpage">1612</infon><infon key="name_0">surname:Pettersen;given-names:E. F.</infon><infon key="pub-id_pmid">15264254</infon><infon key="section_type">REF</infon><infon key="source">J. Comput. Chem.</infon><infon key="type">ref</infon><infon key="volume">25</infon><infon key="year">2004</infon><offset>39425</offset><text>UCSF Chimera–a visualization system for exploratory research and analysis</text></passage><passage><infon key="fpage">261</infon><infon key="lpage">270</infon><infon key="name_0">surname:Lopéz-Blanco;given-names:J. R.</infon><infon key="name_1">surname:Chacón;given-names:P.</infon><infon key="pub-id_pmid">23999189</infon><infon key="section_type">REF</infon><infon key="source">J. Struct. Biol.</infon><infon key="type">ref</infon><infon key="volume">184</infon><infon key="year">2013</infon><offset>39501</offset><text>iMODFIT: efficient and robust flexible fitting based on vibrational analysis in internal coordinates</text></passage><passage><infon key="fpage">1820</infon><infon key="lpage">1825</infon><infon key="name_0">surname:Navaza;given-names:J.</infon><infon key="name_1">surname:Lepault;given-names:J.</infon><infon key="name_2">surname:Rey;given-names:F. A.</infon><infon key="name_3">surname:Alvarez-Rúa;given-names:C.</infon><infon key="name_4">surname:Borge;given-names:J.</infon><infon key="pub-id_pmid">12351826</infon><infon key="section_type">REF</infon><infon key="source">Acta Crystallogr. D Biol.
+Crystallogr</infon><infon key="type">ref</infon><infon key="volume">58</infon><infon key="year">2002</infon><offset>39602</offset><text>On the fitting of model electron densities into EM reconstructions: a reciprocal-space formulation</text></passage><passage><infon key="fpage">651</infon><infon key="lpage">658</infon><infon key="name_0">surname:Siebert;given-names:X.</infon><infon key="name_1">surname:Navaza;given-names:J.</infon><infon key="pub-id_pmid">19564685</infon><infon key="section_type">REF</infon><infon key="source">Acta Crystallogr. D Biol.
+Crystallogr</infon><infon key="type">ref</infon><infon key="volume">65</infon><infon key="year">2009</infon><offset>39701</offset><text>UROX 2.0: an interactive tool for fitting atomic models into electron-microscopy reconstructions</text></passage><passage><infon key="fpage">1792</infon><infon key="lpage">1797</infon><infon key="name_0">surname:Edgar;given-names:R. C.</infon><infon key="pub-id_pmid">15034147</infon><infon key="section_type">REF</infon><infon key="source">Nucleic Acids Res.</infon><infon key="type">ref</infon><infon key="volume">32</infon><infon key="year">2004</infon><offset>39798</offset><text>MUSCLE: multiple sequence alignment with high accuracy and high throughput</text></passage><passage><infon key="fpage">691</infon><infon key="lpage">699</infon><infon key="name_0">surname:Whelan;given-names:S.</infon><infon key="name_1">surname:Goldman;given-names:N.</infon><infon key="pub-id_pmid">11319253</infon><infon key="section_type">REF</infon><infon key="source">Mol. Biol.
+Evol.</infon><infon key="type">ref</infon><infon key="volume">18</infon><infon key="year">2001</infon><offset>39873</offset><text>A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach</text></passage><passage><infon key="section_type">SUPPL</infon><infon key="type">footnote</infon><offset>39995</offset><text>Author Contributions E.K., H.M. and I.G. carried out EM data collection with assistance of M.B. and analyzed the data. D.C. performed cloning, multiple sequence alignment and phylogenetic analysis under the direction of S.E. and I.G., J.P. cloned and purified chimeric proteins under the direction of S.O.C., K.L. and S.W.S.C. purified LdcI, LdcC and LARA under the direction of W.A.H., I.G. conceived and directed the studies and wrote the manuscript with input from E.K.</text></passage><passage><infon key="file">srep24601-f1.jpg</infon><infon key="id">f1</infon><infon key="section_type">FIG</infon><infon key="type">fig_title_caption</infon><offset>40468</offset><text>3D cryoEM reconstructions of LdcC, LdcI-LARA and LdcIa.</text></passage><passage><infon key="file">srep24601-f1.jpg</infon><infon key="id">f1</infon><infon key="section_type">FIG</infon><infon key="type">fig_caption</infon><offset>40524</offset><text>(A,C,E) cryoEM map of the LdcC (A), LdcIa
+(C) and LdcI-LARA (E) decamers with one protomer in light
+grey. In the rest of the protomers, the wing, core and C-terminal domains
+are colored from light to dark in shades of green for LdcC (A), pink
+for LdcIa (C) and blue for LdcI in LdcI-LARA (E).
+In (E), the LARA domain density is shown in dark grey. Two monomers
+making a dimer are delineated. Scale bar 50 Å.
+(B,D,F) One protomer from the cryoEM map of the LdcC (B),
+LdcIa (D) and LdcI-LARA (F) in light grey with
+the pseudoatomic model represented as cartoons and colored as the densities
+in (A,C,E). Each domain is indicated for clarity. Scale bar
+50 Å. See also Figs S1 and S3.</text></passage><passage><infon key="file">srep24601-f2.jpg</infon><infon key="id">f2</infon><infon key="section_type">FIG</infon><infon key="type">fig_title_caption</infon><offset>41210</offset><text>Analysis of conformational rearrangements.</text></passage><passage><infon key="file">srep24601-f2.jpg</infon><infon key="id">f2</infon><infon key="section_type">FIG</infon><infon key="type">fig_caption</infon><offset>41253</offset><text>Superposition of the pseudoatomic models of LdcC, LdcI from LdcI-LARA and
+LdcIa colored as in Fig. 1, and the
+crystal structure of LdcIi in shades of yellow. Only one of the
+two rings of the double toroid is shown for clarity. The dashed circle
+indicates the central region that remains virtually unchanged between all
+the structures, while the periphery undergoes visible movements. Scale bar
+50 Å.</text></passage><passage><infon key="file">srep24601-f3.jpg</infon><infon key="id">f3</infon><infon key="section_type">FIG</infon><infon key="type">fig_title_caption</infon><offset>41656</offset><text>Conformational rearrangements in the enzyme active site.</text></passage><passage><infon key="file">srep24601-f3.jpg</infon><infon key="id">f3</infon><infon key="section_type">FIG</infon><infon key="type">fig_caption</infon><offset>41713</offset><text>(A) LdcIi crystal structure, with one ring represented as a
+grey surface and the second as a cartoon. A monomer with its PLP cofactor is
+delineated. The PLP moieties of the cartoon ring are shown in red.
+(B) The LdcIi dimer extracted from the crystal structure
+of the decamer. One monomer is colored in shades of yellow as in Figs 1 and 2, while the monomer
+related by C2 symmetry is grey. The PLP is red. The active site is boxed.
+(C–F) Close-up views of the active site. The PLP
+moiety in red is from the LdcIi crystal structure. We did not
+attempt to model it in the cryoEM maps. The dimer interface is shown as a
+dashed line and the active site α-helices mentioned in the text
+are highlighted. (C) Compares LdcIi (yellow) and
+LdcIa (pink), (D) compares LdcIa (pink) and
+LdcI-LARA (blue), and (E) compares LdcIi (yellow),
+LdcIa (pink) and LdcI-LARA (blue) simultaneously in order to
+show the progressive shift described in the text. (F) Shows the
+similarity between LdcIa and LdcC at the level of the secondary
+structure elements composing the active site. Colors are as in the other
+figures.</text></passage><passage><infon key="file">srep24601-f4.jpg</infon><infon key="id">f4</infon><infon key="section_type">FIG</infon><infon key="type">fig_title_caption</infon><offset>42813</offset><text>Stretching of the LdcI monomer upon pH-dependent enzyme activation and LARA
+binding.</text></passage><passage><infon key="file">srep24601-f4.jpg</infon><infon key="id">f4</infon><infon key="section_type">FIG</infon><infon key="type">fig_caption</infon><offset>42898</offset><text>(A–C) A slice through the pseudoatomic models of the LdcI
+monomers extracted from the superimposed decamers (Fig.
+2) The rectangle indicates the regions enlarged in
+(D–F). (A) compares LdcIi (yellow)
+and LdcIa (pink), (B) compares LdcIa (pink) and
+LdcI-LARA (blue), and (C) compares LdcIi (yellow),
+LdcIa (pink) and LdcI-LARA (blue) simultaneously in order to
+show the progressive stretching described in the text. The cryoEM density of
+the LARA domain is represented as a grey surface to show the position of the
+binding site and the direction of the movement. (D–F)
+Inserts zooming at the CTD part in proximity of the LARA binding site. Loop
+regions are removed for a clearer visual comparison. An arrow indicates a
+swinging movement.</text></passage><passage><infon key="file">srep24601-f5.jpg</infon><infon key="id">f5</infon><infon key="section_type">FIG</infon><infon key="type">fig_title_caption</infon><offset>43641</offset><text>Analysis of the LdcIC and LdcCI chimeras.</text></passage><passage><infon key="file">srep24601-f5.jpg</infon><infon key="id">f5</infon><infon key="section_type">FIG</infon><infon key="type">fig_caption</infon><offset>43683</offset><text>(A) A slice through the pseudoatomic models of the LdcIa
+(purple) and LdcC (green) monomers extracted from the superimposed decamers
+(Fig. 2). (B) The C-terminal
+β-sheet in LdcIa and LdcC enlarged from
+(A,C) Exchanged primary sequences (capital letters) and
+their immediate vicinity (lower case letters) colored as in
+(A,B), with the corresponding secondary structure elements
+and the amino acid numbering shown. (D,E) A gallery of negative stain
+EM images of (D) the wild type LdcI-RavA cage and (E) the
+LdcCI-RavA cage-like particles. (F) Some representative class
+averages of the LdcCI-RavA cage-like particles. Scale bar
+20 nm.</text></passage><passage><infon key="file">srep24601-f6.jpg</infon><infon key="id">f6</infon><infon key="section_type">FIG</infon><infon key="type">fig_title_caption</infon><offset>44318</offset><text>Sequence analysis of enterobacterial lysine decarboxylases.</text></passage><passage><infon key="file">srep24601-f6.jpg</infon><infon key="id">f6</infon><infon key="section_type">FIG</infon><infon key="type">fig_caption</infon><offset>44378</offset><text>(A) Maximum likelihood tree with the
+“LdcC-like” and the
+“LdcI-like” groups highlighted in green and pink,
+respectively. Only nodes with higher values than 95% are shown (500
+replicates of the original dataset, see Methods for details). Scale bar
+indicates the average number of substitutions per site. (B) Analysis
+of consensus “LdcI-like” and
+“LdcC-like” sequences around the first and second
+C-terminal β-strands. The height of the bars and the letters
+representing the amino acids reflects the degree of conservation of each
+particular position is in the alignment. Amino acids are colored according
+to a polarity color scheme with hydrophobic residues in black, hydrophilic
+in green, acidic in red and basic in blue. Numbering as in E. coli.
+(C) Signature sequences of LdcI and LdcC in the C-terminal
+β-sheet. Polarity differences are highlighted. (D)
+Position and nature of these differences at the surface of the respective
+cryoEM maps with the color code as in B. See also Fig. S7 and Tables S3 and S4.</text></passage></document></collection>

raw_BioC_XML/PMC4852598_raw.xml

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+<!DOCTYPE collection SYSTEM "BioC.dtd">
+<collection><source>PMC</source><date>20201218</date><key>pmc.key</key><document><id>4852598</id><infon key="license">CC BY</infon><passage><infon key="article-id_doi">10.1038/ncomms11337</infon><infon key="article-id_pii">ncomms11337</infon><infon key="article-id_pmc">4852598</infon><infon key="article-id_pmid">27088325</infon><infon key="elocation-id">11337</infon><infon key="license">This work is licensed under a Creative Commons Attribution 4.0
+International License. The images or other third party material in this article are
+included in the article's Creative Commons license, unless indicated otherwise
+in the credit line; if the material is not included under the Creative Commons
+license, users will need to obtain permission from the license holder to reproduce
+the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/</infon><infon key="name_0">surname:van den Berg;given-names:Bert</infon><infon key="name_1">surname:Chembath;given-names:Anupama</infon><infon key="name_2">surname:Jefferies;given-names:Damien</infon><infon key="name_3">surname:Basle;given-names:Arnaud</infon><infon key="name_4">surname:Khalid;given-names:Syma</infon><infon key="name_5">surname:Rutherford;given-names:Julian C.</infon><infon key="section_type">TITLE</infon><infon key="type">front</infon><infon key="volume">7</infon><infon key="year">2016</infon><offset>0</offset><text>Structural basis for Mep2 ammonium transceptor activation by phosphorylation</text></passage><passage><infon key="section_type">ABSTRACT</infon><infon key="type">abstract</infon><offset>77</offset><text>Mep2 proteins are fungal transceptors that play an important role as ammonium sensors in fungal development. Mep2 activity is tightly regulated by phosphorylation, but how this is achieved at the molecular level is not clear. 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. 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. The phosphorylation site in the CTR is solvent accessible and located in a negatively charged pocket ∼30 Å away from the channel exit. 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. The results allow us to propose a model for regulation of eukaryotic ammonium transport by phosphorylation.</text></passage><passage><infon key="section_type">ABSTRACT</infon><infon key="type">abstract</infon><offset>1224</offset><text> Mep2 proteins are tightly regulated fungal ammonium transporters. Here, the authors report the crystal structures of closed states of Mep2 proteins and propose a model for their regulation by comparing them with the open ammonium transporters of bacteria.</text></passage><passage><infon key="section_type">INTRO</infon><infon key="type">paragraph</infon><offset>1481</offset><text>Transceptors are membrane proteins that function not only as transporters but also as receptors/sensors during nutrient sensing to activate downstream signalling pathways. A common feature of transceptors is that they are induced when cells are starved for their substrate. 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). One of the most important unresolved questions in the field is how the transceptors couple to downstream signalling pathways. One hypothesis is that downstream signalling is dependent on a specific conformation of the transporter.</text></passage><passage><infon key="section_type">INTRO</infon><infon key="type">paragraph</infon><offset>2271</offset><text>Mep2 (methylammonium (MA) permease) proteins are ammonium transceptors that are ubiquitous in fungi. 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 environment. Fungi typically have more than one Mep paralogue, for example, Mep1-3 in S. cerevisiae. Of these, only Mep2 proteins function as ammonium receptors/sensors in fungal development. Under conditions of nitrogen limitation, Mep2 initiates a signalling cascade that results in a switch from the yeast form to filamentous (pseudohyphal) growth that may be required for fungal pathogenicity. 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). Compared with Mep1 and Mep3, Mep2 is highly expressed and functions as a low-capacity, high-affinity transporter in the uptake of MA. In addition, Mep2 is also important for uptake of ammonium produced by growth on other nitrogen sources.</text></passage><passage><infon key="section_type">INTRO</infon><infon key="type">paragraph</infon><offset>3393</offset><text>With the exception of the human RhCG structure, no structural information is available for eukaryotic ammonium transporters. By contrast, several bacterial Amt orthologues have been characterized in detail via high-resolution crystal structures and a number of molecular dynamics (MD) studies. All the solved structures including that of RhCG are very similar, establishing the basic architecture of ammonium transporters. The proteins form stable trimers, with each monomer having 11 transmembrane (TM) helices and a central channel for the transport of ammonium. All structures show the transporters in open conformations. Intriguingly, fundamental questions such as the nature of the transported substrate and the transport mechanism are still controversial. Where earlier studies favoured the transport of ammonia gas, recent data and theoretical considerations suggest that Amt/Mep proteins are instead active, electrogenic transporters of either NH4+ (uniport) or NH3/H+ (symport). 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+ symport.</text></passage><passage><infon key="section_type">INTRO</infon><infon key="type">paragraph</infon><offset>4562</offset><text>Ammonium transport is tightly regulated. In animals, this is due to toxicity of elevated intracellular ammonium levels, whereas for microorganisms ammonium is a preferred nitrogen source. In bacteria, amt genes are present in an operon with glnK, encoding a PII-like signal transduction class protein. By binding tightly to Amt proteins without inducing a conformational change in the transporter, GlnK sterically blocks ammonium conductance when nitrogen levels are sufficient. Under conditions of nitrogen limitation, GlnK becomes uridylated, blocking its ability to bind and inhibit Amt proteins. Importantly, eukaryotes do not have GlnK orthologues and have a different mechanism for regulation of ammonium transport activity. In plants, transporter phosphorylation and dephosphorylation are known to regulate activity. In S. cerevisiae, phosphorylation of Ser457 within the C-terminal region (CTR) in the cytoplasm was recently proposed to cause Mep2 opening, possibly via inducing a conformational change.</text></passage><passage><infon key="section_type">INTRO</infon><infon key="type">paragraph</infon><offset>5574</offset><text>To elucidate the mechanism of Mep2 transport regulation, we present here X-ray crystal structures of the Mep2 transceptors from S. cerevisiae and C. albicans. The structures are similar to each other but show considerable differences to all other ammonium transporter structures. The most striking difference is the fact that the Mep2 proteins have closed conformations. The putative phosphorylation site is solvent accessible and located in a negatively charged pocket ∼30 Å away from the channel exit. The channels of phosphorylation-mimicking mutants of C. albicans Mep2 are still closed but show large conformational changes within a conserved part of the CTR. Together with a structure of a C-terminal Mep2 variant lacking the segment containing the phosphorylation site, the results allow us to propose a structural model for phosphorylation-based regulation of eukaryotic ammonium transport.</text></passage><passage><infon key="section_type">RESULTS</infon><infon key="type">title_1</infon><offset>6478</offset><text>Results</text></passage><passage><infon key="section_type">RESULTS</infon><infon key="type">title_2</infon><offset>6486</offset><text>General architecture of Mep2 ammonium transceptors</text></passage><passage><infon key="section_type">RESULTS</infon><infon key="type">paragraph</infon><offset>6537</offset><text>The Mep2 protein of S. cerevisiae (ScMep2) was overexpressed in S. cerevisiae in high yields, enabling structure determination by X-ray crystallography using data to 3.2 Å resolution by molecular replacement (MR) with the archaebacterial Amt-1 structure (see Methods section). Given that the modest resolution of the structure and the limited detergent stability of ScMep2 would likely complicate structure–function studies, several other fungal Mep2 orthologues were subsequently overexpressed and screened for diffraction-quality crystals. Of these, Mep2 from C. albicans (CaMep2) showed superior stability in relatively harsh detergents such as nonyl-glucoside, allowing structure determination in two different crystal forms to high resolution (up to 1.5 Å). Despite different crystal packing (Supplementary Table 1), the two CaMep2 structures are identical to each other and very similar to ScMep2 (Cα r.m.s.d. (root mean square deviation)=0.7 Å for 434 residues), with the main differences confined to the N terminus and the CTR (Fig. 1). Electron density is visible for the entire polypeptide chains, with the exception of the C-terminal 43 (ScMep2) and 25 residues (CaMep2), which are poorly conserved and presumably disordered. Both Mep2 proteins show the archetypal trimeric assemblies in which each monomer consists of 11 TM helices surrounding a central pore. Important functional features such as the extracellular ammonium binding site, the Phe gate and the twin-His motif within the hydrophobic channel are all very similar to those present in the bacterial transporters and RhCG. In the remainder of the manuscript, we will specifically discuss CaMep2 due to the superior resolution of the structure. Unless specifically stated, the drawn conclusions also apply to ScMep2.</text></passage><passage><infon key="section_type">RESULTS</infon><infon key="type">paragraph</infon><offset>8338</offset><text>While the overall architecture of Mep2 is similar to that of the prokaryotic transporters (Cα r.m.s.d. with Amt-1=1.4 Å for 361 residues), there are large differences within the N terminus, intracellular loops (ICLs) ICL1 and ICL3, and the CTR. The N termini of the Mep2 proteins are ∼20–25 residues longer compared with their bacterial counterparts (Figs 1 and 2), substantially increasing the size of the extracellular domain. Moreover, the N terminus of one monomer interacts with the extended extracellular loop ECL5 of a neighbouring monomer. Together with additional, smaller differences in other extracellular loops, these changes generate a distinct vestibule leading to the ammonium binding site that is much more pronounced than in the bacterial proteins. The N-terminal vestibule and the resulting inter-monomer interactions likely increase the stability of the Mep2 trimer, in support of data for plant AMT proteins. However, given that an N-terminal deletion mutant (2-27Δ) grows as well as wild-type (WT) Mep2 on minimal ammonium medium (Fig. 3 and Supplementary Fig. 1), the importance of the N terminus for Mep2 activity is not clear.</text></passage><passage><infon key="section_type">RESULTS</infon><infon key="type">title_2</infon><offset>9498</offset><text>Mep2 channels are closed by a two-tier channel block</text></passage><passage><infon key="section_type">RESULTS</infon><infon key="type">paragraph</infon><offset>9551</offset><text>The largest differences between the Mep2 structures and the other known ammonium transporter structures are located on the intracellular side of the membrane. In the vicinity of the Mep2 channel exit, the cytoplasmic end of TM2 has unwound, generating a longer ICL1 even though there are no insertions in this region compared to the bacterial proteins (Figs 2 and 4). ICL1 has also moved inwards relative to its position in the bacterial Amts. The largest backbone movements of equivalent residues within ICL1 are ∼10 Å, markedly affecting the conserved basic RxK motif (Fig. 4). The head group of Arg54 has moved ∼11 Å relative to that in Amt-1, whereas the shift of the head group of the variable Lys55 residue is almost 20 Å. The side chain of Lys56 in the basic motif points in an opposite direction in the Mep2 structures compared with that of, for example, Amt-1 (Fig. 4). In addition to changing the RxK motif, the movement of ICL1 has another, crucial functional consequence. At the C-terminal end of TM1, the side-chain hydroxyl group of the relatively conserved Tyr49 (Tyr53 in ScMep2) makes a strong hydrogen bond with the ɛ2 nitrogen atom of the absolutely conserved His342 of the twin-His motif (His348 in ScMep2), closing the channel (Figs 4 and 5). In bacterial Amt proteins, this Tyr side chain is rotated ∼4 Å away as a result of the different conformation of TM1, leaving the channel open and the histidine available for its putative role in substrate transport (Supplementary Fig. 2).</text></passage><passage><infon key="section_type">RESULTS</infon><infon key="type">paragraph</infon><offset>11074</offset><text>Compared with ICL1, the backbone conformational changes observed for the neighbouring ICL2 are smaller, but large shifts are nevertheless observed for the conserved residues Glu140 and Arg141 (Fig. 4). Finally, the important ICL3 linking the pseudo-symmetrical halves (TM1-5 and TM6-10) of the transporter is also shifted up to ∼10 Å and forms an additional barrier that closes the channel on the cytoplasmic side (Fig. 5). This two-tier channel block likely ensures that very little ammonium transport will take place under nitrogen-sufficient conditions. The closed state of the channel might also explain why no density, which could correspond to ammonium (or water), is observed in the hydrophobic part of the Mep2 channel close to the twin-His motif. Significantly, this is also true for ScMep2, which was crystallized in the presence of 0.2 M ammonium ions (see Methods section).</text></passage><passage><infon key="section_type">RESULTS</infon><infon key="type">paragraph</infon><offset>11967</offset><text>The final region in Mep2 that shows large differences compared with the bacterial transporters is the CTR. In Mep2, the CTR has moved away and makes relatively few contacts with the main body of the transporter, generating a more elongated protein (Figs 1 and 4). By contrast, in the structures of bacterial proteins, the CTR is docked tightly onto the N-terminal half of the transporters (corresponding to TM1-5), resulting in a more compact structure. This is illustrated by the positions of the five universally conserved residues within the CTR, that is, Arg415(370), Glu421(376), Gly424(379), Asp426(381) and Tyr 435(390) in CaMep2(Amt-1) (Fig. 2). These residues include those of the ‘ExxGxD' motif, which when mutated generate inactive transporters. In Amt-1 and other bacterial ammonium transporters, these CTR residues interact with residues within the N-terminal half of the protein. On one side, the Tyr390 hydroxyl in Amt-1 is hydrogen bonded with the side chain of the conserved His185 at the C-terminal end of loop ICL3. At the other end of ICL3, the backbone carbonyl groups of Gly172 and Lys173 are hydrogen bonded to the side chain of Arg370. Similar interactions were also modelled in the active, non-phosphorylated plant AtAmt-1;1 structure (for example, Y467-H239 and D458-K71). The result of these interactions is that the CTR ‘hugs' the N-terminal half of the transporters (Fig. 4). Also noteworthy is Asp381, the side chain of which interacts strongly with the positive dipole on the N-terminal end of TM2. This interaction in the centre of the protein may be particularly important to stabilize the open conformations of ammonium transporters. In the Mep2 structures, none of the interactions mentioned above are present.</text></passage><passage><infon key="section_type">RESULTS</infon><infon key="type">title_2</infon><offset>13717</offset><text>Phosphorylation target site is at the periphery of Mep2</text></passage><passage><infon key="section_type">RESULTS</infon><infon key="type">paragraph</infon><offset>13773</offset><text>Recently Boeckstaens et al. provided evidence that Ser457 in ScMep2 (corresponding to Ser453 in CaMep2) is phosphorylated by the TORC1 effector kinase Npr1 under nitrogen-limiting conditions. In the absence of Npr1, plasmid-encoded WT Mep2 in a S. cerevisiae mep1-3Δ strain (triple mepΔ) does not allow growth on low concentrations of ammonium, suggesting that the transporter is inactive (Fig. 3 and Supplementary Fig. 1). Conversely, the phosphorylation-mimicking S457D variant is active both in the triple mepΔ background and in a triple mepΔ npr1Δ strain (Fig. 3). Mutation of other potential phosphorylation sites in the CTR did not support growth in the npr1Δ background. Collectively, these data suggest that phosphorylation of Ser457 opens the Mep2 channel to allow ammonium uptake. Ser457 is located in a part of the CTR that is conserved in a subgroup of Mep2 proteins, but which is not present in bacterial proteins (Fig. 2). This segment (residues 450–457 in ScMep2 and 446–453 in CaMep2) was dubbed an autoinhibitory (AI) region based on the fact that its removal generates an active transporter in the absence of Npr1 (Fig. 3).</text></passage><passage><infon key="section_type">RESULTS</infon><infon key="type">paragraph</infon><offset>14939</offset><text>Where is the AI region and the Npr1 phosphorylation site located? Our structures reveal that surprisingly, the AI region is folded back onto the CTR and is not located near the centre of the trimer as expected from the bacterial structures (Fig. 4). The AI region packs against the cytoplasmic ends of TM2 and TM4, physically linking the main body of the transporter with the CTR via main chain interactions and side-chain interactions of Val447, Asp449, Pro450 and Arg452 (Fig. 6). The AI regions have very similar conformations in CaMep2 and ScMep2, despite considerable differences in the rest of the CTR (Fig. 6). Strikingly, the Npr1 target serine residue is located at the periphery of the trimer, far away (∼30 Å) from any channel exit (Fig. 6). Despite its location at the periphery of the trimer, the electron density for the serine is well defined in both Mep2 structures and corresponds to the non-phosphorylated state (Fig. 6). This makes sense since the proteins were expressed in rich medium and confirms the recent suggestion by Boeckstaens et al. that the non-phosphorylated form of Mep2 corresponds to the inactive state. For ScMep2, Ser457 is the most C-terminal residue for which electron density is visible, indicating that the region beyond Ser457 is disordered. In CaMep2, the visible part of the sequence extends for two residues beyond Ser453 (Fig. 6). The peripheral location and disorder of the CTR beyond the kinase target site should facilitate the phosphorylation by Npr1. The disordered part of the CTR is not conserved in ammonium transporters (Fig. 2), suggesting that it is not important for transport. Interestingly, a ScMep2 457Δ truncation mutant in which a His-tag directly follows Ser457 is highly expressed but has low activity (Fig. 3 and Supplementary Fig. 1b), suggesting that the His-tag interferes with phosphorylation by Npr1. The same mutant lacking the His-tag has WT properties (Supplementary Fig. 1b), confirming that the region following the phosphorylation site is dispensable for function.</text></passage><passage><infon key="section_type">RESULTS</infon><infon key="type">title_2</infon><offset>16987</offset><text>Mep2 lacking the AI region is conformationally heterogeneous</text></passage><passage><infon key="section_type">RESULTS</infon><infon key="type">paragraph</infon><offset>17048</offset><text>Given that Ser457/453 is far from any channel exit (Fig. 6), the crucial question is how phosphorylation opens the Mep2 channel to generate an active transporter. Boeckstaens et al. proposed that phosphorylation does not affect channel activity directly, but instead relieves inhibition by the AI region. The data behind this hypothesis is the observation that a ScMep2 449-485Δ deletion mutant lacking the AI region is highly active in MA uptake both in the triple mepΔ and triple mepΔ npr1Δ backgrounds, implying that this Mep2 variant has a constitutively open channel. We obtained a similar result for ammonium uptake by the 446Δ mutant (Fig. 3), supporting the data from Marini et al. We then constructed and purified the analogous CaMep2 442Δ truncation mutant and determined the crystal structure using data to 3.4 Å resolution. The structure shows that removal of the AI region markedly increases the dynamics of the cytoplasmic parts of the transporter. This is not unexpected given the fact that the AI region bridges the CTR and the main body of Mep2 (Fig. 6). Density for ICL3 and the CTR beyond residue Arg415 is missing in the 442Δ mutant, and the density for the other ICLs including ICL1 is generally poor with visible parts of the structure having high B-factors (Fig. 7). Interestingly, however, the Tyr49-His342 hydrogen bond that closes the channel in the WT protein is still present (Fig. 7 and Supplementary Fig. 2). Why then does this mutant appear to be constitutively active? We propose two possibilities. The first one is that the open state is disfavoured by crystallization because of lower stability or due to crystal packing constraints. The second possibility is that the Tyr–His hydrogen bond has to be disrupted by the incoming substrate to open the channel. The latter model would fit well with the NH3/H+ symport model in which the proton is relayed by the twin-His motif. The importance of the Tyr–His hydrogen bond is underscored by the fact that its removal in the ScMep2 Y53A mutant results in a constitutively active transporter (Fig. 3).</text></passage><passage><infon key="section_type">RESULTS</infon><infon key="type">title_2</infon><offset>19155</offset><text>Phosphorylation causes a conformational change in the CTR</text></passage><passage><infon key="section_type">RESULTS</infon><infon key="type">paragraph</infon><offset>19213</offset><text>Do the Mep2 structures provide any clues regarding the potential effect of phosphorylation? The side-chain hydroxyl of Ser457/453 is located in a well-defined electronegative pocket that is solvent accessible (Fig. 6). The closest atoms to the serine hydroxyl group are the backbone carbonyl atoms of Asp419, Glu420 and Glu421, which are 3–4 Å away. We therefore predict that phosphorylation of Ser453 will result in steric clashes as well as electrostatic repulsion, which in turn might cause substantial conformational changes within the CTR. To test this hypothesis, we determined the structure of the phosphorylation-mimicking R452D/S453D protein (hereafter termed ‘DD mutant'), using data to a resolution of 2.4 Å. The additional mutation of the arginine preceding the phosphorylation site was introduced (i) to increase the negative charge density and make it more comparable to a phosphate at neutral pH, and (ii) to further destabilize the interactions of the AI region with the main body of the transporter (Fig. 6). The ammonium uptake activity of the S. cerevisiae version of the DD mutant is the same as that of WT Mep2 and the S453D mutant, indicating that the mutations do not affect transporter functionality in the triple mepΔ background (Fig. 3). Unexpectedly, the AI segment containing the mutated residues has only undergone a slight shift compared with the WT protein (Fig. 8 and Supplementary Fig. 3). By contrast, the conserved part of the CTR has undergone a large conformational change involving formation of a 12-residue-long α-helix from Leu427 to Asp438. In addition, residues Glu420-Leu423 including Glu421 of the ExxGxD motif are now disordered (Fig. 8 and Supplementary Fig. 3). Overall, ∼20 residues are affected by the introduced mutations. This is the first time a large conformational change has been observed in an ammonium transporter as a result of a mutation, and confirms previous hypotheses that phosphorylation causes structural changes in the CTR. To exclude the possibility that the additional R452D mutation is responsible for the observed changes, we also determined the structure of the ‘single D' S453D mutant. As shown in Supplementary Fig. 4, the consequence of the single D mutation is very similar to that of the DD substitution, with conformational changes and increased dynamics confined to the conserved part of the CTR (Supplementary Fig. 4). To supplement the crystal structures, we also performed modelling and MD studies of WT CaMep2, the DD mutant and phosphorylated protein (S453J). In the WT structure, the acidic residues Asp419, Glu420 and Glu421 are within hydrogen bonding distance of Ser453. After 200 ns of MD simulation, the interactions between these residues and Ser453 remain intact. The protein backbone has an average r.m.s.d. of only ∼3 Å during the 200-ns simulation, indicating that the protein is stable. There is flexibility in the side chains of the acidic residues so that they are able to form stable hydrogen bonds with Ser453. In particular, persistent hydrogen bonds are observed between the Ser453 hydroxyl group and the acidic group of Glu420, and also between the amine group of Ser453 and the backbone carbonyl of Glu420 (Supplementary Fig. 5). The DD mutant is also stable during the simulations, but the average backbone r.m.s.d of ∼3.6 Å suggests slightly more conformational flexibility than WT. As the simulation proceeds, the side chains of the acidic residues move away from Asp452 and Asp453, presumably to avoid electrostatic repulsion. For example, the distance between the Asp453 acidic oxygens and the Glu420 acidic oxygens increases from ∼7 to &gt;22 Å after 200 ns simulations, and thus these residues are not interacting. The protein is structurally stable throughout the simulation with little deviation in the other parts of the protein. Finally, the S453J mutant is also stable throughout the 200-ns simulation and has an average backbone deviation of ∼3.8 Å, which is similar to the DD mutant. The movement of the acidic residues away from Arg452 and Sep453 is more pronounced in this simulation in comparison with the movement away from Asp452 and Asp453 in the DD mutant. The distance between the phosphate of Sep453 and the acidic oxygen atoms of Glu420 is initially ∼11 Å, but increases to &gt;30 Å after 200 ns. The short helix formed by residues Leu427 to Asp438 unravels during the simulations to a disordered state. The remainder of the protein is not affected (Supplementary Fig. 5). Thus, the MD simulations support the notion from the crystal structures that phosphorylation generates conformational changes in the conserved part of the CTR. However, the conformational changes for the phosphomimetic mutants in the crystals are confined to the CTR (Fig. 8), and the channels are still closed (Supplementary Fig. 2). One possible explanation is that the mutants do not accurately mimic a phosphoserine, but the observation that the S453D and DD mutants are fully active in the absence of Npr1 suggests that the mutations do mimic the effect of phosphorylation (Fig. 3). The fact that the S453D structure was obtained in the presence of 10 mM ammonium ions suggests that the crystallization process favours closed states of the Mep2 channels.</text></passage><passage><infon key="section_type">DISCUSS</infon><infon key="type">title_1</infon><offset>24519</offset><text>Discussion</text></passage><passage><infon key="section_type">DISCUSS</infon><infon key="type">paragraph</infon><offset>24530</offset><text>Knowledge about ammonium transporter structure has been obtained from experimental and theoretical studies on bacterial family members. In addition, a number of biochemical and genetic studies are available for bacterial, fungal and plant proteins. These efforts have advanced our knowledge considerably but have not yet yielded atomic-level answers to several important mechanistic questions, including how ammonium transport is regulated in eukaryotes and the mechanism of ammonium signalling. In Arabidopsis thaliana Amt-1;1, phosphorylation of the CTR residue T460 under conditions of high ammonium inhibits transport activity, that is, the default (non-phosphorylated) state of the plant transporter is open. Interestingly, phosphomimetic mutations introduced into one monomer inactivate the entire trimer, indicating that (i) heterotrimerization occurs and (ii) the CTR mediates allosteric regulation of ammonium transport activity via phosphorylation. Owing to the lack of structural information for plant AMTs, the details of channel closure and inter-monomer crosstalk are not yet clear. Contrasting with the plant transporters, the inactive states of Mep2 proteins under conditions of high ammonium are non-phosphorylated, with channels that are closed on the cytoplasmic side. The reason why similar transporters such as A. thaliana Amt-1;1 and Mep2 are regulated in opposite ways by phosphorylation (inactivation in plants and activation in fungi) is not known. In fungi, preventing ammonium entry via channel closure in ammonium transporters would be one way to alleviate ammonium toxicity, in addition to ammonium excretion via Ato transporters and amino-acid secretion.</text></passage><passage><infon key="section_type">DISCUSS</infon><infon key="type">paragraph</infon><offset>26215</offset><text>By determining the first structures of closed ammonium transporters and comparing those structures with the permanently open bacterial proteins, we demonstrate that Mep2 channel closure is likely due to movements of the CTR and ICL1 and ICL3. More specifically, the close interactions between the CTR and ICL1/ICL3 present in open transporters are disrupted, causing ICL3 to move outwards and block the channel (Figs 4 and 9a). In addition, ICL1 has shifted inwards to contribute to the channel closure by engaging His2 from the twin-His motif via hydrogen bonding with a highly conserved tyrosine hydroxyl group. Upon phosphorylation by the Npr1 kinase in response to nitrogen limitation, the region around the conserved ExxGxD motif undergoes a conformational change that opens the channel (Fig. 9). Importantly, the structural similarities in the TM parts of Mep2 and AfAmt-1 (Fig. 5a) suggest that channel opening/closure does not require substantial changes in the residues lining the channel. How exactly the channel opens and whether opening is intra-monomeric are still open questions; it is possible that the change in the CTR may disrupt its interactions with ICL3 of the neighbouring monomer (Fig. 9b), which could result in opening of the neighbouring channel via inward movement of its ICL3. Owing to the crosstalk between monomers, a single phosphorylation event might lead to opening of the entire trimer, although this has not yet been tested (Fig. 9b). Whether or not Mep2 channel opening requires, in addition to phosphorylation, disruption of the Tyr–His2 interaction by the ammonium substrate is not yet clear.</text></passage><passage><infon key="section_type">DISCUSS</infon><infon key="type">paragraph</infon><offset>27848</offset><text>Is our model for opening and closing of Mep2 channels valid for other eukaryotic ammonium transporters? Our structural data support previous studies and clarify the central role of the CTR and cytoplasmic loops in the transition between closed and open states. However, even the otherwise highly similar Mep2 proteins of S. cerevisiae and C. albicans have different structures for their CTRs (Fig. 1 and Supplementary Fig. 6). In addition, the AI region of the CTR containing the Npr1 kinase site is conserved in only a subset of fungal transporters, suggesting that the details of the structural changes underpinning regulation vary. Nevertheless, given the central role of absolutely conserved residues within the ICL1-ICL3-CTR interaction network (Fig. 4), we propose that the structural basics of fungal ammonium transporter activation are conserved. The fact that Mep2 orthologues of distantly related fungi are fully functional in ammonium transport and signalling in S. cerevisiae supports this notion. It should also be noted that the tyrosine residue interacting with His2 is highly conserved in fungal Mep2 orthologues, suggesting that the Tyr–His2 hydrogen bond might be a general way to close Mep2 proteins.</text></passage><passage><infon key="section_type">DISCUSS</infon><infon key="type">paragraph</infon><offset>29070</offset><text>With regards to plant AMTs, it has been proposed that phosphorylation at T460 generates conformational changes that would close the neighbouring pore via the C terminus. This assumption was based partly on a homology model for Amt-1;1 based on the (open) archaebacterial AfAmt-1 structure, which suggested that the C terminus of Amt-1;1 would extend further to the neighbouring monomer. Our Mep2 structures show that this assumption may not be correct (Fig. 4 and Supplementary Fig. 6). In addition, the considerable differences between structurally resolved CTR domains means that the exact environment of T460 in Amt-1;1 is also not known (Supplementary Fig. 6). Based on the available structural information, we consider it more likely that phosphorylation-mediated pore closure in Amt-1;1 is intra-monomeric, via disruption of the interactions between the CTR and ICL1/ICL3 (for example, Y467-H239 and D458-K71). There is generally no equivalent for CaMep2 Tyr49 in plant AMTs, indicating that a Tyr–His2 hydrogen bond as observed in Mep2 may not contribute to the closed state in plant transporters.</text></passage><passage><infon key="section_type">DISCUSS</infon><infon key="type">paragraph</infon><offset>30177</offset><text>We propose that intra-monomeric CTR-ICL1/ICL3 interactions lie at the basis of regulation of both fungal and plant ammonium transporters; close interactions generate open channels, whereas the lack of ‘intra-' interactions leads to inactive states. The need to regulate in opposite ways may be the reason why the phosphorylation sites are in different parts of the CTR, that is, centrally located close to the ExxGxD motif in AMTs and peripherally in Mep2. In this way, phosphorylation can either lead to channel closing (in the case of AMTs) or channel opening in the case of Mep2. Our model also provides an explanation for the observation that certain mutations within the CTR completely abolish transport activity. An example of an inactivating residue is the glycine of the ExxGxD motif of the CTR. Mutation of this residue (G393 in EcAmtB; G456 in AtAmt-1;1) inactivates transporters as diverse as Escherichia coli AmtB and A. thaliana Amt-1;1 (refs). Such mutations likely cause structural changes in the CTR that prevent close contacts between the CTR and ICL1/ICL3, thereby stabilizing a closed state that may be similar to that observed in Mep2.</text></passage><passage><infon key="section_type">DISCUSS</infon><infon key="type">paragraph</infon><offset>31335</offset><text>Regulation and modulation of membrane transport by phosphorylation is known to occur in, for example, aquaporins and urea transporters, and is likely to be a common theme for eukaryotic channels and transporters. Recently, phosphorylation was also shown to modulate substrate affinity in nitrate transporters. With respect to ammonium transport, phosphorylation has thus far only been shown for A. thaliana AMTs and for S. cerevisiae Mep2 (refs). However, the absence of GlnK proteins in eukaryotes suggests that phosphorylation-based regulation of ammonium transport may be widespread. Nevertheless, as discussed above, considerable differences may exist between different species.</text></passage><passage><infon key="section_type">DISCUSS</infon><infon key="type">paragraph</infon><offset>32018</offset><text>With respect to Mep2-mediated signalling to induce pseudohyphal growth, two models have been put forward as to how this occurs and why it is specific to Mep2 proteins. In one model, signalling is proposed to depend on the nature of the transported substrate, which might be different in certain subfamilies of ammonium transporters (for example, Mep1/Mep3 versus Mep2). For example, NH3 uniport or symport of NH3/H+ might result in changes in local pH, but NH4+ uniport might not, and this difference might determine signalling. In the other model, signalling is thought to require a distinct conformation of the Mep2 transporter occurring during the transport cycle. While the current study does not specifically address the mechanism of signalling underlying pseudohyphal growth, our structures do show that Mep2 proteins can assume different conformations.</text></passage><passage><infon key="section_type">DISCUSS</infon><infon key="type">paragraph</infon><offset>32878</offset><text>It is clear that ammonium transport across biomembranes remains a fascinating and challenging field in large part due to the unique properties of the substrate. Our Mep2 structural work now provides a foundation for future studies to uncover the details of the structural changes that occur during eukaryotic ammonium transport and signaling, and to assess the possibility to utilize small molecules to shut down ammonium sensing and downstream signalling pathways in pathogenic fungi.</text></passage><passage><infon key="section_type">METHODS</infon><infon key="type">title_1</infon><offset>33364</offset><text>Methods</text></passage><passage><infon key="section_type">METHODS</infon><infon key="type">title_2</infon><offset>33372</offset><text>Mep2 overexpression and purification</text></passage><passage><infon key="section_type">METHODS</infon><infon key="type">paragraph</infon><offset>33409</offset><text>Ammonium transporter genes were amplified from genomic DNA or cDNA by PCR (Phusion, New England Biolabs). In both ScMEP2 and CaMEP2, Asn4 was replaced by a glutamine to prevent glycosylation. In order to allow transformation of yeast by recombination, the following primer extensions were used: forward 5′-GAAAAAACCCCGGATTCTAGAACTAGTGGATCCTCC-3′ and reverse 5′-TGACTCGAGTTATGCACCGTGGTGGTGATGGTGATG-3′. These primers result in a construct that lacks the cleavable N- and C-terminal tags present in the original vector, and replaces these with a C-terminal hexa-histidine tag. Recombination in yeast strain W303 pep4Δ was carried out using ∼50–100 ng of SmaI-digested vector 83νΔ (ref.) and at least a fourfold molar excess of PCR product via the lithium acetate method. Transformants were selected on SCD -His plates incubated at 30 °C. Construction of mutant CaMEP2 genes was done using the Q5 site-directed mutagenesis kit (NEB) per manufacturer's instructions. Three CaMep2 mutants were made for crystallization: the first mutant is a C-terminal truncation mutant 442Δ, lacking residues 443–480 including the AI domain. The second mutant, R452D/S453D, mimics the protein phosphorylated at Ser453. Given that phosphate is predominantly charged −2 at physiological pH, we introduced the second aspartate residue for Arg452. However, we also constructed the ‘single D', S453D CaMep2 variant.</text></passage><passage><infon key="section_type">METHODS</infon><infon key="type">paragraph</infon><offset>34827</offset><text>For expression, cells were grown in shaker flasks at 30 °C for ∼24 h in synthetic minimal medium lacking histidine and with 1% (w/v) glucose to a typical OD600 of 6–8. Cells were subsequently spun down for 15 min at 4,000g and resuspended in YP medium containing 1.5% (w/v) galactose, followed by another 16–20 h growth at 30 °C/160 r.p.m. and harvesting by centrifugation. Final OD600 values typically reached 18–20. Cells were lysed by bead beating (Biospec) for 5 × 1 min with 1 min intervals on ice, or by 1–2 passes through a cell disrupter operated at 35,000 p.s.i. (TS-Series 0.75 kW; Constant Systems). Membranes were collected from the suspension by centrifugation at 200,000g for 90 min (45Ti rotor; Beckmann Coulter). Membrane protein extraction was performed by homogenization in a 1:1 (w/w) mixture of dodecyl-β-D-maltoside and decyl-β-D-maltoside (DDM/DM) followed by stirring at 4 °C overnight. Typically, 1 g (1% w/v) of total detergent was used for membranes from 2 l of cells. The membrane extract was centrifuged for 35 min at 200,000g and the supernatant was loaded onto a 10-ml Nickel column (Chelating Sepharose; GE Healthcare) equilibrated in 20 mM Tris/300 mM NaCl/0.2% DDM, pH 8. The column was washed with 15 column volumes buffer containing 30 mM imidazole and eluted in 3 column volumes with 250 mM imidazole. Proteins were purified to homogeneity by gel filtration chromatography in 10 mM HEPES/100 mM NaCl/0.05% DDM, pH 7–7.5. For polishing and detergent exchange, a second gel filtration column was performed using various detergents. In the case of ScMep2, diffracting crystals were obtained only with 0.05% decyl-maltose neopentyl glycol. For the more stable CaMep2 protein, we obtained crystals in, for example, nonyl-glucoside, decyl-maltoside and octyl-glucose neopentyl glycol. Proteins were concentrated to 7–15 mg ml−1 using 100 kDa cutoff centrifugal devices (Millipore), flash-frozen and stored at −80 °C before use.</text></passage><passage><infon key="section_type">METHODS</infon><infon key="type">title_2</infon><offset>36860</offset><text>Crystallization and structure determination</text></passage><passage><infon key="section_type">METHODS</infon><infon key="type">paragraph</infon><offset>36904</offset><text>Crystallization screening trials by sitting drop vapour diffusion were set up at 4 and 20 °C using in-house screens and the MemGold 1 and 2 screens (Molecular Dimensions) with a Mosquito crystallization robot. Crystals were harvested directly from the initial trials or optimized by sitting or hanging drop vapour diffusion using larger drops (typically 2–3 μl total volume). Bar-shaped crystals for ScMep2 diffracting to 3.2 Å resolution were obtained from 50 mM 2-(N-morpholino)ethanesulfonic acid (MES)/0.2 M di-ammonium hydrogen phosphate/30% PEG 400, pH 6. They belong to space group P212121 and have nine molecules (three trimers) in the asymmetric unit (AU). Well-diffracting crystals for CaMep2 were obtained in space group P3 from 0.1 M MES/0.2 M lithium sulphate/20% PEG400, pH 6 (two molecules per AU). An additional crystal form in space group R3 was grown in 0.04 M Tris/0.04 M NaCl/27% PEG350 MME, pH 8 (one molecule per AU). Diffracting crystals for the phosporylation-mimicking CaMep2 DD mutant were obtained in space group P6322 from 0.1 M sodium acetate/15–20% PEG400, pH 5 (using decyl-maltoside as detergent; one molecule per AU), while S453D mutant crystals grew in 24% PEG400/0.05 M sodium acetate, pH 5.4/0.05 M magnesium acetate tetrahydrate/10 mM NH4Cl (space group R32; one molecule per AU). Finally, the 442Δ truncation mutant gave crystals under many different conditions, but most of these diffracted poorly or not at all. A reasonable low-resolution data set (3.4 Å resolution) was eventually obtained from a crystal grown in 24% PEG400/0.05 M sodium acetate/0.05 M magnesium acetate, pH 6.1 (space group R32). Diffraction data were collected at the Diamond Light Source and processed with XDS or HKL2000 (ref. ).</text></passage><passage><infon key="section_type">METHODS</infon><infon key="type">paragraph</infon><offset>38689</offset><text>For MR, a search model was constructed with Sculptor within Phenix, using a sequence alignment of ScMep2 with Archaeoglobus fulgidus Amt-1 (PDB ID 2B2H; ∼40% sequence identity to ScMep2). A clear solution with nine molecules (three trimers) in the AU was obtained using Phaser. The model was subsequently completed by iterative rounds of manual building within Coot followed by refinement within Phenix. The structures for WT CaMep2 were solved using the best-defined monomer of ScMep2 (60% sequence identity with CaMep2) in MR with Phaser, followed by automated model building within Phenix. Finally, the structures of the three mutant CaMep2 proteins were solved using WT CaMep2 as the search model. The data collection and refinement statistics for all six solved structures have been summarized in Supplementary Tables 1 and 2.</text></passage><passage><infon key="section_type">METHODS</infon><infon key="type">title_2</infon><offset>39523</offset><text>Growth assays</text></passage><passage><infon key="section_type">METHODS</infon><infon key="type">paragraph</infon><offset>39537</offset><text>The S. cerevisiae haploid triple mepΔ strain (Σ1278b MATα mep1::LEU2 mep2::LEU2 mep3::G418 ura3-52) and triple mepΔ npr1Δ strain (Σ1278b MATα mep1::LEU2 mep2::LEU2 mep3::G418 npr1::NAT1 ura3-52) were generated by integrating the NAT1 resistance gene at one NPR1 locus in the diploid strain MLY131 (ref.), followed by isolation of individual haploid strains. Cells were grown in synthetic minimal medium with glucose (2%) as the carbon source and ammonium sulphate (1 mM) or glutamate (0.1%) as the nitrogen source. Yeast cells were transformed as described. All DNA sequences encoding epitope-tagged ScMep2 and its mutant derivatives were generated by PCR and homologous recombination using the vector pRS316 (ref. ). In each case, the ScMEP2 sequences included the ScMEP2 promoter (1 kb), the ScMEP2 terminator and sequences coding for a His-6 epitope at the C-terminal end of the protein. All Mep2-His fusions contain the N4Q mutation to prevent glycosylation of Mep2 (ref.). All newly generated plasmid inserts were verified by DNA sequencing. For growth assays, S. cerevisiae cells containing plasmids expressing ScMep2 or mutant derivatives were grown overnight in synthetic minimal glutamate medium, washed, spotted by robot onto solid agar plates and culture growth followed by time course photography. Images were then processed to quantify the growth of each strain over 3 days as described.</text></passage><passage><infon key="section_type">METHODS</infon><infon key="type">title_2</infon><offset>40966</offset><text>Protein modelling</text></passage><passage><infon key="section_type">METHODS</infon><infon key="type">paragraph</infon><offset>40984</offset><text>The MODELLER (version 9.15) software package was used to build protein structures for MD simulations. This method was required to construct two complete protein models, the double mutant R452D/S453D (with the four missing residues from the X-ray structure added) and also the construct in which the mutation at position 452 is reverted to R, and D453 is replaced with a phosphoserine. The quality of these models was assessed using normalized Discrete Optimized Protein Energy (DOPE) values and the molpdf assessment function within the MODELLER package. The model R452D/S453D mutant has a molpdf assessment score of 1854.05, and a DOPE assessment score of -60920.55. The model of the S453J mutant has a molpdf assessment score of 1857.01 and a DOPE assessment score of −61032.15.</text></passage><passage><infon key="section_type">METHODS</infon><infon key="type">title_2</infon><offset>41767</offset><text>MD simulations</text></passage><passage><infon key="section_type">METHODS</infon><infon key="type">paragraph</infon><offset>41782</offset><text>WT and model structures were embedded into a pre-equilibrated lipid bilayer composed of 512 dipalmitoylphosphatidylcholine lipids using the InflateGRO2 computer programme. The bilayers were then solvated with the SPC water model and counterions were added to achieve a charge neutral state. All simulations were performed with the GROMACS package (version 4.5.5), and the GROMOS96 43a1p force field. During simulation time, the temperature was maintained at 310 K using the Nosé-Hoover thermostat with a coupling constant of 0.5 ps. Pressure was maintained at 1 bar using semi-isotropic coupling with the Parrinello-Rahman barostat and a time constant of 5 ps. Electrostatic interactions were treated using the smooth particle mesh Ewald algorithm with a short-range cutoff of 0.9 nm. Van der Waals interactions were truncated at 1.4 nm with a long-range dispersion correction applied to energy and pressure. The neighbour list was updated every five steps. All bonds were constrained with the LINCS algorithm, so that a 2-fs time step could be applied throughout. The phospholipid parameters for the dipalmitoylphosphatidylcholine lipids were based on the work of Berger. The embedded proteins were simulated for 200 ns each; a repeat simulation was performed for each system with different initial velocities to ensure reproducibility. To keep the c.p.u. times within reasonable limits, all simulations were performed on Mep2 monomers. This is also consistent with previous simulations for E. coli AmtB.</text></passage><passage><infon key="section_type">METHODS</infon><infon key="type">title_1</infon><offset>43303</offset><text>Additional information</text></passage><passage><infon key="section_type">METHODS</infon><infon key="type">paragraph</infon><offset>43326</offset><text>Accession codes: The atomic coordinates and the associated structure factors have been deposited in the Protein Data Bank (http:// www.pdbe.org) with accession codes 5AEX (ScMep2), 5AEZ(CaMep2; R3), 5AF1(CaMep2; P3), 5AID(CaMep2; 442D), 5AH3 (CaMep2; R452D/S453D) and 5FUF (CaMep2; S453D).</text></passage><passage><infon key="section_type">METHODS</infon><infon key="type">paragraph</infon><offset>43616</offset><text>How to cite this article: van den Berg, B. et al. Structural basis for Mep2 ammonium transceptor activation by phosphorylation. Nat. Commun. 7:11337 doi: 10.1038/ncomms11337 (2016).</text></passage><passage><infon key="section_type">SUPPL</infon><infon key="type">title_1</infon><offset>43798</offset><text>Supplementary Material</text></passage><passage><infon key="fpage">556</infon><infon key="lpage">564</infon><infon key="name_0">surname:Holsbeeks;given-names:I.</infon><infon key="name_1">surname:Lagatie;given-names:O.</infon><infon key="name_2">surname:Van
+Nuland;given-names:A.</infon><infon key="name_3">surname:Van de Velde;given-names:S.</infon><infon key="name_4">surname:Thevelein;given-names:J.
+M.</infon><infon key="pub-id_pmid">15450611</infon><infon key="section_type">REF</infon><infon key="source">Trends Biochem. Sci.</infon><infon key="type">ref</infon><infon key="volume">29</infon><infon key="year">2004</infon><offset>43821</offset><text>The eukaryotic plasma membrane as a nutrient-sensing device</text></passage><passage><infon key="fpage">254</infon><infon key="lpage">299</infon><infon key="name_0">surname:Conrad;given-names:M.</infon><infon key="pub-id_pmid">24483210</infon><infon key="section_type">REF</infon><infon key="source">FEMS Microbiol. Rev.</infon><infon key="type">ref</infon><infon key="volume">38</infon><infon key="year">2014</infon><offset>43881</offset><text>Nutrient sensing and signaling in the yeast Saccharomyces cerevisiae</text></passage><passage><infon key="fpage">D251</infon><infon key="lpage">D258</infon><infon key="name_0">surname:Saier;given-names:M. H.</infon><infon key="name_1">surname:Reddy;given-names:V. S.</infon><infon key="name_2">surname:Tamang;given-names:D.
+G.</infon><infon key="name_3">surname:Vastermark;given-names:A.</infon><infon key="pub-id_pmid">24225317</infon><infon key="section_type">REF</infon><infon key="source">Nucleic Acids
+Res.</infon><infon key="type">ref</infon><infon key="volume">42</infon><infon key="year">2014</infon><offset>43950</offset><text>The transporter classification database</text></passage><passage><infon key="fpage">4282</infon><infon key="lpage">4293</infon><infon key="name_0">surname:Marini;given-names:A. M.</infon><infon key="name_1">surname:Soussi-Boudekou;given-names:S.</infon><infon key="name_2">surname:Vissers;given-names:S.</infon><infon key="name_3">surname:Andre;given-names:B.</infon><infon key="pub-id_pmid">9234685</infon><infon key="section_type">REF</infon><infon key="source">Mol. Cell Biol.</infon><infon key="type">ref</infon><infon key="volume">17</infon><infon key="year">1997</infon><offset>43990</offset><text>A family of ammonium transporters in Saccharomyces cerevisiae</text></passage><passage><infon key="fpage">e24275</infon><infon key="name_0">surname:Van Zeebroeck;given-names:G.</infon><infon key="name_1">surname:Kimpe;given-names:M.</infon><infon key="name_2">surname:Vandormael;given-names:P.</infon><infon key="name_3">surname:Thevelein;given-names:J. M.</infon><infon key="pub-id_pmid">21912684</infon><infon key="section_type">REF</infon><infon key="source">PLoS ONE</infon><infon key="type">ref</infon><infon key="volume">6</infon><infon key="year">2011</infon><offset>44052</offset><text>A split-ubiquitin two-hybrid screen for proteins physically interacting with the yeast amino acid transceptor Gap1 and ammonium transceptor Mep2</text></passage><passage><infon key="fpage">1236</infon><infon key="lpage">1247</infon><infon key="name_0">surname:Lorenz;given-names:M. C.</infon><infon key="name_1">surname:Heitman;given-names:J.</infon><infon key="pub-id_pmid">9482721</infon><infon key="section_type">REF</infon><infon key="source">EMBO J.</infon><infon key="type">ref</infon><infon key="volume">17</infon><infon key="year">1998</infon><offset>44197</offset><text>The MEP2 ammonium permease regulates pseudohyphal differentiation in Saccharomyces cerevisiae</text></passage><passage><infon key="fpage">345</infon><infon key="lpage">355</infon><infon key="name_0">surname:Shnaiderman;given-names:C.</infon><infon key="name_1">surname:Miyara;given-names:I.</infon><infon key="name_2">surname:Kobiler;given-names:I.</infon><infon key="name_3">surname:Sherman;given-names:A.</infon><infon key="name_4">surname:Prusky;given-names:D.</infon><infon key="pub-id_pmid">23387470</infon><infon key="section_type">REF</infon><infon key="source">Mol. Plant Microbe Interact.</infon><infon key="type">ref</infon><infon key="volume">26</infon><infon key="year">2013</infon><offset>44291</offset><text>Differential activation of ammonium transporters during the accumulation of ammonia by Colletotrichum gloeosporioides and its effect on appressoria formation andpathogenicity</text></passage><passage><infon key="fpage">3028</infon><infon key="lpage">3039</infon><infon key="name_0">surname:Rutherford;given-names:J. C.</infon><infon key="name_1">surname:Chua;given-names:G.</infon><infon key="name_2">surname:Hughes;given-names:T.</infon><infon key="name_3">surname:Cardenas;given-names:M.
+E.</infon><infon key="name_4">surname:Heitman;given-names:J.</infon><infon key="pub-id_pmid">18434596</infon><infon key="section_type">REF</infon><infon key="source">Mol. Biol. Cell</infon><infon key="type">ref</infon><infon key="volume">19</infon><offset>44466</offset><text>A Mep2-dependent transcriptional profile links permease function to gene expression during pseudohyphal growth in Saccharomyces cerevisiae</text></passage><passage><infon key="fpage">649</infon><infon key="lpage">669</infon><infon key="name_0">surname:Biswas;given-names:K.</infon><infon key="name_1">surname:Morschhäuser;given-names:J.</infon><infon key="pub-id_pmid">15819622</infon><infon key="section_type">REF</infon><infon key="source">Mol. Microbiol.</infon><infon key="type">ref</infon><infon key="volume">56</infon><infon key="year">2005</infon><offset>44605</offset><text>The Mep2p ammonium permease controls nitrogen starvation-induced filamentous growth in Candida albicans</text></passage><passage><infon key="fpage">21362</infon><infon key="lpage">21370</infon><infon key="name_0">surname:Boeckstaens;given-names:M.</infon><infon key="name_1">surname:André;given-names:B.</infon><infon key="name_2">surname:Marini;given-names:A. M.</infon><infon key="pub-id_pmid">18508774</infon><infon key="section_type">REF</infon><infon key="source">J. Biol.
+Chem.</infon><infon key="type">ref</infon><infon key="volume">283</infon><infon key="year">2008</infon><offset>44709</offset><text>Distinct transport mechanisms in yeast ammonium transport/sensor proteins of the Mep/Amt/Rh family and impact on filamentation</text></passage><passage><infon key="fpage">534</infon><infon key="lpage">546</infon><infon key="name_0">surname:Boeckstaens;given-names:M.</infon><infon key="name_1">surname:André;given-names:B.</infon><infon key="name_2">surname:Marini;given-names:A. M.</infon><infon key="pub-id_pmid">17493133</infon><infon key="section_type">REF</infon><infon key="source">Mol. Microbiol.</infon><infon key="type">ref</infon><infon key="volume">64</infon><infon key="year">2007</infon><offset>44836</offset><text>The yeast ammonium transport protein Mep2 and its positive regulator, the Npr1 kinase, play an important role in normal and pseudohyphal growth on various nitrogen media through retrieval of excreted ammonium</text></passage><passage><infon key="fpage">9638</infon><infon key="lpage">9643</infon><infon key="name_0">surname:Gruswitz;given-names:F.</infon><infon key="pub-id_pmid">20457942</infon><infon key="section_type">REF</infon><infon key="source">Proc.
+Natl Acad. Sci. USA</infon><infon key="type">ref</infon><infon key="volume">107</infon><infon key="year">2010</infon><offset>45045</offset><text>Function of human Rh based on structure of RhCG at 2.1A</text></passage><passage><infon key="fpage">1587</infon><infon key="lpage">1594</infon><infon key="name_0">surname:Khademi;given-names:S.</infon><infon key="pub-id_pmid">15361618</infon><infon key="section_type">REF</infon><infon key="source">Science</infon><infon key="type">ref</infon><infon key="volume">305</infon><infon key="year">2004</infon><offset>45101</offset><text>Mechanism of ammonia transport by Amt/MEP/Rh: structure of AmtB at 1.35A</text></passage><passage><infon key="fpage">14994</infon><infon key="lpage">14999</infon><infon key="name_0">surname:Andrade;given-names:S. L.</infon><infon key="name_1">surname:Dickmanns;given-names:A.</infon><infon key="name_2">surname:Ficner;given-names:R.</infon><infon key="name_3">surname:Einsle;given-names:O.</infon><infon key="pub-id_pmid">16214888</infon><infon key="section_type">REF</infon><infon key="source">Proc. Natl Acad. Sci. USA</infon><infon key="type">ref</infon><infon key="volume">102</infon><infon key="year">2005</infon><offset>45174</offset><text>Crystal structure of the archaeal ammonium transporter Amt-1 from Archaeoglobus fulgidus</text></passage><passage><infon key="fpage">39492</infon><infon key="lpage">39498</infon><infon key="name_0">surname:Javelle;given-names:A.</infon><infon key="pub-id_pmid">17040913</infon><infon key="section_type">REF</infon><infon key="source">J. Biol. Chem.</infon><infon key="type">ref</infon><infon key="volume">281</infon><infon key="year">2006</infon><offset>45263</offset><text>An unusual twin-his arrangement in the pore of ammonia channels is essential for substrate conductance</text></passage><passage><infon key="fpage">10419</infon><infon key="lpage">10427</infon><infon key="name_0">surname:Wang;given-names:S.</infon><infon key="name_1">surname:Orabi;given-names:E. A.</infon><infon key="name_2">surname:Baday;given-names:S.</infon><infon key="name_3">surname:Bernèche;given-names:S.</infon><infon key="name_4">surname:Lamoureux;given-names:G.</infon><infon key="pub-id_pmid">22631217</infon><infon key="section_type">REF</infon><infon key="source">J. Am. Chem. Soc.</infon><infon key="type">ref</infon><infon key="volume">134</infon><infon key="year">2012</infon><offset>45366</offset><text>Ammonium transporters achieve charge transfer by fragmenting their substrate</text></passage><passage><infon key="fpage">e62745</infon><infon key="name_0">surname:Wang;given-names:J.</infon><infon key="pub-id_pmid">23667517</infon><infon key="section_type">REF</infon><infon key="source">PLoS ONE</infon><infon key="type">ref</infon><infon key="volume">8</infon><infon key="year">2013</infon><offset>45443</offset><text>Ammonium transport proteins with changes in one of the conserved pore histidines have different performance in ammonia and methylamine conduction</text></passage><passage><infon key="fpage">10876</infon><infon key="lpage">10884</infon><infon key="name_0">surname:Lin;given-names:Y.</infon><infon key="name_1">surname:Cao;given-names:Z.</infon><infon key="name_2">surname:Mo;given-names:Y.</infon><infon key="pub-id_pmid">16910683</infon><infon key="section_type">REF</infon><infon key="source">J. Am.
+Chem. Soc.</infon><infon key="type">ref</infon><infon key="volume">128</infon><infon key="year">2006</infon><offset>45589</offset><text>Molecular dynamics simulations on the Escherichia coli ammonia channel protein AmtB: mechanism of ammonia/ammonium transport</text></passage><passage><infon key="fpage">3970</infon><infon key="lpage">3975</infon><infon key="name_0">surname:Akgun;given-names:U.</infon><infon key="name_1">surname:Khademi;given-names:S.</infon><infon key="pub-id_pmid">21368153</infon><infon key="section_type">REF</infon><infon key="source">Proc. Natl
+Acad. Sci. USA</infon><infon key="type">ref</infon><infon key="volume">108</infon><infon key="year">2011</infon><offset>45714</offset><text>Periplasmic vestibule plays an important role for solute recruitment, selectivity, and gating in the Rh/Amt/MEP superfamily</text></passage><passage><infon key="fpage">17090</infon><infon key="lpage">17095</infon><infon key="name_0">surname:Zheng;given-names:L.</infon><infon key="name_1">surname:Kostrewa;given-names:D.</infon><infon key="name_2">surname:Bernèche;given-names:S.</infon><infon key="name_3">surname:Winkler;given-names:F. K.</infon><infon key="name_4">surname:Li;given-names:X. D.</infon><infon key="pub-id_pmid">15563598</infon><infon key="section_type">REF</infon><infon key="source">Proc. Natl Acad. Sci. USA</infon><infon key="type">ref</infon><infon key="volume">101</infon><infon key="year">2004</infon><offset>45838</offset><text>The mechanism of ammonia transport based on the crystal structure of AmtB of Escherichia coli</text></passage><passage><infon key="fpage">7091</infon><infon key="lpage">7098</infon><infon key="name_0">surname:Baday;given-names:S.</infon><infon key="name_1">surname:Wang;given-names:S.</infon><infon key="name_2">surname:Lamoureux;given-names:G.</infon><infon key="name_3">surname:Bernèche;given-names:S.</infon><infon key="pub-id_pmid">24021113</infon><infon key="section_type">REF</infon><infon key="source">Biochemistry</infon><infon key="type">ref</infon><infon key="volume">52</infon><infon key="year">2013</infon><offset>45932</offset><text>Different hydration patterns in the pores of AmtB and RhCG could determine their transport mechanisms</text></passage><passage><infon key="fpage">628</infon><infon key="lpage">695</infon><infon key="name_0">surname:van Heeswijk;given-names:W. C.</infon><infon key="name_1">surname:Westerhoff;given-names:H. V.</infon><infon key="name_2">surname:Boogerd;given-names:F. C.</infon><infon key="pub-id_pmid">24296575</infon><infon key="section_type">REF</infon><infon key="source">Microbiol. Mol. Biol. Rev.</infon><infon key="type">ref</infon><infon key="volume">77</infon><infon key="year">2013</infon><offset>46034</offset><text>Nitrogen assimilation in Escherichia coli: putting molecular data into a systems perspective</text></passage><passage><infon key="fpage">9995</infon><infon key="lpage">10000</infon><infon key="name_0">surname:Wacker;given-names:T.</infon><infon key="name_1">surname:Garcia-Celma;given-names:J. J.</infon><infon key="name_2">surname:Lewe;given-names:P.</infon><infon key="name_3">surname:Andrade;given-names:S. L.</infon><infon key="pub-id_pmid">24958855</infon><infon key="section_type">REF</infon><infon key="source">Proc. Natl Acad. Sci. USA</infon><infon key="type">ref</infon><infon key="volume">111</infon><infon key="year">2014</infon><offset>46127</offset><text>Direct observation of electrogenic NH4(+) transport in ammonium transport (Amt) proteins</text></passage><passage><infon key="fpage">11650</infon><infon key="lpage">11655</infon><infon key="name_0">surname:Neuhäuser;given-names:B.</infon><infon key="name_1">surname:Ludewig;given-names:U.</infon><infon key="pub-id_pmid">24634212</infon><infon key="section_type">REF</infon><infon key="source">J. Biol. Chem.</infon><infon key="type">ref</infon><infon key="volume">289</infon><infon key="year">2014</infon><offset>46216</offset><text>Uncoupling of ionic currents from substrate transport in the plant ammonium transporter AtAMT1;2</text></passage><passage><infon key="fpage">95</infon><infon key="lpage">102</infon><infon key="name_0">surname:Monfort;given-names:P.</infon><infon key="name_1">surname:Kosenko;given-names:E.</infon><infon key="name_2">surname:Erceg;given-names:S.</infon><infon key="name_3">surname:Canales;given-names:J. J.</infon><infon key="name_4">surname:Felipo;given-names:V.</infon><infon key="pub-id_pmid">12020609</infon><infon key="section_type">REF</infon><infon key="source">Neurochem. Int.</infon><infon key="type">ref</infon><infon key="volume">41</infon><infon key="year">2002</infon><offset>46313</offset><text>Molecular mechanism of acute ammonia toxicity: role of NMDA receptors</text></passage><passage><infon key="fpage">11</infon><infon key="lpage">14</infon><infon key="name_0">surname:Thomas;given-names:G.</infon><infon key="name_1">surname:Coutts;given-names:G.</infon><infon key="name_2">surname:Merrick;given-names:M.</infon><infon key="pub-id_pmid">10637624</infon><infon key="section_type">REF</infon><infon key="source">Trends Genet.</infon><infon key="type">ref</infon><infon key="volume">16</infon><infon key="year">2000</infon><offset>46383</offset><text>The glnKamtB operon. A conserved gene pair in prokaryotes</text></passage><passage><infon key="fpage">42</infon><infon key="lpage">47</infon><infon key="name_0">surname:Gruswitz;given-names:F.</infon><infon key="name_1">surname:O'Connell;given-names:J.;suffix:III</infon><infon key="name_2">surname:Stroud;given-names:R.
+M.</infon><infon key="pub-id_pmid">17190799</infon><infon key="section_type">REF</infon><infon key="source">Proc. Natl Acad.
+Sci. USA</infon><infon key="type">ref</infon><infon key="volume">104</infon><infon key="year">2006</infon><offset>46441</offset><text>Inhibitory complex of the transmembrane ammonia channel, AmtB, and the cytosolic regulatory protein, GlnK, at 1.96A</text></passage><passage><infon key="fpage">29558</infon><infon key="lpage">29567</infon><infon key="name_0">surname:Durand;given-names:A.</infon><infon key="name_1">surname:Merrick;given-names:M.</infon><infon key="pub-id_pmid">16864585</infon><infon key="section_type">REF</infon><infon key="source">J. Biol. Chem.</infon><infon key="type">ref</infon><infon key="volume">281</infon><infon key="year">2006</infon><offset>46557</offset><text>In vitro analysis of the Escherichia coli AmtB-GlnK complex reveals a stoichiometric interaction and sensitivity to ATP and 2-oxoglutarate</text></passage><passage><infon key="fpage">736</infon><infon key="lpage">738</infon><infon key="name_0">surname:Lanquar;given-names:V.</infon><infon key="name_1">surname:Frommer;given-names:W. B.</infon><infon key="pub-id_pmid">20418663</infon><infon key="section_type">REF</infon><infon key="source">Plant Signal.
+Behav.</infon><infon key="type">ref</infon><infon key="volume">5</infon><infon key="year">2010</infon><offset>46696</offset><text>Adjusting ammonium uptake via phosphorylation</text></passage><passage><infon key="fpage">3101</infon><infon key="lpage">3110</infon><infon key="name_0">surname:Boeckstaens;given-names:M.</infon><infon key="name_1">surname:Llinares;given-names:E.</infon><infon key="name_2">surname:Van
+Vooren;given-names:P.</infon><infon key="name_3">surname:Marini;given-names:A. M.</infon><infon key="pub-id_pmid">24476960</infon><infon key="section_type">REF</infon><infon key="source">Nat. Commun.</infon><infon key="type">ref</infon><infon key="volume">5</infon><infon key="year">2014</infon><offset>46742</offset><text>The TORC1 effector kinase Npr1 fine tunes the inherent activity of the Mep2 ammonium transport protein</text></passage><passage><infon key="fpage">1361</infon><infon key="lpage">1373</infon><infon key="name_0">surname:Graff;given-names:L.</infon><infon key="pub-id_pmid">21127027</infon><infon key="section_type">REF</infon><infon key="source">J. Exp. Bot.</infon><infon key="type">ref</infon><infon key="volume">62</infon><infon key="year">2011</infon><offset>46845</offset><text>N- terminal cysteines affect oligomer stability of the allosterically regulated ammonium transporter LeAMT1;1</text></passage><passage><infon key="fpage">161</infon><infon key="lpage">171</infon><infon key="name_0">surname:Severi;given-names:E.</infon><infon key="name_1">surname:Javelle;given-names:A.</infon><infon key="name_2">surname:Merrick;given-names:M.</infon><infon key="pub-id_pmid">17453422</infon><infon key="section_type">REF</infon><infon key="source">Mol. Membr. Biol.</infon><infon key="type">ref</infon><infon key="volume">24</infon><infon key="year">2007</infon><offset>46955</offset><text>The conserved carboxy-terminal region of the ammonia channel AmtB plays a critical role in channel function</text></passage><passage><infon key="fpage">195</infon><infon key="lpage">198</infon><infon key="name_0">surname:Loqué;given-names:D.</infon><infon key="name_1">surname:Lalonde;given-names:S.</infon><infon key="name_2">surname:Looger;given-names:L. L.</infon><infon key="name_3">surname:von
+Wirén;given-names:N.</infon><infon key="name_4">surname:Frommer;given-names:W. B.</infon><infon key="pub-id_pmid">17293878</infon><infon key="section_type">REF</infon><infon key="source">Nature</infon><infon key="type">ref</infon><infon key="volume">446</infon><infon key="year">2007</infon><offset>47063</offset><text>A cytosolic trans-activation domain essential for ammonium uptake</text></passage><passage><infon key="fpage">974</infon><infon key="lpage">984</infon><infon key="name_0">surname:Yuan;given-names:L.</infon><infon key="pub-id_pmid">23463773</infon><infon key="section_type">REF</infon><infon key="source">Plant
+Cell</infon><infon key="type">ref</infon><infon key="volume">25</infon><infon key="year">2013</infon><offset>47129</offset><text>Allosteric regulation of transport activity by heterotrimerization of Arabidopsis ammonium transporter complexes in vivo</text></passage><passage><infon key="fpage">e351</infon><infon key="name_0">surname:Hess;given-names:D. C.</infon><infon key="name_1">surname:Lu;given-names:W.</infon><infon key="name_2">surname:Rabinowitz;given-names:J.
+D.</infon><infon key="name_3">surname:Botstein;given-names:D.</infon><infon key="pub-id_pmid">17048990</infon><infon key="section_type">REF</infon><infon key="source">PLoS
+Biol.</infon><infon key="type">ref</infon><infon key="volume">4</infon><infon key="year">2006</infon><offset>47250</offset><text>Ammonium toxicity and potassium limitation in yeast</text></passage><passage><infon key="fpage">259</infon><infon key="lpage">275</infon><infon key="name_0">surname:Smith;given-names:D. G.</infon><infon key="name_1">surname:Garcia-Pedrajas;given-names:M. D.</infon><infon key="name_2">surname:Gold;given-names:S. E.</infon><infon key="name_3">surname:Perlin;given-names:M. H.</infon><infon key="pub-id_pmid">14507379</infon><infon key="section_type">REF</infon><infon key="source">Mol.
+Microbiol.</infon><infon key="type">ref</infon><infon key="volume">50</infon><infon key="year">2003</infon><offset>47302</offset><text>Isolation and characterization from pathogenic fungi of genes encoding ammonium permeases and their roles in dimorphism</text></passage><passage><infon key="fpage">187</infon><infon key="lpage">201</infon><infon key="name_0">surname:Teichert;given-names:S.</infon><infon key="name_1">surname:Rutherford;given-names:J. C.</infon><infon key="name_2">surname:Wottawa;given-names:M.</infon><infon key="name_3">surname:Heitman;given-names:J.</infon><infon key="name_4">surname:Tudzynski;given-names:B.</infon><infon key="pub-id_pmid">18083831</infon><infon key="section_type">REF</infon><infon key="source">Eukaryot. Cell</infon><infon key="type">ref</infon><infon key="volume">7</infon><infon key="year">2008</infon><offset>47422</offset><text>Impact of ammonium permeases mepA, mepB, and mepC on nitrogen-regulated secondary metabolism in Fusarium fujikuroi</text></passage><passage><infon key="fpage">411</infon><infon key="lpage">430</infon><infon key="name_0">surname:Javelle;given-names:A.</infon><infon key="pub-id_pmid">12519192</infon><infon key="section_type">REF</infon><infon key="source">Mol.
+Microbiol.</infon><infon key="type">ref</infon><infon key="volume">47</infon><infon key="year">2003</infon><offset>47537</offset><text>Molecular characterization, function and regulation of ammonium transporters (Amt) and ammonium-metabolizing enzymes (GS, NADP-GDH) in the ectomycorrhizal fungus Hebeloma cylindrosporum</text></passage><passage><infon key="fpage">2580</infon><infon key="lpage">2588</infon><infon key="name_0">surname:Törnroth-Horsefield;given-names:S.</infon><infon key="name_1">surname:Hedfalk;given-names:K.</infon><infon key="name_2">surname:Fischer;given-names:G.</infon><infon key="name_3">surname:Lindkvist-Petersson;given-names:K.</infon><infon key="name_4">surname:Neutze;given-names:R.</infon><infon key="section_type">REF</infon><infon key="source">FEBS
+Lett.</infon><infon key="type">ref</infon><infon key="volume">584</infon><infon key="year">2006</infon><offset>47723</offset><text>Structural insights into eukaryotic aquaporin regulation</text></passage><passage><infon key="fpage">79</infon><infon key="lpage">107</infon><infon key="name_0">surname:Klein;given-names:J. D.</infon><infon key="pub-id_pmid">25298340</infon><infon key="section_type">REF</infon><infon key="source">Subcell.
+Biochem.</infon><infon key="type">ref</infon><infon key="volume">73</infon><infon key="year">2014</infon><offset>47780</offset><text>Expression of urea transporters and their regulation</text></passage><passage><infon key="fpage">68</infon><infon key="lpage">72</infon><infon key="name_0">surname:Parker;given-names:J. L.</infon><infon key="name_1">surname:Newstead;given-names:S.</infon><infon key="pub-id_pmid">24572366</infon><infon key="section_type">REF</infon><infon key="source">Nature</infon><infon key="type">ref</infon><infon key="volume">507</infon><infon key="year">2014</infon><offset>47833</offset><text>Molecular basis of nitrate uptake by the plant nitrate transporter NRT1.1</text></passage><passage><infon key="fpage">695</infon><infon key="lpage">707</infon><infon key="name_0">surname:Hays;given-names:F. A.</infon><infon key="name_1">surname:Roe-Zurz;given-names:Z.</infon><infon key="name_2">surname:Stroud;given-names:R. M.</infon><infon key="pub-id_pmid">20946832</infon><infon key="section_type">REF</infon><infon key="source">Methods Enzymol.</infon><infon key="type">ref</infon><infon key="volume">470</infon><infon key="year">2010</infon><offset>47907</offset><text>Overexpression and purification of integral membrane proteins in yeast</text></passage><passage><infon key="fpage">125</infon><infon key="lpage">132</infon><infon key="name_0">surname:Kabsch;given-names:W.</infon><infon key="section_type">REF</infon><infon key="source">Acta Crystallogr.</infon><infon key="type">ref</infon><infon key="volume">D66</infon><infon key="year">2010</infon><offset>47978</offset><text>XDS</text></passage><passage><infon key="fpage">307</infon><infon key="lpage">326</infon><infon key="name_0">surname:Otwinowski;given-names:Z.</infon><infon key="name_1">surname:Minor;given-names:W.</infon><infon key="section_type">REF</infon><infon key="source">Methods Enzymol.</infon><infon key="type">ref</infon><infon key="volume">276</infon><infon key="year">2003</infon><offset>47982</offset><text>Processing of X-ray diffraction data collected in oscillation mode</text></passage><passage><infon key="fpage">352</infon><infon key="lpage">367</infon><infon key="name_0">surname:Afonine;given-names:P. V.</infon><infon key="section_type">REF</infon><infon key="source">Acta Crystallogr.</infon><infon key="type">ref</infon><infon key="volume">D68</infon><infon key="year">2012</infon><offset>48049</offset><text>Towards automated crystallographic structure refinement with phenix.refine</text></passage><passage><infon key="fpage">458</infon><infon key="lpage">464</infon><infon key="name_0">surname:McCoy;given-names:A. J.</infon><infon key="name_1">surname:Grosse-Kunstleve;given-names:R. W.</infon><infon key="name_2">surname:Storoni;given-names:L. C.</infon><infon key="name_3">surname:Read;given-names:R. J.</infon><infon key="section_type">REF</infon><infon key="source">Acta
+Crystallogr.</infon><infon key="type">ref</infon><infon key="volume">D61</infon><infon key="year">2005</infon><offset>48124</offset><text>Likelihood-enhanced fast translation functions</text></passage><passage><infon key="fpage">2126</infon><infon key="lpage">2132</infon><infon key="name_0">surname:Emsley;given-names:P.</infon><infon key="name_1">surname:Cowtan;given-names:K.</infon><infon key="section_type">REF</infon><infon key="source">Acta
+Crystallogr.</infon><infon key="type">ref</infon><infon key="volume">D60</infon><infon key="year">2004</infon><offset>48171</offset><text>Coot: model-building tools for molecular graphics</text></passage><passage><infon key="fpage">339</infon><infon key="lpage">346</infon><infon key="name_0">surname:Schiestl;given-names:R. H.</infon><infon key="name_1">surname:Gietz;given-names:R. D.</infon><infon key="pub-id_pmid">2692852</infon><infon key="section_type">REF</infon><infon key="source">Curr. Genet.</infon><infon key="type">ref</infon><infon key="volume">16</infon><infon key="year">1989</infon><offset>48221</offset><text>High efficiency transformation of intact yeast cells using single stranded nucleic acids as a carrier</text></passage><passage><infon key="fpage">201</infon><infon key="lpage">216</infon><infon key="name_0">surname:Ma;given-names:H.</infon><infon key="name_1">surname:Kunes;given-names:S.</infon><infon key="name_2">surname:Schatz;given-names:P.
+J.</infon><infon key="name_3">surname:Botstein;given-names:D.</infon><infon key="pub-id_pmid">2828185</infon><infon key="section_type">REF</infon><infon key="source">Gene</infon><infon key="type">ref</infon><infon key="volume">58</infon><infon key="year">1987</infon><offset>48323</offset><text>Plasmid construction by homologous recombination in yeast</text></passage><passage><infon key="fpage">552</infon><infon key="lpage">564</infon><infon key="name_0">surname:Marini;given-names:A. M.</infon><infon key="name_1">surname:André;given-names:B.</infon><infon key="pub-id_pmid">11069679</infon><infon key="section_type">REF</infon><infon key="source">Mol. Microbiol.</infon><infon key="type">ref</infon><infon key="volume">38</infon><infon key="year">2000</infon><offset>48381</offset><text>In vivo N-glycosylation of the Mep2 high-affinity ammonium transporter of Saccharomyces cerevisiae reveals an extracytosolic N-terminus</text></passage><passage><infon key="fpage">e1001362</infon><infon key="name_0">surname:Addinall;given-names:S. G.</infon><infon key="pub-id_pmid">21490951</infon><infon key="section_type">REF</infon><infon key="source">PLoS Genet.</infon><infon key="type">ref</infon><infon key="volume">7</infon><infon key="year">2011</infon><offset>48517</offset><text>Quantitative fitness analysis shows that NMD proteins and many other protein complexes suppress or enhance distinct telomere cap defects</text></passage><passage><infon key="fpage">291</infon><infon key="lpage">325</infon><infon key="name_0">surname:Marti-Renom;given-names:M. A.</infon><infon key="pub-id_pmid">10940251</infon><infon key="section_type">REF</infon><infon key="source">Annu. Rev. Biophys. Biomol. Struct.</infon><infon key="type">ref</infon><infon key="volume">29</infon><infon key="year">2000</infon><offset>48654</offset><text>Comparative protein structure modeling of genes and genomes</text></passage><passage><infon key="fpage">2657</infon><infon key="lpage">2669</infon><infon key="name_0">surname:Schmidt;given-names:T. H.</infon><infon key="name_1">surname:Kandt;given-names:C.</infon><infon key="pub-id_pmid">22989154</infon><infon key="section_type">REF</infon><infon key="source">J. Chem.
+Inf. Model.</infon><infon key="type">ref</infon><infon key="volume">52</infon><infon key="year">2012</infon><offset>48714</offset><text>LAMBADA and InflateGRO2: efficient membrane alignment and insertion of membrane proteins for molecular dynamics simulations</text></passage><passage><infon key="fpage">331</infon><infon key="lpage">342</infon><infon key="name_0">surname:Berendsen;given-names:H. J. C.</infon><infon key="name_1">surname:Postma;given-names:J. P.</infon><infon key="name_2">surname:van
+Gunsteren;given-names:W. F.</infon><infon key="name_3">surname:Hermans;given-names:J.</infon><infon key="section_type">REF</infon><infon key="source">Interaction models for water in relation to protein hydration Intermolecular Forces</infon><infon key="type">ref</infon><infon key="year">1981</infon><offset>48838</offset></passage><passage><infon key="fpage">1701</infon><infon key="lpage">1718</infon><infon key="name_0">surname:Van Der Spoel;given-names:D.</infon><infon key="pub-id_pmid">16211538</infon><infon key="section_type">REF</infon><infon key="source">J. Comput. Chem.</infon><infon key="type">ref</infon><infon key="volume">26</infon><infon key="year">2005</infon><offset>48839</offset><text>GROMACS: fast, flexible, and free</text></passage><passage><infon key="fpage">511</infon><infon key="lpage">519</infon><infon key="name_0">surname:Nosé;given-names:S.</infon><infon key="section_type">REF</infon><infon key="source">J. Chem. Phys.</infon><infon key="type">ref</infon><infon key="volume">81</infon><infon key="year">1984</infon><offset>48873</offset><text>A unified formulation of the constant temperature molecular dynamics methods</text></passage><passage><infon key="fpage">1695</infon><infon key="name_0">surname:Hoover;given-names:W. G.</infon><infon key="section_type">REF</infon><infon key="source">Phys.
+Rev. A</infon><infon key="type">ref</infon><infon key="volume">31</infon><infon key="year">1985</infon><offset>48950</offset><text>Canonical dynamics: equilibrium phase-space distributions</text></passage><passage><infon key="fpage">7182</infon><infon key="lpage">7190</infon><infon key="name_0">surname:Parrinello;given-names:M.</infon><infon key="name_1">surname:Rahman;given-names:A.</infon><infon key="section_type">REF</infon><infon key="source">J. Appl. Phys.</infon><infon key="type">ref</infon><infon key="volume">52</infon><infon key="year">1981</infon><offset>49008</offset><text>Polymorphic transitions in single crystals: a new molecular dynamics method</text></passage><passage><infon key="fpage">8577</infon><infon key="lpage">8593</infon><infon key="name_0">surname:Essmann;given-names:U.</infon><infon key="section_type">REF</infon><infon key="source">J. Chem. Phys.</infon><infon key="type">ref</infon><infon key="volume">103</infon><infon key="year">1995</infon><offset>49084</offset><text>A smooth particle mesh Ewald method</text></passage><passage><infon key="fpage">1463</infon><infon key="lpage">1472</infon><infon key="name_0">surname:Hess;given-names:B.</infon><infon key="name_1">surname:Bekker;given-names:H.</infon><infon key="name_2">surname:Berendsen;given-names:H.
+J.</infon><infon key="name_3">surname:Fraaije;given-names:J. G.</infon><infon key="section_type">REF</infon><infon key="source">J.
+Comput. Chem.</infon><infon key="type">ref</infon><infon key="volume">18</infon><infon key="year">1997</infon><offset>49120</offset><text>LINCS: a linear constraint solver for molecular simulations</text></passage><passage><infon key="fpage">2002</infon><infon key="lpage">2013</infon><infon key="name_0">surname:Berger;given-names:O.</infon><infon key="name_1">surname:Edholm;given-names:O.</infon><infon key="name_2">surname:Jähnig;given-names:F.</infon><infon key="pub-id_pmid">9129804</infon><infon key="section_type">REF</infon><infon key="source">Biophys. J.</infon><infon key="type">ref</infon><infon key="volume">72</infon><infon key="year">1997</infon><offset>49180</offset><text>Molecular dynamics simulations of a fluid bilayer of dipalmitoylphosphatidylcholine at full hydration, constant pressure, and constant temperature</text></passage><passage><infon key="section_type">REF</infon><infon key="type">ref</infon><offset>49327</offset><text> The PyMOL Molecular Graphics System. version 1.7.4 (Schrödinger, LLC).</text></passage><passage><infon key="section_type">SUPPL</infon><infon key="type">footnote</infon><offset>49400</offset><text>Author contributions B.v.d.B. performed the experiments related to Mep2 structure determination, designed research and wrote the paper. A.C. performed ammonium growth experiments of Mep variants. D.J. and S.K. performed modelling studies and MD simulations. A.B. collected the X-ray synchrotron data and maintained the Newcastle Structural Biology Laboratory. J.C.R. designed research related to the S. cerevisiae growth assays.</text></passage><passage><infon key="file">ncomms11337-f1.jpg</infon><infon key="id">f1</infon><infon key="section_type">FIG</infon><infon key="type">fig_title_caption</infon><offset>49829</offset><text>X-ray crystal structures of Mep2 transceptors.</text></passage><passage><infon key="file">ncomms11337-f1.jpg</infon><infon key="id">f1</infon><infon key="section_type">FIG</infon><infon key="type">fig_caption</infon><offset>49876</offset><text>(a) Monomer cartoon models viewed from the side for (left) A.
+fulgidus Amt-1 (PDB ID 2B2H), S. cerevisiae Mep2 (middle) and
+C. albicans Mep2 (right). The cartoons are in rainbow
+representation. The region showing ICL1 (blue), ICL3 (green) and the CTR
+(red) is boxed for comparison. (b) CaMep2 trimer viewed from the
+intracellular side (right). One monomer is coloured as in a and one
+monomer is coloured by B-factor (blue, low; red; high). The CTR is boxed.
+(c) Overlay of ScMep2 (grey) and CaMep2 (rainbow), illustrating
+the differences in the CTRs. All structure figures were generated with
+Pymol.</text></passage><passage><infon key="file">ncomms11337-f2.jpg</infon><infon key="id">f2</infon><infon key="section_type">FIG</infon><infon key="type">fig_title_caption</infon><offset>50476</offset><text>Sequence conservation in ammonium transporters.</text></passage><passage><infon key="file">ncomms11337-f2.jpg</infon><infon key="id">f2</infon><infon key="section_type">FIG</infon><infon key="type">fig_caption</infon><offset>50524</offset><text>ClustalW alignment of CaMep2, ScMep2, A. fulgidus Amt-1, E.
+coli AmtB and A. thaliana Amt-1;1. The secondary structure
+elements observed for CaMep2 are indicated, with the numbers corresponding
+to the centre of the TM segment. Important regions are labelled. The
+conserved RxK motif in ICL1 is boxed in blue, the ER motif in ICL2 in cyan,
+the conserved ExxGxD motif of the CTR in red and the AI region in yellow.
+Coloured residues are functionally important and correspond to those of the
+Phe gate (blue), the binding site Trp residue (magenta) and the twin-His
+motif (red). The Npr1 kinase site in the AI region is highlighted pink. The
+grey sequences at the C termini of CaMep2 and ScMep2 are not visible in the
+structures and are likely disordered.</text></passage><passage><infon key="file">ncomms11337-f3.jpg</infon><infon key="id">f3</infon><infon key="section_type">FIG</infon><infon key="type">fig_title_caption</infon><offset>51276</offset><text>Growth of ScMep2 variants on low ammonium medium.</text></passage><passage><infon key="file">ncomms11337-f3.jpg</infon><infon key="id">f3</infon><infon key="section_type">FIG</infon><infon key="type">fig_caption</infon><offset>51326</offset><text>(a) The triple mepΔ strain (black) and triple
+mepΔ npr1Δ strain (grey) containing plasmids
+expressing WT and variant ScMep2 were grown on minimal medium containing
+1 mM ammonium sulphate. The quantified cell density reflects
+logarithmic growth after 24 h. Error bars are the s.d. for three
+replicates of each strain (b) The strains used in a were also
+serially diluted and spotted onto minimal agar plates containing glutamate
+(0.1%) or ammonium sulphate (1 mM), and grown for 3 days at
+30 °C.</text></passage><passage><infon key="file">ncomms11337-f4.jpg</infon><infon key="id">f4</infon><infon key="section_type">FIG</infon><infon key="type">fig_title_caption</infon><offset>51832</offset><text>Structural differences between Mep2 and bacterial ammonium
+transporters.</text></passage><passage><infon key="file">ncomms11337-f4.jpg</infon><infon key="id">f4</infon><infon key="section_type">FIG</infon><infon key="type">fig_caption</infon><offset>51905</offset><text>(a) ICL1 in AfAmt-1 (light blue) and CaMep2 (dark blue), showing
+unwinding and inward movement in the fungal protein. (b) Stereo
+diagram viewed from the cytosol of ICL1, ICL3 (green) and the CTR (red) in
+AfAmt-1 (light colours) and CaMep2 (dark colours). The side chains of
+residues in the RxK motif as well as those of Tyr49 and His342 are labelled.
+The numbering is for CaMep2. (c) Conserved residues in ICL1-3 and the
+CTR. Views from the cytosol for CaMep2 (left) and AfAmt-1, highlighting the
+large differences in conformation of the conserved residues in ICL1 (RxK
+motif; blue), ICL2 (ER motif; cyan), ICL3 (green) and the CTR (red). The
+labelled residues are analogous within both structures. In b and
+c, the centre of the trimer is at top.</text></passage><passage><infon key="file">ncomms11337-f5.jpg</infon><infon key="id">f5</infon><infon key="section_type">FIG</infon><infon key="type">fig_title_caption</infon><offset>52652</offset><text>Channel closures in Mep2.</text></passage><passage><infon key="file">ncomms11337-f5.jpg</infon><infon key="id">f5</infon><infon key="section_type">FIG</infon><infon key="type">fig_caption</infon><offset>52678</offset><text>(a) Stereo superposition of AfAmt-1 and CaMep2 showing the residues of
+the Phe gate, His2 of the twin-His motif and the tyrosine residue Y49 in TM1
+that forms a hydrogen bond with His2 in CaMep2. (b) Surface views
+from the side in rainbow colouring, showing the two-tier channel block
+(indicated by the arrows) in CaMep2.</text></passage><passage><infon key="file">ncomms11337-f6.jpg</infon><infon key="id">f6</infon><infon key="section_type">FIG</infon><infon key="type">fig_title_caption</infon><offset>53000</offset><text>The Npr1 kinase target Ser453 is dephosphorylated and located in an
+electronegative pocket.</text></passage><passage><infon key="file">ncomms11337-f6.jpg</infon><infon key="id">f6</infon><infon key="section_type">FIG</infon><infon key="type">fig_caption</infon><offset>53092</offset><text>(a) Stereoviews of CaMep2 showing 2Fo–Fc
+electron density (contoured at 1.0 σ) for CTR residues
+Asp419-Met422 and for Tyr446-Thr455 of the AI region. For clarity, the
+residues shown are coloured white, with oxygen atoms in red and nitrogen
+atoms in blue. The phosphorylation target residue Ser453 is labelled in
+bold. (b) Overlay of the CTRs of ScMep2 (grey) and CaMep2 (green),
+showing the similar electronegative environment surrounding the
+phosphorylation site (P). The AI regions are coloured magenta. (c)
+Cytoplasmic view of the Mep2 trimer indicating the large distance between
+Ser453 and the channel exits (circles; Ile52 lining the channel exit is
+shown).</text></passage><passage><infon key="file">ncomms11337-f7.jpg</infon><infon key="id">f7</infon><infon key="section_type">FIG</infon><infon key="type">fig_title_caption</infon><offset>53761</offset><text>Effect of removal of the AI region on Mep2 structure.</text></passage><passage><infon key="file">ncomms11337-f7.jpg</infon><infon key="id">f7</infon><infon key="section_type">FIG</infon><infon key="type">fig_caption</infon><offset>53815</offset><text>(a) Side views for WT CaMep2 (left) and the truncation mutant
+442Δ (right). The latter is shown as a putty model according to
+B-factors to illustrate the disorder in the protein on the cytoplasmic side.
+Missing regions are labelled. (b) Stereo superpositions of WT CaMep2
+and the truncation mutant. 2Fo–Fc electron
+density (contoured at 1.0 σ) for residues Tyr49 and His342 is
+shown for the truncation mutant.</text></passage><passage><infon key="file">ncomms11337-f8.jpg</infon><infon key="id">f8</infon><infon key="section_type">FIG</infon><infon key="type">fig_title_caption</infon><offset>54233</offset><text>Phosphorylation causes conformational changes in the CTR.</text></passage><passage><infon key="file">ncomms11337-f8.jpg</infon><infon key="id">f8</infon><infon key="section_type">FIG</infon><infon key="type">fig_caption</infon><offset>54291</offset><text>(a) Cytoplasmic view of the DD mutant trimer, with WT CaMep2
+superposed in grey for one of the monomers. The arrow indicates the
+phosphorylation site. The AI region is coloured magenta. (b) Monomer
+side-view superposition of WT CaMep2 and the DD mutant, showing the
+conformational change and disorder around the ExxGxD motif. Side chains for
+residues 452 and 453 are shown as stick models.</text></passage><passage><infon key="file">ncomms11337-f9.jpg</infon><infon key="id">f9</infon><infon key="section_type">FIG</infon><infon key="type">fig_title_caption</infon><offset>54681</offset><text>Schematic model for phosphorylation-based regulation of Mep2 ammonium
+transporters.</text></passage><passage><infon key="file">ncomms11337-f9.jpg</infon><infon key="id">f9</infon><infon key="section_type">FIG</infon><infon key="type">fig_caption</infon><offset>54765</offset><text>(a) In the closed, non-phosphorylated state (i), the CTR (magenta) and
+ICL3 (green) are far apart with the latter blocking the intracellular
+channel exit (indicated with a hatched circle). Upon phosphorylation and
+mimicked by the CaMep2 S453D and DD mutants (ii), the region around the
+ExxGxD motif undergoes a conformational change that results in the CTR
+interacting with the inward-moving ICL3, opening the channel (full circle)
+(iii). The arrows depict the movements of important structural elements. The
+open-channel Mep2 structure is represented by archaebacterial Amt-1 and
+shown in lighter colours consistent with Fig. 4. As
+discussed in the text, similar structural arrangements may occur in plant
+AMTs. In this case however, the open channel corresponds to the
+non-phosphorylated state; phosphorylation breaks the CTR–ICL3
+interactions leading to channel closure. (b) Model based on AMT
+transporter analogy showing how phosphorylation of a
+Mep2 monomer might allosterically open channels in the entire trimer via
+disruption of the interactions between the CTR and ICL3 of a neighbouring
+monomer (arrow).</text></passage></document></collection>