Báo cáo Y học: Herbaspirillum seropedicae signal transduction protein PII is structurally similar to the enteric GlnK

Eur. J. Biochem. 269, 3296–3303 (2002) Ó FEBS 2002 doi:10.1046/j.1432-1033.2002.03011.x Herbaspirillum seropedicae signal transduction protein PII is structurally similar to the enteric GlnK Elaine Machado Benelli1, Martin Buck2, Igor Polikarpov3, Emanuel Maltempi de Souza1, Leonardo M. Cruz1 and Fabio O. Pedrosa1 1Department of Biochemistry, Universidade Federal do Parana, Curitiba, Brazil; 2Department of Biological Science, Imperial College of Science, Technology & Medicine, Sir Alexander Fleming Building, Imperial College Road, London, UK; 3Laboratorio Nacional de Luz Sincrotron, Campinas, Brazil PII-like proteins are signal transduction proteins found in bacteria, archaea and eukaryotes. They mediate a variety of cellular responses. A second PII-like protein, called GlnK, has been found in several organisms. In the diazotroph Herbaspirillumseropedicae,PIIproteinisinvolvedinsensing nitrogen levels and controlling nitrogen fixation genes. In this work, the crystal structure of the unliganded H. sero-pedicae PII was solved by X-ray diffraction. H. seropedicae PII has a Gly residue, Gly108 preceding Pro109 and the main-chainformsabturn.Theglycineatposition108allows a bend in the C-terminal main-chain, thereby modifying the surface of the cleft between monomers and potentially Control of nitrogen metabolism in many bacteria utilizes a conserved mechanism of intracellular signalling to regulate patterns of gene expression and enzyme activity necessary for adapting to changes in the quality and abundance of nitrogen sources. The NifA protein is the transcriptional activator of nitrogen fixation (nif) genes in the majority of diazotrophs within the Proteobacteria. In several of these organisms, nifA expression is controlled by the general nitrogen regulation Ntr system, which, in turn, is controlled by the state of the glnB product, the PII protein. Under nitrogen excess, PII interacts with NtrB resulting in the dephosphorylation of the transcriptional activator NtrC-P and diminished nifA expression. Under limiting nitrogen, PII is uridylylated by GlnD and this allows NtrB to phosphorylate NtrC. In the c-subdivision of the Proteo-bacteria, nif gene expression is regulated by NifA and NifL: under high ammonium or oxygen levels NifL inhibits NifA activity,whereasundernitrogenlimitingconditionsandlow oxygen NifA is active. In K. pneumoniae GlnK, a paralogue of PII, interacts with the NifL–NifA complex, to relieve NifA inhibition by NifL [12,13,16,]. In Azotobacter vinela- Correspondence to E. Machado Benelli, Department of Biochemistry, Universidade Federal do Parana, C. Postal 19046, Curitiba, Brazil. E-mail: benelli@bio.ufpr.br Abbreviations: NtrB, nitrogen regulation protein B; NtrC, nitrogen regulation protein C; GlnD, uridylylating enzyme; NifA, nitrogen fixation protein A; NifL, nitrogen fixation protein L; EcPII, Escheri-chiacoliglnBproduct;EcGlnK,EscherichiacoliglnKproduct;HsPII, Herbispirillum seropedicae glnB product; KpPII, K. pneumoniae glnB product; KpGlnK, K. pneumoniae glnK product. (Received 29 January 2002, revised 15 February 2002, accepted 22 May 2002) changing function. The structure suggests that the C-terminal region of PII proteins may be involved in specificityoffunction,andnonentericdiazotrophsarefound to have the C-terminal consensus XGXDAX(107–112). We arealsoproposingbindingsitesforATPand2-oxoglutarate based on the structural alignment of PII with PII-ATP/ GlnK-ATP, 5-carboxymethyl-2-hydroxymuconate iso-merase and 4-oxalocrotonate tautomerase bound to the inhibitor 2-oxo-3-pentynoate. Keywords: nitrogen regulation; PII X-ray structure; crystal packing, Herbaspirillum seropedicae; G lnK. ndii only the GlnK protein is present and it controls the activity of NifA by the interaction with NifL and the complexNifL–NifAissensitiveto2-oxoglutaratelevels[20]. Although extensively studied in bacteria, PII-like proteins are present in all three kingdoms of life. For recent reviews see Ninfa & Atkinson [24], Thomas et al. [33] and Mag-asanik [21]. In Herbaspirillum seropedicae, a member of the bsubdi-visionofProteobacteria,theglnAntrBCandglnBgeneshave been identified [6,26], suggesting that an Ntr PII-dependent signal transducer cascade senses the nitrogen levels in this organism. In H. seropedicae, nifA expression is also dependent on phosphorylated NtrC (NtrC-P), but NifL hasnot been found. However,theactivity ofNifAisknown to be controlled by the PII protein, as in Azospirillum brasilense, a member of the asubdivision of the Proteobac-teria [2,3]. The mechanism involved in this control is not known. Souza et al. [30] observed that the activity of a H. seropedicae N-terminal domain-truncated NifA (DNTD) was independent of ammonium levels, suggesting that the N-terminal domain (NTD) plays a role in the control of NifA activity by ammonium. Arsene et al. [3] made a similar observation in A. brasilense and suggested that PII-UMP may interact with the NTD of NifA to change its activity. The residue Tyr18 from the NTD of NifA seems to be involved in the interaction between PII and NifA [2]. PII proteins interact directly with a variety of ligands, including ATP and 2-oxoglutarate. The structure of the EcPII protein and the paralogue EcGlnK have been solved in the presence and absence of ATP [7,9,35,36]. Here we reportthecrystalstructureofunligandedH. seropedicaePII (HsPII) at 2.1 A resolution and compare this with the available structures from E. coli. Although in amino-acid Ó FEBS 2002 Structural similarities between PII and GlnK (Eur. J. Biochem. 269) 3297 sequence HsPII shows higher identity to EcPII than EcGlnK, distinct structural differences are evident, placing HsPII closer to the unliganded and ATPbound forms of EcGlnK in three-dimensional structure. We suggest a correlation of the structural differences with the specialized functions of PII-like proteins in diazotrophs. It seems that function may be related to conformational flexibility exhibited by PII and GlnK proteins, as indicated by a comparison of crystal packing arrangements seen in several different crystal forms of PII-like proteins [7,9,35]. Changes inEcPIIstructureassociatedwithATPbindingsupportthis view and indicate that C-terminal structures can be ligand dependent [35]. When EcPII is bound to ATP the C-terminal structure is similar to that in unliganded EcGlnK [36] and unliganded HsPII (this paper). We note similarities in quaternary and subunit tertiary structure with other proteins, unrelated to PII by amino-acid sequence, that interact with a-ketoacids, suggesting the existence of a family of a-ketoacid interacting proteins. EXPERIMENTAL PROCEDURES Protein purification HsPII protein was overexpressed in E. coli RB9065kDE3, a glnB glnD mutant background lysogenized with kDE3 for T7 RNA polymerase production and purified as described by Benelli et al. [5]. The purified HsPII protein was dialysed in a buffer containing 10 mM Tris/HCl pH 8.0, 50 mM NaCl, 20% glycerol and 0.1 mM EDTA and concentrated in a Centricon-3 filter prior to crystallization. Crystallization Crystallizations used either the sitting or hanging drop vapour diffusion method at 18 °C in Limbro tissue culture plates. An initial Hampton crystallization screen of both native and N-terminal hexa histidine-tagged HsPII yielded promising microcrystals. Conditions were optimized by addition of a number of additives [10]. HsPII protein (14 mgÆmL)1) and His6–PII protein (13 mgÆmL)1) in Tris/ HCl 10 mM pH 8.0, NaCl 50 mM, glycerol 20% and EDTA 0.1 mM were used in crystallization experiments. A tetragonal crystal form of native PII was grown from hanging drops containing protein solution mixed in a 1 : 1 ratio with well solution (15.8% ethyleneglycol). A trigonal crystal form was grown by vapour diffusion in sitting drops. The reservoir solution contained 0.1 M sodium acetate pH 4.6, 30% methylpentadiol and 0.15 mgÆmL)1 of dextran sulfate. The drops contained 1 lL of protein solution and 1 lL of reservoir solution. The orthorhombic crystal form grew, using the hanging drop method, in 30% methylpentadiol, 0.1 mM sodium cacodylate pH 6.5 and 0.2 mM magnesium acetate. Initial tests on a copper rotating anode revealed diffraction to 3 A from the tetragonal and trigonal crystal forms (Table 1). Crystals of His6–PII were obtained by the hanging drop method at 18 °C. The reservoir solution contained 0.5 mL of 0.1 M sodium citrate pH 6 and 10% PEG6K and the drop contained 1 lL of protein solution (13 mgÆmL)1) and 1 lL of reservoir solution. The His6–PII crystal form diffracted to 6 A with the rotating anode source, and was not further characterized. Table 1. Summary of X-ray data collection and crystallographic refinement statistics. Data collectiona,b Space group Unit cell dimensions Solvent content (%) Max. resolution (A) Unique reflections Redundancy Completeness (%) Average I/rI P212121 a ¼ 78.41 A, b ¼ 82.36 A, c ¼ 100.95 A 68 2.1 36523 3 94 (95) 13 (1) P3221 a ¼ b ¼ 121.74 A, c ¼ 65.24 A a ¼ b ¼ 90°, c ¼ 120° 68 3.0 21170 3 98 (99) 12 (2) P43212 a ¼ b ¼ 88.81 A, c ¼ 116.91 A 61 3.2 8163 4 100 (100) 14 (4) R ¼ S|I ) < I > |/S|I| 0.057 0.078 0.187 Refinement in orthorhombic crystal formc,d,e Data range (A) Reflections (F > 0) Completeness (%) Reflections in free set Non-H atoms Residues Rms bond lengths (A) Rms bond angles (deg) Rms B-factors for bonded atoms (A2) Rfree (%) Rcryst (%) 13.0–2.1 36331 94.4 1820 4313 560 0.018 0.044 4.2 27.2 20.3 a Values in parentheses correspond to the highest resolution shell; 2.15–2.10 A (2415 reflections) for the orthorhombic form; 3.05–3.00 A (815 reflections) for the trigonal form; 3.25–3.20 A (393 reflections) for the tetragonal form. b The resolution cut-off was defined so that 50% of reflections in the highest resolution shell had I >3 r. c Rms deviations in bond lengths and angles are given from ideal values. d Rcryst ¼ S||Fo|–|Fc||/S|Fo|. e Rfree is as for Rcryst but calculated for a test set comprising 1820 reflections not used in the refinement. 3298 E. Machado Benelli et al. (Eur. J. Biochem. 269) Data collection and processing Asummaryofthedatacollectionandrefinementstatisticsis given in Table 1. Diffraction data were collected from a single crystal of each form at 120 K using a 30-cm MAR imaging plate detector system on a RIGAKU RU-200B generatorwithacopperanodeanddoublefocusingmirrors. A 2.1-A data set on the orthorhombic crystal form was collected at 120 K using synchrotron radiation at a wavelength of 1.38 A, using a MAR 345 imaging plate on the protein crystallography beamline [28,29] at the Brazilian National Synchrotron Laboratory (Campinas, Brazil). The crystal initially diffracted to 1.9 A, but the high resolution reflections gradually decayed during data collec-tion. The diffraction data were consistent with space group P212121,withthecellparametersa ¼ 78.41 A,b ¼82.36 A, c ¼ 100.95 A. The data were integrated, reduced and scaled using DENZO and SCALEPACK [25], respectively. Intensities were then converted to structure factors using the method of French & Wilson [11] as implemented in TRUNCATE [8]. Structure solution and refinement The structure of HsPII was solved in three space groups by molecular replacement in AMORE [23]. Selected crystallo-graphic data are given in Table 1. The complete EcPII monomer structure (PDB accession no. 2PII; [7]) and a truncated model lacking the uridylylation site loop and the C-terminal tail, residues 40–54 and 96–112, respectively, werebothusedassearchmodelstosolvethetrigonalcrystal form. Both monomer and trimer forms, generated by the crystallographicthreefoldaxisinspacegroupP63,wereused as search models. All calculations performed used 10 to 4 A data. Only when the trimer was used as a search model did the first peak in the cross rotation function correspond to the correct solution. A solution could not be found with the entire monomer structure, only with the truncated mono-mer model. Initial refinement of the whole model included noncrystallographic symmetry averaging and yielded a crystallography R-factor of 37%, the electron density map calculated at this stage indicated that residues 38–51 and 104–112 were not in correct positions. Model building was subsequently carried out on the truncated model only. The electron density for the rest of the protein was well defined; therefore itwas possibleto substitute all EcPII residues with the corresponding HsPII residues. Electron densities for residues 38 and 39 were so poor that they both had to be removed. Additional electron densities were apparent for two residues preceding Asp54 and five after Val96. The current model including residues 1–37 and 52–110 was obtained after a few rounds of model adjustment followed by refinement in REFMAC [22]. The tetragonal crystal form was solved using the trigonal HsPIImodelafterthefirstbuildinwhichalltheaminoacids different from EcPII were changed. This model included residues 1–37 and 54–96. The structure of the orthorhombic crystal form was solved using the trigonal HsPII containing residues1–35and55–107.Molecularreplacement,including rotation and translation functions followed by rigid body refinement, was carried out using 10 to 3.3 A data and resulted in an R-value of 39.6% and correlation coefficient of 60.3%. Ó FEBS 2002 Refinement was carried out using the program REFMAC [22] from the CCP4 suite of the program [8]. Eighty cycles of positional and B-factor refinement of the molecular replacement model against all the data between 10 A and 2.1 A resolution resulted in a model with Rcryst 30.0% and Rfree 36.1%. Model building was carried out using the programe O [18]. The orthorhombic HsPII model was built into 2Fo ) Fc and Fo ) Fc difference maps, residues were placed in well defined 2 r electron density maps. Eleven cycles of model building and refinement resulted in an R-factor of 23.1%. and Rfree of 29.8% In the last cycle, 125 moleculesofwaterwereaddedandtheR-factorsdroppedto 20.3 and 27.3%, respectively. The final model comprises residues 1–37 and 51–112 (monomer A), 1–36 and 43–107 (monomer B), 1–36 and 57–112 (monomer C), 1–37 and 50–112 (monomer D), 1–35 and 57–105 (monomer E) and 1–35 and 57–112 (monomer F). The residue Lys68 is placed as Ala in chains B, D and F because the electron density of the lateral chain of Lys was not observed in these chains. ThestereochemicalqualityofthefinalmodeloftheHsPII proteinwasverifiedbyPROCHECK [19].Thecoordinateswere deposited in the Protein Data Bank as the code 1HWU. RESULTS AND DISCUSSION Overall structure HsPII was overproduced and purified from E. coli and found to be a trimer of 36 kDa in solution, as are the EcPII and EcGlnK proteins [24]. The crystal structure was solved by molecular replacement using EcPII as the search model (see Materials and methods). Several different crystal forms of HsPII were grown (Table 1). The structural model was obtainedfromtheorthorhombiccrystalswhichdiffractedat 2.1 A. Monomers of the HsPII trimer are accommodated around a central threefold axis (Fig. 1A). The core of the HsPII monomer has a double bab motif (Figs 1B and 2A). The structural scaffold (the bstrands, the ahelices and the short B-loop) is well conserved in available PII-like struc-tures (Fig. 1B). Major differences amongst structures are in the T-loop (which contains the uridylylation site, Tyr51) and C-loop. HsPII is similar to EcGlnK, EcGlnK-ATP and EcPII-ATP in its C-loop (Figs 1B and 2A). The bstrands of the bab motif line the central cavity of the HsPII trimer, with the ahelices at the periphery of the molecule (Fig. 1A). The bottom edge of the central cavity is negativelycharged(Fig. 2B,part i)owingtothepresenceof Glu97 (Ala in EcPII and Gln in EcGlnK) and Glu95. The entrance of the central cavity is partially restricted by Gln94 with lateral chains directed towards its interior. Gln94 is substituted by Phe in EcPII and Ala in EcGlnK. The entrance from the top is restricted by Thr31, whose lateral chain is oriented to the interior of the cavity. The interior wall of the cavity is largely hydrophilic. Most of the intersubunit interactions that maintain the EcPII and EcGlnK trimers occur between conserved residues and are therefore also preserved in the HsPII structure, for example between Lys34 and Glu32 and Lys60 and Glu62 or Asp62 (in EcGlnK) (Fig. 2A,B, part ii). The salt bridge between residues Lys2 and Glu95 in EcPII appears to be substituted by Lys2 and Asp97 in HsPII. Furthermore, the interaction between residues Asp71 and Arg98 of different chains seen Ó FEBS 2002 Structural similarities between PII and GlnK (Eur. J. Biochem. 269) 3299 Fig. 1. Ribbon diagrams of the trimeric HsPII (A) and monomeric HsPII, EcPII, EcPII-ATP, EcGlnK and EcGlnK-ATP (B). (A) A ribbon diagram of the structure of the trimeric HsPII, each chain in a different colour. The bsheets of the bab motif line the central cavity of the trimer with the ahelices at the periph-ery. (B) Ribbon diagrams ofthe monomersof HsPII (i), EcPII (ii), EcPII-ATP (iii), EcGlnK (iv) and EcGlnK-ATP (v). Secondary struc-tures are colour coded: green bsheets, b1–4, blue helices, a1–2 and 310 helix and orange loops. The monomers share the same bab motif with the major structural differences residing in the loops T and C. inEcPIIdoesnotexistintheHsPIIstructure.Theseresidues are substituted by Glu and Gln, respectively. The lateral cleft created in the interface of each monomer of HsPII (Figs 1A and 2B, part iii) is similar to that observedinEcGlnKbutsmallerthaninEcPII.InHsPIIthe clefts are partially obstructed by C-terminal sequences. The bend of the main chain at Gly108 pushes residues Pro109, Asp110, Ala111 and Val112 into the cleft (Fig. 2B, part ii). Around the lateral cleft in the HsPII protein there is a salt bridge between Asp66 and Lys68 which does not appear in EcPII or EcGlnK (Fig. 2B, parts i and iii). This bridge is close to the C-terminal region and might mediate the interactions between PII and its receptors. Single amino-acid modifications of EcPII protein around the cleft produced mutant proteins (residues Thr83, Gly89 and Lys90) with impaired binding of the ligands 2-oxoglutarate and ATP [17] (Fig. 4C). None of the C-terminal residues seem to interact directly with ATP in the EcGlnK or EcPII proteins, for which structures of the complexes with ATP are available [35,36]. However these C-terminal residues are closer to the lateral cleft in EcGlnK compared to EcPII and might therefore influence binding of ATP indirectly. It is reasonable to propose that the structure of the C-terminal regionisimportantforeffectorbindingtoPII,althoughtthe effector need not directly interact with the C-terminal sequence (discussed below). The HsPII protein requires 2-oxoglutarate for uridylylation by the GlnD protein whereas the EcPII requires both 2-oxoglutarate and ATP, and the affinity constant for 2-oxoglutarate binding to HsPII is considerably higher than that of EcPII [5]. The bottom face of the HsPII trimer comprises mainly negatively charged residues (Fig. 2B, part i). Positive charges are located around the B-loop, which is probably involved in ATP interactions. In this region, HsPII Arg101 and Arg103 are separated by the lateral chain of Ile102 whereas in EcPII these residues are closer. This may explain why in the presence of excess 2-oxoglutarate Kact for ATP binding to HsPII is higher (100 lM) than that for EcPII ( 3 lM) [5,17]. The T- and C-loops The T-loop of PII-like proteins frequently includes a tyrosine which is the site of uridylylation. Where structures of the T-loop are available for EcPII and EcGlnK, crystal packing contacts appear to stabilize the T-loop in an artificially ordered conformation. In HsPII the part of T-loop that could be built shows a high temperature factor, and is exposed to the solvent. In the orthorhombic HsPII crystal there are two PII trimers per asymmetric unit. As 3300 E. Machado Benelli et al. (Eur. J. Biochem. 269) Ó FEBS 2002 Fig. 2. Alignments of the HsPII with EcPII and HsPII with EcGlnK amino-acid sequences (A) and molecular surface of the HsPII trimer (B). (A) Alignments of the HsPII with EcPII and HsPII with EcGlnK amino-acid sequences. The identity (73%) and similarity (86%) of HsPII to EcPII is higher than HsPII to EcGlnK (67% and 76%, respectively). Secondary structural elements are labelled above and below the sequence. The ahelix, bstrands, 310 helix and loops are coloured in green,blue,darkgreenandblack,respectively. (B) Molecular surface of the HsPII trimer colour-coded with acidic residue side-chains in red, basic side-chains in blue and others in white. T-loop residues 37–51 are not included. Residuesreferredinthetextarelabelledonthe monomer (i) The negatively charge bottom face ofthe trimer;(ii)the top face of the trimer and(iii)molecularsurfaceofthelateralcleftof the HsPII trimer. The salt bridge between Asp66A and Arg68A, located close to the C-terminal region, may mediate interaction between PII and its receptors. packing contacts are different for each monomer in these two trimers, the monomers were refined independently. The final rmsd values for the overlay of all atoms of the two trimers was 0.42 A. Electron density inall HsPII monomers to residues 38–53, which are within the T-loop, were not completely visible and the C-loop could be built in four of the six monomers (monomer A, C, D and F) present in unit of cell (see Experimental procedures). Those residues of the HsPII T-loop that can be traced represent a conformation unaffected by crystal packing contacts and are presumably in the preferred conformation of the T-loop as exists in the absence of interacting ligands such as ATP and 2-oxoglut-arate.ThelimitedamountofHsPIIT-loopthatisstructured shows significant conformational differences compared to those sequences ordered by packing contacts in the crystals of EcPII and EcGlnK (Fig. 1B). This implies that changes in conformation across much of the T-loop are possible duringthenormalfunctioningofthePII-likeproteins[1,35]. The K. pneumoniae glnK product (KpGlnK) and EcG-lnK proteins function to relieve NifL inhibition of NifA activity under nitrogen-limiting growth conditions. Arcon-deguy et al. [1], investigated the importance of the KpGlnK T-loop residues 43, 52 and 54 on the control of K. pneu-moniae NifA activity. Both EcGlnK and KpGlnK proteins have high sequence identity to EcPII. However, EcPII expressed from the chromosome is unable to substitute for the GlnKs with respect to NifLA [13,16]. Arcondeguy et al. (2000) suggested that residue 54 is the most important residue in the T-loop for distinguishing between PII and GlnK in controlling NifL activity. Residue 54 in HsPII is aspartate, as in K. pneumoniae glnB product (KpPII) and EcPII. However HsPII differs functionally from EcPII and KpPII,andisabletoactivateNifAinanE. colibackground containing NifL when expressed from a low copy number plasmid, as does EcGlnK, but not EcPII or KpPII (A. C. Bonatto, E. M. Souza, F. O. Pedrosa & E. M. Benelli, unpublished results). This suggests that some determinants of functionality that distinguish PII from GlnK must reside outside the T-loop. Consistent with this a second HsPII-like protein has been discovered, with the same T-loop sequence as the HsPII studied here (L. Noindorf, M. B. Steffens, E. M. Souza, F. O. Pedrosa & L. Chubatsu, unpublished data). This protein was called GlnK because it has higher identity to EcGlnK than EcPII and it is encoded by a glnK gene which is located on the glnKamtB operon. The HsPII and HsGlnK proteins are 78.6% identical and 93.75% similar and one of the seven different amino acids is in the C-terminal (Pro109 HsPII is substituted by Lys109 HsGlnK). Despite, the high homology between these proteins they are functionally different. The H. seropedicae glnB mutant has normal GS activity and biosynthesis but it is unable to fix nitrogen, suggesting that in vivo HsGlnK is unable to substitute HsPII [6]. The C-terminal structure of PII The structure of the C-terminal region of HsPII could be entirelybuiltonlyforoneofthemonomersintheasymmetric unit. In contrast to the C-terminal region of EcPII, which containsabsheet,theC-terminalofHsPIIcontainsaturnof ... - tailieumienphi.vn