FRINK Linked Data Fragments server

Matches in SemOpenAlex for { <https://semopenalex.org/work/W2063896337> ?p ?o ?g. }

• W2063896337 endingPage "34104" @default.
• W2063896337 startingPage "34096" @default.
• W2063896337 abstract "ATP phosphoribosyl transferase (ATP-PRT) joins ATP and 5-phosphoribosyl-1-pyrophosphate (PRPP) in a highly regulated reaction that initiates histidine biosynthesis. The unusual hetero-octameric version of ATP-PRT includes four HisGS catalytic subunits based on the periplasmic binding protein fold and four HisZ regulatory subunits that resemble histidyl-tRNA synthetases. Here, we present the first structure of a PRPP-bound ATP-PRT at 2.9 Å and provide a structural model for allosteric activation based on comparisons with other inhibited and activated ATP-PRTs from both the hetero-octameric and hexameric families. The activated state of the octameric enzyme is characterized by an interstitial phosphate ion in the HisZ-HisG interface and new contacts between the HisZ motif 2 loop and the HisGS dimer interface. These contacts restructure the interface to recruit conserved residues to the active site, where they activate pyrophosphate to promote catalysis. Additionally, mutational analysis identifies the histidine binding sites within a region highly conserved between HisZ and the functional HisRS. Through the oligomerization and functional re-assignment of protein domains associated with aminoacylation and phosphate binding, the HisZ-HisG octameric ATP-PRT acquired the ability to initiate the synthesis of a key metabolic intermediate in an allosterically regulated fashion. ATP phosphoribosyl transferase (ATP-PRT) joins ATP and 5-phosphoribosyl-1-pyrophosphate (PRPP) in a highly regulated reaction that initiates histidine biosynthesis. The unusual hetero-octameric version of ATP-PRT includes four HisGS catalytic subunits based on the periplasmic binding protein fold and four HisZ regulatory subunits that resemble histidyl-tRNA synthetases. Here, we present the first structure of a PRPP-bound ATP-PRT at 2.9 Å and provide a structural model for allosteric activation based on comparisons with other inhibited and activated ATP-PRTs from both the hetero-octameric and hexameric families. The activated state of the octameric enzyme is characterized by an interstitial phosphate ion in the HisZ-HisG interface and new contacts between the HisZ motif 2 loop and the HisGS dimer interface. These contacts restructure the interface to recruit conserved residues to the active site, where they activate pyrophosphate to promote catalysis. Additionally, mutational analysis identifies the histidine binding sites within a region highly conserved between HisZ and the functional HisRS. Through the oligomerization and functional re-assignment of protein domains associated with aminoacylation and phosphate binding, the HisZ-HisG octameric ATP-PRT acquired the ability to initiate the synthesis of a key metabolic intermediate in an allosterically regulated fashion. Phosphoribosyl transferases (PRTs) 5The abbreviations used are: PRT, phosphoribosyl transferase; HisRS, histidyl-tRNA synthetase; PRPP, 5-phosphoribosyl-1-pyrophosphate; PR-ATP, N-1-(5′-phosphoribosyl)-ATP; ATP-PRT, ATP phosphoribosyl transferase.5The abbreviations used are: PRT, phosphoribosyl transferase; HisRS, histidyl-tRNA synthetase; PRPP, 5-phosphoribosyl-1-pyrophosphate; PR-ATP, N-1-(5′-phosphoribosyl)-ATP; ATP-PRT, ATP phosphoribosyl transferase. catalyze the attack of a nitrogenous and/or aromatic base on 5-phosphoribosyl-1-pyrophosphate (PRPP), and thereby participate in essential reactions in the biosynthesis of nucleotides and the amino acids tryptophan and histidine (1Musick W.D. CRC Crit. Rev. Biochem. 1981; 11: 1-34Crossref PubMed Scopus (144) Google Scholar, 2Schramm V.L. Grubmeyer C. Prog. Nucleic Acids Res. Mol. Biol. 2004; 78: 261-304Crossref PubMed Scopus (44) Google Scholar). The largest family (type I) of these structurally diverse enzymes includes many nucleotide salvage enzymes that share a five-stranded parallel β sheet fold with a substrate binding hood domain (3Smith J.L. Nat. Struct. Biol. 1999; 6: 502-504Crossref PubMed Scopus (23) Google Scholar, 4Sinha S.C. Smith J.L. Curr. Opin. Struct. Biol. 2001; 11: 733-739Crossref PubMed Scopus (85) Google Scholar). The folds of type II (5Eads J.C. Ozturk D. Wexler T.B. Grubmeyer C. Sacchettini J.C. Structure. 1997; 5: 47-58Abstract Full Text Full Text PDF PubMed Scopus (95) Google Scholar) and type III enzymes (6Mayans O. Ivens A. Nissen L.J. Kirschner K. Wilmanns M. EMBO J. 2002; 21: 3245-3254Crossref PubMed Scopus (28) Google Scholar) are distinct from the class I enzymes, and the type III enzymes resemble nucleoside phosphorylase. Among the PRTs with complex quaternary structures and sophisticated regulation are the glutamine PRPP amidotransferase, which catalyzes the first committed step of purine biosynthesis (7Smith J.L. Zaluzec E.J. Wery J.P. Niu L. Switzer R.L. Zalkin H. Satow Y. Science. 1994; 264: 1427-1433Crossref PubMed Scopus (223) Google Scholar), and ATP phosphoribosyl transferase (ATP-PRT), which joins ATP and PRPP to initiate synthesis of histidine (8Martin R.G. J. Biol. Chem. 1963; 238: 257-268Abstract Full Text PDF Google Scholar, 9Voll M.J. Appella E. Martin R.G. J. Biol. Chem. 1967; 242: 1760-1767Abstract Full Text PDF PubMed Google Scholar). Glutamine PRPP amidotransferase and ATP-PRT both exhibit pathway end product inhibition, and regulation by cellular energy levels (7Smith J.L. Zaluzec E.J. Wery J.P. Niu L. Switzer R.L. Zalkin H. Satow Y. Science. 1994; 264: 1427-1433Crossref PubMed Scopus (223) Google Scholar, 10Winkler M.E. Neidhardt F.C. Escherichia coli and Salmonella Typhimurium, Cellular and Molecular Biology. 1. American Society for Microbiology, Washington, D. C.1987: 395-411Google Scholar). ATP-PRT is competitively inhibited by AMP and ADP (8Martin R.G. J. Biol. Chem. 1963; 238: 257-268Abstract Full Text PDF Google Scholar, 11Brenner M. Ames B.N. Voge H.J. Metabolic Regulation. 5. Academic Press, New York1971: 349-387Crossref Google Scholar, 12Morton D.P. Parsons S.M. Arch. Biochem. Biophys. 1976; 175: 677-686Crossref PubMed Scopus (37) Google Scholar, 13Morton D.P. Parsons S.M. Arch. Biochem. Biophys. 1977; 181: 643-648Crossref PubMed Scopus (24) Google Scholar) and non-competitively inhibited by histidine (Fig. 1) (8Martin R.G. J. Biol. Chem. 1963; 238: 257-268Abstract Full Text PDF Google Scholar, 13Morton D.P. Parsons S.M. Arch. Biochem. Biophys. 1977; 181: 643-648Crossref PubMed Scopus (24) Google Scholar). Despite decades of investigation, the structural basis of this regulation, and for PRTs in general, is not well understood. ATP-PRTs constitute two distinct subfamilies with different quaternary structures but share a conserved catalytic domain that currently represents the sole member of a fourth (type IV) PRT family. The nominally hexameric “long form,” (or HisGL) enzymes (14Parsons S.M. Koshland Jr., D.E. J. Biol. Chem. 1974; 249: 4119-4126Abstract Full Text PDF PubMed Google Scholar, 15Bell R.M. Parsons S.M. Dubravac S.A. Redfield A.G. Koshland Jr., D.E. J. Biol. Chem. 1974; 249: 4110-4118Abstract Full Text PDF PubMed Google Scholar, 16Klungsoyr L. Kryvi H. Biochim. Biophys. Acta. 1971; 227: 327-336Crossref PubMed Scopus (22) Google Scholar) were characterized during early efforts to understand amino acid biosynthesis regulation in enteric bacteria (10Winkler M.E. Neidhardt F.C. Escherichia coli and Salmonella Typhimurium, Cellular and Molecular Biology. 1. American Society for Microbiology, Washington, D. C.1987: 395-411Google Scholar, 11Brenner M. Ames B.N. Voge H.J. Metabolic Regulation. 5. Academic Press, New York1971: 349-387Crossref Google Scholar). Structures of the HisGL subfamily recently determined include apo and histidine-AMP complexes from Mycobacterium tuberculosis ATP-PRT (17Cho Y. Sharma V. Sacchettini J.C. J. Biol. Chem. 2003; 278: 8333-8339Abstract Full Text Full Text PDF PubMed Scopus (74) Google Scholar), and AMP-bound and N-1-(5′-phosphoribosyl)-ATP (PR-ATP product) bound complexes of HisGL ATP-PRT from Escherichia coli (18Lohkamp B. McDermott G. Campbell S.A. Coggins J.R. Lapthorn A.J. J. Mol. Biol. 2004; 336: 131-144Crossref PubMed Scopus (45) Google Scholar). The hexameric HisGL enzymes possesses a bi-lobal catalytic domain reminiscent of periplasmic binding proteins that bind sulfate, phosphate, and other small ligands (19Quiocho F.A. Ledvina P.S. Mol. Microbiol. 1996; 20: 17-25Crossref PubMed Scopus (450) Google Scholar, 20Wang Z. Luecke H. Yao N. Quiocho F.A. Nat. Struct. Biol. 1997; 4: 519-522Crossref PubMed Scopus (93) Google Scholar). The second ATP-PRT subfamily (“short form”; HisGS) is defined by hetero-octameric enzymes composed of two subunit types (21Sissler M. Delorme C. Bond J. Ehrlich S.D. Renault P. Francklyn C. Proc. Natl. Acad. Sci. U. S. A. 1999; 96: 8985-8990Crossref PubMed Scopus (115) Google Scholar). The catalytic subunit is denoted HisGS to reflect its relationship with HisGL (∼25% sequence identity), as well as the absence of 85–100 residues that comprise the C-terminal regulatory region in the long form (21Sissler M. Delorme C. Bond J. Ehrlich S.D. Renault P. Francklyn C. Proc. Natl. Acad. Sci. U. S. A. 1999; 96: 8985-8990Crossref PubMed Scopus (115) Google Scholar, 22Bond J.P. Francklyn C. J. Mol. Evol. 2000; 50: 339-347Crossref PubMed Scopus (28) Google Scholar). Hetero-octameric ATP-PRTs possess a second subunit type, HisZ, which is related to the catalytic domain of functional histidyl-tRNA synthetases (HisRSs), but is inactive on its own (21Sissler M. Delorme C. Bond J. Ehrlich S.D. Renault P. Francklyn C. Proc. Natl. Acad. Sci. U. S. A. 1999; 96: 8985-8990Crossref PubMed Scopus (115) Google Scholar, 22Bond J.P. Francklyn C. J. Mol. Evol. 2000; 50: 339-347Crossref PubMed Scopus (28) Google Scholar, 23Delorme C. Ehrlich S.D. Renault P. J. Bacteriol. 1992; 174: 6571-6579Crossref PubMed Google Scholar). The hetero-octamer is assembled from two dimers each of HisGS and HisZ (24Bovee M.L. Champagne K.S. Demeler B. Francklyn C.S. Biochemistry. 2002; 41: 11838-11846Crossref PubMed Scopus (24) Google Scholar), and both are required to reconstitute catalytic activity (21Sissler M. Delorme C. Bond J. Ehrlich S.D. Renault P. Francklyn C. Proc. Natl. Acad. Sci. U. S. A. 1999; 96: 8985-8990Crossref PubMed Scopus (115) Google Scholar). The recent structure of the histidine-bound ATP-PRT complex from Thermotoga maritima provided the first view of the short form variant subfamily, and confirmed predicted structural relationships between HisGS and HisGL, and between HisZ and HisRS (25Vega M.C. Zou P. Fernandez F.J. Murphy G.E. Sterner R. Popoz A. Wilmanns M. Mol. Microbiol. 2005; 55: 675-686Crossref PubMed Scopus (23) Google Scholar). However, no conclusions could be drawn about the structural basis of PRT function and its activation. Here, we present phosphate-bound and PRPP-bound structures of the hetero-octameric ATP-PRTs that represent the first illustrations of the activated state. Comparison of these structures to the apo-, histidine/AMP, and PR-ATP-bound hexameric complexes of HisGL, and the histidine-bound complex of the hetero-octameric subfamily reveals a common activation mechanism resembling those of glycosyltransferases in general. These new structures define a specific structural role of the aminoacyl-tRNA synthetase-like subunit in the allosteric activation of the PRT reaction, and thereby illustrate how catalytic function emerged from the collaborative adaptation of two functionally distinct ancestral protein domains. Construction of Mutant Proteins—Mutant versions (E130A and Y268F/Y269F) of the HisZ-HisG ATP-PRT were derived from a Lactococcus lactis pQE30 expression construct (21Sissler M. Delorme C. Bond J. Ehrlich S.D. Renault P. Francklyn C. Proc. Natl. Acad. Sci. U. S. A. 1999; 96: 8985-8990Crossref PubMed Scopus (115) Google Scholar) by use of the QuikChange® procedure (Stratagene). The double-stranded primers were 45 nucleotides in length, and the mutations were verified by DNA sequencing. Overexpression and Purification of Native and Selenomethionyl HisZ-HisG ATP-PRT—The octameric ATP-PRT complex from L. lactis was purified from an E. coli overexpression strain according to a previously published protocol (24Bovee M.L. Champagne K.S. Demeler B. Francklyn C.S. Biochemistry. 2002; 41: 11838-11846Crossref PubMed Scopus (24) Google Scholar). Selenomethionyl-octameric ATP-PRT was overexpressed by inhibiting the methionine pathway (26Doublié S. Methods Enzymol. 1997; 276: 523-530Crossref PubMed Scopus (788) Google Scholar), and purified in the same fashion as the wild type enzyme. Pooled fractions from the final hydroxylapatite column were concentrated to 15–17 mg/ml, dialyzed into 50 mm Na2PO4 (pH 6.0), 300 mm NaCl, 10% (v/v) glycerol, 10 mm β-mercaptoethanol, and stored at 4 °C for crystallization experiments. Crystallization and Data Collection—Crystals of the L. lactis complex were obtained by incubation at 12 °C by the hanging drop method using 2 μl of well solution (15–25% (v/v) polyethylene glycol 400, 0.1 m Tris-HCl, pH 7.5, 0.2 m MgCl2) and 2 μl of protein sample at 10–16 mg/ml and 10 mm ATP (or 10 mm N-1-methyl-ATP and 5 mm PRPP) in the drop. The growth of well ordered crystals was dependent on ATP or N-1-methyl-ATP, although the ATP molecule was not visible in the final electron density maps. Initial selenomethionyl crystals were obtained by essentially the same procedures, and then improved by microseeding. Crystals grown in the presence of ATP were derivatized with 2.5 mm sodium tungstate dihydrate (Na2WO4-2H2O). Cryoprotection was performed by addition of 17–18% glycerol before flash cooling in liquid nitrogen. All crystals grew to ∼0.4 × 0.2 × 0.03 mm3 in an orthorhombic space group (P21212) with unit cell parameters of a = 151.68 Å, b = 222.93 Å, c = 86.38 Å. There are four molecules each of HisG and HisZ per asymmetric unit, with an estimated solvent content of 57%. X-ray data were collected at 100 K on a Brandeis B1.2, ADSC Q315, or an ADSC Q4 CCD detector on beamlines X12C, X25, or X26C, respectively, at the National Synchrotron Light Source (Upton, NY). Complete selenomethionyl MAD data sets to 3.1 Å were collected for peak and remote wavelengths on X25, and another remote data set at X26C. The PO4-bound dataset served as the reference for refinement, and was collected at 1.2124 Å on beamline X26C from a tungstate-derivatized crystal that diffracted to 2.9 Å. An additional 3.2-Å dataset was collected from a crystal grown in the presence of N-1-ATP and PRPP. All datasets were processed and scaled using DENZO and SCALEPACK (27Otwinowski Z. Minor W. Methods Enzymol. 1997; 276: 307-326Crossref Scopus (38251) Google Scholar), and the data statistics are summarized in TABLE ONE.TABLE ONEData collection, phasing, and refinement statistics for HisZG ATP-PRTaseSe-PeakSe-Remote1Se-Remote2PRPPaN1-methyl-ATP and PRPP substrates were co-crystallized with the HisZG ATP-PRTasePO4-boundbATP was present in the mother liquor during crystallizationData collectionResolution (Å)40–3.140–3.240–3.129–3.2540–2.9Unique reflections53,89959,47250,70646,27265,583Redundancy97444CompletenesscThe numbers in parentheses are the statistics for the highest resolution shell, %95.6 (78.2)91.6 (65.2)99.3 (97.8)98.1 (93.7)96.7 (82.7)RmergedRmerge = Σ|I–〈I〉|/ΣI, where 〈I〉 is the average intensity from multiple observations of symmetry-related reflections, %0.109 (0.447)0.114 (0.363)0.085 (0.474)0.123 (0.404)0.075 (0.467)Overall I/sigma18.17 (2.06)15.01 (2.09)14.3 (2.11)9.52 (2.28)15.72 (2.09)Phasing statisticsRisoeRiso = Σ|FPH–FP|/Σ|FP|, where FP is the observed structure factor amplitude for the reference data set (Se-Peak), and FPH is the observed structure factor amplitude for the heavy atom derivative0.0720.0780.2190.149No. of sites44 Se44 Se44 Se2 WO4Phasing power1.1Overall FOMfFigure of merit, before and after density modification0.39/0.64Refinement statisticsPO4-boundPRPPRworkgRwork and Rfree = Σhkl||Fo|–|Fc||/Σhkl|Fo|, where Fo and Fc are the observed and calculated structure factor amplitudes. Rfree was calculated with ∼5.0% of the reflections not used in refinement, %24.4724.70RfreegRwork and Rfree = Σhkl||Fo|–|Fc||/Σhkl|Fo|, where Fo and Fc are the observed and calculated structure factor amplitudes. Rfree was calculated with ∼5.0% of the reflections not used in refinement, %28.5530.14rms deviationsBond length, Å0.00950.0095Bond angles, °1.411.32B-factor, (Å2)Average for all atoms7767Wilson plot7964a N1-methyl-ATP and PRPP substrates were co-crystallized with the HisZG ATP-PRTaseb ATP was present in the mother liquor during crystallizationc The numbers in parentheses are the statistics for the highest resolution shelld Rmerge = Σ|I–〈I〉|/ΣI, where 〈I〉 is the average intensity from multiple observations of symmetry-related reflectionse Riso = Σ|FPH–FP|/Σ|FP|, where FP is the observed structure factor amplitude for the reference data set (Se-Peak), and FPH is the observed structure factor amplitude for the heavy atom derivativef Figure of merit, before and after density modificationg Rwork and Rfree = Σhkl||Fo|–|Fc||/Σhkl|Fo|, where Fo and Fc are the observed and calculated structure factor amplitudes. Rfree was calculated with ∼5.0% of the reflections not used in refinement Open table in a new tab Structure Determination and Refinement—Twenty of the 48 possible selenium sites in the asymmetric unit were initially determined with SHELXD (28Uson I. Sheldrick G.M. Curr. Opin. Struct. Biol. 1999; 9: 643-648Crossref PubMed Scopus (259) Google Scholar). These sites were refined with SOLVE (29Terwilliger T.C. Berendzen J. Acta Crystallogr. D. Biol. Crystallogr. 1999; 55: 849-861Crossref PubMed Scopus (3216) Google Scholar), allowing identification of 24 additional selenium atoms. Further heavy atom refinement and phasing of the resulting 44 selenium atom substructure, followed by density modification using the 4-fold non-crystallographic symmetry with RESOLVE (30Terwilliger T.C. Acta Crystallogr. D Biol. Crystallogr. 2000; 56: 965-972Crossref PubMed Scopus (1628) Google Scholar), resulted in an interpretable electron density map. Model building was accomplished with the program O (31Jones T.A. Zou J.Y. Cowan S.W. Kjeldgaard M. Acta Crystystallogr. Sect. A. 1991; 47: 110-119Crossref PubMed Scopus (12999) Google Scholar). Subsequent rounds of refinement were performed using CNS (32Brunger A. Adams P. Clore G. DeLano W.L. Gros P. Grosse-Kunstleve R.W. Jiang J.S. Kuszewski J. Nilges M. Pannu N.S. Read R.J. Rice L.M. Simonson T. Warren G.L. Acta Crystallogr. D. Biol. Crystallogr. 1998; 54: 905-921Crossref PubMed Scopus (16918) Google Scholar). Simulated annealing with a 4-fold NCS restraint was alternated with manual rebuilding. TLS refinement using REFMAC within the CCP4 suite (33Collaborative Computational Project N. Acta Crystallogr. D. Biol. Crystallogr. 1994; 50: 760-763Crossref PubMed Scopus (19667) Google Scholar) proved valuable in reducing the free R factor. The PRPP bound model was refined using rigid body refinement followed by simulated annealing in CNS (32Brunger A. Adams P. Clore G. DeLano W.L. Gros P. Grosse-Kunstleve R.W. Jiang J.S. Kuszewski J. Nilges M. Pannu N.S. Read R.J. Rice L.M. Simonson T. Warren G.L. Acta Crystallogr. D. Biol. Crystallogr. 1998; 54: 905-921Crossref PubMed Scopus (16918) Google Scholar). The PRPP-bound and PO4-bound structures contained a total of 2064 and 2056 residues of 2116, respectively. In the final models all non-glycine residues fell into the allowed regions of the Ramachandran plot. Refinement statistics are reported in TABLE ONE. Histidine Inhibition Assays—ATP phosphoribosyl transferase activity was measured by following the formation of PR-ATP at 22 °C over time (9Voll M.J. Appella E. Martin R.G. J. Biol. Chem. 1967; 242: 1760-1767Abstract Full Text PDF PubMed Google Scholar). Reactions included ATP-PRT at a concentration of 100 nm, and were initiated with PRPP. The absorbance at 290 nm was detected every 9 s for 10 min using a BioMate5 spectrophotometer. End product inhibition was examined by the inclusion of 1 mm histidine. The base-line absorbance was established by setting A290 to zero for the reaction mixture before adding PRPP. Each experiment was repeated at least five times. Overall Structure and Monomer Architecture—The 2.9-Å crystal structure of the phosphate-bound (ATP activated) L. lactis hetero-octameric ATP-PRT was solved by multiwavelength anomalous diffraction, and a PRPP-bound (N-1-methyl-ATP activated) form was refined to 3.2 Å (TABLE ONE). Because of the fact that these forms were crystallized in the presence of ATP or N-1-methyl-ATP (which sedimentation velocity experiments suggest stabilize the 10.7 S R-form of the complex (24Bovee M.L. Champagne K.S. Demeler B. Francklyn C.S. Biochemistry. 2002; 41: 11838-11846Crossref PubMed Scopus (24) Google Scholar)), they presumably represent the active form of the complex. The overall architecture of the L. lactis complex features an X-shaped central core composed of the HisRS-like HisZ subunits, with dimers of HisGS catalytic subunits inserted into either end (Fig. 2a), and is generally similar to the histidine-bound complex from T. maritima (25Vega M.C. Zou P. Fernandez F.J. Murphy G.E. Sterner R. Popoz A. Wilmanns M. Mol. Microbiol. 2005; 55: 675-686Crossref PubMed Scopus (23) Google Scholar). The HisGS subunits closely resemble HisGL subunits from the hexameric ATP-PRTs (17Cho Y. Sharma V. Sacchettini J.C. J. Biol. Chem. 2003; 278: 8333-8339Abstract Full Text Full Text PDF PubMed Scopus (74) Google Scholar, 18Lohkamp B. McDermott G. Campbell S.A. Coggins J.R. Lapthorn A.J. J. Mol. Biol. 2004; 336: 131-144Crossref PubMed Scopus (45) Google Scholar), but lack the C-terminal histidine binding domain (Fig. 2b). The HisGS fold consists of two α/β domains connected by a twisted β ribbon. Domain I (residues 1–90 and 178–205) folds into a six-stranded mixed β sheet flanked by five α helices, whereas domain II (residues 91–177) comprises a five-stranded β sheet with one helical crossover connection above and two below. The active site lies in the crevice between these two domains. The HisZ subunits (Fig. 2c) feature the seven-stranded antiparallel β sheet flanked by 3–4 α helices and class defining motifs found in HisRS (34Arnez J.G. Harris D.C. Mitschler A. Rees B. Francklyn C.S. Moras D. EMBO J. 1995; 14: 4143-4155Crossref PubMed Scopus (129) Google Scholar) and class II aminoacyl-tRNA synthetase paralogs (35Nakatsu T. Kato H. Oda J. Nat. Struct. Biol. 1998; 5: 15-19Crossref PubMed Scopus (65) Google Scholar, 36Carrodeguas J.A. Theis K. Bogenhagen D.F. Kisker C. Mol. Cell. 2001; 7: 43-54Abstract Full Text Full Text PDF PubMed Scopus (109) Google Scholar), but possess an α-helical insertion domain with a different topology. The HisGS and HisZ monomers from the PRPP-bound (L. lactis) and histidine-bound (T. maritima) complexes can be readily superimposed, but there are notable structural differences. In the phosphate-bound and PRPP-bound L. lactis complexes, residues 30–35 of HisGS form a poorly structured loop, whereas these constitute a well ordered β strand in the histidine-bound T. maritima complex (Fig. 3a, arrow) (25Vega M.C. Zou P. Fernandez F.J. Murphy G.E. Sterner R. Popoz A. Wilmanns M. Mol. Microbiol. 2005; 55: 675-686Crossref PubMed Scopus (23) Google Scholar). Conversely, residues 142–147 comprise helix Gα6 in the phosphate-bound and PRPP-bound complexes, but lose substantial helical character in the histidine-bound complex. In the L. lactis complexes, the loop and Gα6 are critical components of the HisGS dimer interface that undergo conformational changes in response to activation. Dimeric Interactions and the HisZ-HisG Interface—The two monomers in each HisGS dimer pack in an antiparallel fashion, creating a hydrophobic interface defined by contacts between Ile-47, Phe-57, and Ile-62 from domain I with Leu-143′ and Val-147′ from domain II (Fig. 4a). Hydrogen bonds between Asn-52 and Glu-138′, and between Asp-53 and the main chain NH of Glu-138′ also strengthen the dimer. The HisZ dimer is stabilized by the symmetrical interaction of Zα1 and Zα1′ in the bottom of the interface, and extensive hydrophobic interactions from aromatic residues that lie under the antiparallel β ribbons that arch over the interface (Fig. 4b). Notably, the histidine-bound T. maritima and L. lactis PRPP-bound complexes differ with respect to the motif 2 loop. Whereas all four motif 2 loops are ordered in the T. maritima complex, only one motif 2 loop is ordered in each of the HisZ dimers in the L. lactis complexes. The four HisZ-HisG interfaces in the phosphate-bound and PRPP-bound L. lactis complexes feature the interaction of HisGS domain I (especially Gβ5 and Gα8–α9) with the insertion domain and antiparallel β sheet of HisZ (Fig. 5a). In the two HisZ subunits with ordered motif 2 loops, the loop interacts directly with helix Gα2 in the HisGS dimer interface (Fig. 5b). Principal contacts include salt bridges between Lys-118 and Arg-120 in the motif 2 loop with Glu-59 and Asp-77, which are located at the C termini of Gα2 and Gα3 in HisGS, respectively (Fig. 5b). Notably, this motif 2 loop/HisGS dimer interaction is conspicuously absent in the T. maritima histidine-bound complex (25Vega M.C. Zou P. Fernandez F.J. Murphy G.E. Sterner R. Popoz A. Wilmanns M. Mol. Microbiol. 2005; 55: 675-686Crossref PubMed Scopus (23) Google Scholar). The PRPP- and histidine-bound complexes are also distinguished by an interstitial phosphate ion seen in the two L. lactis HisZ-HisG interfaces with ordered motif 2 loops, but not in the T. maritima complex (Fig. 5a). The position of the phosphate is fixed by Tyr-82 and Lys-189 in HisGS, and Lys-275 and Tyr-277 from HisZ. The association of the interstitial phosphate with the two HisZ subunits possessing ordered motif 2 loops, as well as the high degree of conservation of the residues serving as its ligands (supplemental materials Fig. S1a and S1b) suggests that its presence is not merely a crystallization artifact. By virtue of its location in the HisZ-HisG interface, and its absence in the T. maritima histidine-bound complex, the interstitial phosphate may work in concert with the HisZ motif 2 loop to alter the structure of the HisGS dimer interface, thereby promoting transition to the activated state. The PRPP Binding Site and Activation of PRT Function—Prior sedimentation analysis of the hetero-octameric L. lactis complex revealed that ATP stabilizes a 10.7 S activated R state, whereas histidine and AMP in combination promote transition to a 9.5 S inhibited T state (24Bovee M.L. Champagne K.S. Demeler B. Francklyn C.S. Biochemistry. 2002; 41: 11838-11846Crossref PubMed Scopus (24) Google Scholar). The phosphate-bound and PRPP-bound L. lactis complexes were crystallized in the presence of ATP and N-1-ATP, respectively. Even though no density was seen for ATP, the sedimentation analysis supports the assignment of these L. lactis complexes to the R state. In contrast, the T. maritima histidine-bound hetero-octamer represents a putative histidine-inhibited T state complex (25Vega M.C. Zou P. Fernandez F.J. Murphy G.E. Sterner R. Popoz A. Wilmanns M. Mol. Microbiol. 2005; 55: 675-686Crossref PubMed Scopus (23) Google Scholar). Similarly, the hexameric M. tuberculosis histidine/AMP bound HisGL (17Cho Y. Sharma V. Sacchettini J.C. J. Biol. Chem. 2003; 278: 8333-8339Abstract Full Text Full Text PDF PubMed Scopus (74) Google Scholar) and PR-ATP bound E. coli HisGL complexes (18Lohkamp B. McDermott G. Campbell S.A. Coggins J.R. Lapthorn A.J. J. Mol. Biol. 2004; 336: 131-144Crossref PubMed Scopus (45) Google Scholar) represent, respectively, inhibited and activated forms. The structural alignment of HisG monomers from all published ATP-PRT structures revealed that pairs of monomers representing the same state (i.e. “activated” or “inhibited”) exhibited lower root mean square deviations (normalized to 100 Cα) than pairs representing different states (TABLE TWO). Thus, the identity of the bound ligand was a more reliable indicator of structural similarity than whether or not the two proteins belonged to the same subclass (i.e. HisGS or HisGL). The observed structural differences between active and inhibited states are therefore not merely artifacts of comparing enzymes from different organisms.TABLE TWONormalized root mean square deviations (rmsd) calculated for pairwise superpositions of HisGS and HisGL monomers from various ATP-PRT structures Alignments were created using the Fast_force subroutine of LSQMAN from the O package (31Jones T.A. Zou J.Y. Cowan S.W. Kjeldgaard M. Acta Crystystallogr. Sect. A. 1991; 47: 110-119Crossref PubMed Scopus (12999) Google Scholar). The runs were performed using a fragment size of 50, a step size of 25, and 100 as the minimum number of residues to match. The choice of the algorithm was dictated by the uneven number of Cα carbons in the comparison of HisGL and HisGS monomers. The values to the left of the hyphen in the parentheses represent the raw root mean square deviation in Å, which was calculated over the number Cα carbons given to the right of the hyphen. All Cα atoms from the individual HisG monomers were used as input in the search for the best alignment. The values in bold type represent root mean square deviations normalized to 100 Cα atoms for comparison, according to the formula: rmsd100=rmsd/1+lnn/100, where n is the number of amino acid residues in the raw calculation. The normalized values therefore provide a statistical basis on which to compare superpositions within and across the HisGL and HisGS families.MtHisGL, apo (1NH7)MtHisGL, inhibited His/AMP (1NH8)EcHisGL, active PR-ATP (1Q1K)EcHisGL, inhibited AMP (1H3D)TmHisGS, apo (1O64)TmHisGS, inhibited His/AMP (1USY)L1HisGS, active PO4 (1Z7M)L1HisGS, active PRPP (1Z7N)1NH71NH80.76(1.06/205)1Q1K1.201.14(1.77/251)(1.54/20" @default.
• W2063896337 created "2016-06-24" @default.
• W2063896337 creator A5001476495 @default.
• W2063896337 creator A5033892718 @default.
• W2063896337 creator A5036925851 @default.
• W2063896337 creator A5039011979 @default.
• W2063896337 creator A5088798352 @default.
• W2063896337 date "2005-10-01" @default.
• W2063896337 modified "2023-10-18" @default.
• W2063896337 title "Activation of the Hetero-octameric ATP Phosphoribosyl Transferase through Subunit Interface Rearrangement by a tRNA Synthetase Paralog" @default.
• W2063896337 cites W1480394609 @default.
• W2063896337 cites W1483187151 @default.
• W2063896337 cites W1504680953 @default.
• W2063896337 cites W1507594708 @default.
• W2063896337 cites W1539796472 @default.
• W2063896337 cites W1576979747 @default.
• W2063896337 cites W1588869927 @default.
• W2063896337 cites W1726597626 @default.
• W2063896337 cites W1777525352 @default.
• W2063896337 cites W192686486 @default.
• W2063896337 cites W1941046107 @default.
• W2063896337 cites W1965277349 @default.
• W2063896337 cites W1970561265 @default.
• W2063896337 cites W1971970683 @default.
• W2063896337 cites W1978422652 @default.
• W2063896337 cites W1982648542 @default.
• W2063896337 cites W1987129456 @default.
• W2063896337 cites W1987933268 @default.
• W2063896337 cites W1990257248 @default.
• W2063896337 cites W1995017064 @default.
• W2063896337 cites W1997194941 @default.
• W2063896337 cites W1998238795 @default.
• W2063896337 cites W2001641653 @default.
• W2063896337 cites W2013083986 @default.
• W2063896337 cites W2014224553 @default.
• W2063896337 cites W2018859828 @default.
• W2063896337 cites W2025936024 @default.
• W2063896337 cites W2027484071 @default.
• W2063896337 cites W2030030132 @default.
• W2063896337 cites W2031386057 @default.
• W2063896337 cites W2034202145 @default.
• W2063896337 cites W2036550916 @default.
• W2063896337 cites W2040402586 @default.
• W2063896337 cites W2047518536 @default.
• W2063896337 cites W2047807358 @default.
• W2063896337 cites W2052448379 @default.
• W2063896337 cites W2055956723 @default.
• W2063896337 cites W2080640253 @default.
• W2063896337 cites W2093873576 @default.
• W2063896337 cites W2094348523 @default.
• W2063896337 cites W2111468050 @default.
• W2063896337 cites W2135464698 @default.
• W2063896337 cites W2143694829 @default.
• W2063896337 cites W66180445 @default.
• W2063896337 cites W6981869 @default.
• W2063896337 cites W83378798 @default.
• W2063896337 doi "https://doi.org/10.1074/jbc.m505041200" @default.
• W2063896337 hasPubMedId "https://pubmed.ncbi.nlm.nih.gov/16051603" @default.
• W2063896337 hasPublicationYear "2005" @default.
• W2063896337 type Work @default.
• W2063896337 sameAs 2063896337 @default.
• W2063896337 citedByCount "32" @default.
• W2063896337 countsByYear W20638963372012 @default.
• W2063896337 countsByYear W20638963372015 @default.
• W2063896337 countsByYear W20638963372016 @default.
• W2063896337 countsByYear W20638963372017 @default.
• W2063896337 countsByYear W20638963372018 @default.
• W2063896337 countsByYear W20638963372019 @default.
• W2063896337 countsByYear W20638963372020 @default.
• W2063896337 countsByYear W20638963372021 @default.
• W2063896337 countsByYear W20638963372022 @default.
• W2063896337 countsByYear W20638963372023 @default.
• W2063896337 crossrefType "journal-article" @default.
• W2063896337 hasAuthorship W2063896337A5001476495 @default.
• W2063896337 hasAuthorship W2063896337A5033892718 @default.
• W2063896337 hasAuthorship W2063896337A5036925851 @default.
• W2063896337 hasAuthorship W2063896337A5039011979 @default.
• W2063896337 hasAuthorship W2063896337A5088798352 @default.
• W2063896337 hasBestOaLocation W20638963371 @default.
• W2063896337 hasConcept C104292427 @default.
• W2063896337 hasConcept C104317684 @default.
• W2063896337 hasConcept C112243037 @default.
• W2063896337 hasConcept C153911025 @default.
• W2063896337 hasConcept C153957851 @default.
• W2063896337 hasConcept C181199279 @default.
• W2063896337 hasConcept C185592680 @default.
• W2063896337 hasConcept C2776376580 @default.
• W2063896337 hasConcept C55493867 @default.
• W2063896337 hasConcept C67705224 @default.
• W2063896337 hasConcept C86803240 @default.
• W2063896337 hasConcept C95444343 @default.
• W2063896337 hasConceptScore W2063896337C104292427 @default.
• W2063896337 hasConceptScore W2063896337C104317684 @default.
• W2063896337 hasConceptScore W2063896337C112243037 @default.
• W2063896337 hasConceptScore W2063896337C153911025 @default.
• W2063896337 hasConceptScore W2063896337C153957851 @default.
• W2063896337 hasConceptScore W2063896337C181199279 @default.
• W2063896337 hasConceptScore W2063896337C185592680 @default.

• next