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1.
Biochemistry ; 63(2): 230-240, 2024 Jan 16.
Article in English | MEDLINE | ID: mdl-38150593

ABSTRACT

The first step of histidine biosynthesis in Acinetobacter baumannii, the condensation of ATP and 5-phospho-α-d-ribosyl-1-pyrophosphate to produce N1-(5-phospho-ß-d-ribosyl)-ATP (PRATP) and pyrophosphate, is catalyzed by the hetero-octameric enzyme ATP phosphoribosyltransferase, a promising target for antibiotic design. The catalytic subunit, HisGS, is allosterically activated upon binding of the regulatory subunit, HisZ, to form the hetero-octameric holoenzyme (ATPPRT), leading to a large increase in kcat. Here, we present the crystal structure of ATPPRT, along with kinetic investigations of the rate-limiting steps governing catalysis in the nonactivated (HisGS) and activated (ATPPRT) forms of the enzyme. A pH-rate profile showed that maximum catalysis is achieved above pH 8.0. Surprisingly, at 25 °C, kcat is higher when ADP replaces ATP as substrate for ATPPRT but not for HisGS. The HisGS-catalyzed reaction is limited by the chemical step, as suggested by the enhancement of kcat when Mg2+ was replaced by Mn2+, and by the lack of a pre-steady-state burst of product formation. Conversely, the ATPPRT-catalyzed reaction rate is determined by PRATP diffusion from the active site, as gleaned from a substantial solvent viscosity effect. A burst of product formation could be inferred from pre-steady-state kinetics, but the first turnover was too fast to be directly observed. Lowering the temperature to 5 °C allowed observation of the PRATP formation burst by ATPPRT. At this temperature, the single-turnover rate constant was significantly higher than kcat, providing additional evidence for a step after chemistry limiting catalysis by ATPPRT. This demonstrates allosteric activation by HisZ accelerates the chemical step.


Subject(s)
ATP Phosphoribosyltransferase , Acinetobacter baumannii , ATP Phosphoribosyltransferase/chemistry , Diphosphates , Acinetobacter baumannii/metabolism , Catalytic Domain , Kinetics , Adenosine Triphosphate/metabolism , Catalysis
2.
Nat Commun ; 13(1): 7607, 2022 Dec 09.
Article in English | MEDLINE | ID: mdl-36494361

ABSTRACT

ATP phosphoribosyltransferase catalyses the first step of histidine biosynthesis and is controlled via a complex allosteric mechanism where the regulatory protein HisZ enhances catalysis by the catalytic protein HisGS while mediating allosteric inhibition by histidine. Activation by HisZ was proposed to position HisGS Arg56 to stabilise departure of the pyrophosphate leaving group. Here we report active-site mutants of HisGS with impaired reaction chemistry which can be allosterically restored by HisZ despite the HisZ:HisGS interface lying ~20 Å away from the active site. MD simulations indicate HisZ binding constrains the dynamics of HisGS to favour a preorganised active site where both Arg56 and Arg32 are poised to stabilise leaving-group departure in WT-HisGS. In the Arg56Ala-HisGS mutant, HisZ modulates Arg32 dynamics so that it can partially compensate for the absence of Arg56. These results illustrate how remote protein-protein interactions translate into catalytic resilience by restoring damaged electrostatic preorganisation at the active site.


Subject(s)
ATP Phosphoribosyltransferase , ATP Phosphoribosyltransferase/chemistry , Catalytic Domain , Histidine/metabolism , Allosteric Regulation
3.
Biochemistry ; 58(28): 3078-3086, 2019 07 16.
Article in English | MEDLINE | ID: mdl-31251578

ABSTRACT

ATP phosphoribosyltransferase (ATPPRT) catalyzes the first step of histidine biosynthesis, being allosterically inhibited by the final product of the pathway. Allosteric inhibition of long-form ATPPRTs by histidine has been extensively studied, but inhibition of short-form ATPPRTs is poorly understood. Short-form ATPPRTs are hetero-octamers formed by four catalytic subunits (HisGS) and four regulatory subunits (HisZ). HisGS alone is catalytically active and insensitive to histidine. HisZ enhances catalysis by HisGS in the absence of histidine but mediates allosteric inhibition in its presence. Here, steady-state and pre-steady-state kinetics establish that histidine is a noncompetitive inhibitor of short-form ATPPRT and that inhibition does not occur by dissociating HisGS from the hetero-octamer. The crystal structure of ATPPRT in complex with histidine and the substrate 5-phospho-α-d-ribosyl-1-pyrophosphate was determined, showing histidine bound solely to HisZ, with four histidine molecules per hetero-octamer. Histidine binding involves the repositioning of two HisZ loops. The histidine-binding loop moves closer to histidine to establish polar contacts. This leads to a hydrogen bond between its Tyr263 and His104 in the Asp101-Leu117 loop. The Asp101-Leu117 loop leads to the HisZ-HisGS interface, and in the absence of histidine, its motion prompts HisGS conformational changes responsible for catalytic activation. Following histidine binding, interaction with the histidine-binding loop may prevent the Asp101-Leu117 loop from efficiently sampling conformations conducive to catalytic activation. Tyr263Phe-PaHisZ-containing PaATPPRT, however, is less susceptible though not insensitive to histidine inhibition, suggesting the Tyr263-His104 interaction may be relevant to yet not solely responsible for transmission of the allosteric signal.


Subject(s)
ATP Phosphoribosyltransferase/antagonists & inhibitors , ATP Phosphoribosyltransferase/chemistry , Histidine/chemistry , Histidine/pharmacology , ATP Phosphoribosyltransferase/metabolism , Allosteric Regulation/drug effects , Allosteric Regulation/physiology , Crystallography/methods , Histidine/metabolism , Protein Binding/physiology , Protein Structure, Secondary
4.
Biophys J ; 116(10): 1887-1897, 2019 05 21.
Article in English | MEDLINE | ID: mdl-31053263

ABSTRACT

Allosteric regulation plays an important role in the control of metabolic flux in biosynthetic pathways. In microorganisms, many enzymes in these pathways adopt different strategies of allostery to allow the tuning of their activities in response to metabolic demand. Thus, it is important to uncover the mechanism of allosteric signal transmission to fully comprehend the complex control of enzyme function and its evolution. ATP-phosphoribosyltransferase (ATP-PRT), as the first enzyme in the histidine biosynthetic pathway, is allosterically regulated by histidine and offers a good platform for the study of allostery. Two forms of ATP-PRT, namely long and short forms, were discovered that show different arrangements of their regulatory machinery. Crystal structures of the long-form ATP-PRT have revealed overall conformational changes in the inhibited state, but the observed changes in the active state are quite subtle, making the elucidation of its allosteric mechanism difficult. Here, we combine computational methods (ligand docking, quantum mechanics/molecular mechanics optimization, and molecular dynamic simulations) with experimental studies to probe the signal transmission between remote allosteric and active sites. Our results reveal that distinct conformational ensembles of the catalytic domain with different dynamic properties exist in the ligand-free and histidine-bound enzymes. These ensembles display different capabilities in supporting the catalytic and allosteric function of ATP-PRT. The findings give insight into the underlying mechanism of allostery and allow us to propose that the hinge twisting within the catalytic domain is the key for both enhancement of catalysis and provision of regulation in ATP-PRT enzymes.


Subject(s)
ATP Phosphoribosyltransferase/chemistry , ATP Phosphoribosyltransferase/metabolism , Biocatalysis , Histidine/biosynthesis , Allosteric Regulation , Catalytic Domain , Molecular Dynamics Simulation
5.
Biochem J ; 475(16): 2681-2697, 2018 08 31.
Article in English | MEDLINE | ID: mdl-30072492

ABSTRACT

In the first committed step of histidine biosynthesis, adenosine 5'-triphosphate (ATP) and 5-phosphoribosyl-α1-pyrophosphate (PRPP), in the presence of ATP phosphoribosyltransferase (ATP-PRT, EC 2.4.2.17), yield phosphoribosyl-ATP. ATP-PRTs are subject to feedback inhibition by histidine that allosterically binds between the regulatory domains. Histidine biosynthetic pathways of bacteria, lower eukaryotes, and plants are considered promising targets for the design of antibiotics, antifungal agents, and herbicides because higher organisms are histidine heterotrophs. Plant ATP-PRTs are similar to one of the two types of their bacterial counterparts, the long-type ATP-PRTs. A biochemical and structural study of ATP-PRT from the model legume plant, Medicago truncatula (MedtrATP-PRT1) is reported herein. Two crystal structures, presenting homohexameric MedtrATP-PRT1 in its relaxed (R-) and histidine-bound, tense (T-) states allowed to observe key features of the enzyme and provided the first structural insights into an ATP-PRT from a eukaryotic organism. In particular, they show pronounced conformational reorganizations during R-state to T-state transition that involves substantial movements of domains. This rearrangement requires a trans- to cis- switch of a peptide backbone within the hinge region of MedtrATP-PRT1. A C-terminal α-helix, absent in bacteria, reinforces the hinge that is constituted by two peptide strands. As a result, conformations of the R- and T-states are significantly different from the corresponding states of prokaryotic enzymes with known 3-D structures. Finally, adenosine 5'-monophosphate (AMP) bound at the active site is consistent with a competitive (and synergistic with histidine) nature of AMP inhibition.


Subject(s)
ATP Phosphoribosyltransferase/chemistry , ATP Phosphoribosyltransferase/metabolism , Histidine/biosynthesis , Medicago truncatula/enzymology , Plant Proteins/chemistry , Plant Proteins/metabolism , ATP Phosphoribosyltransferase/genetics , Crystallography, X-Ray , Histidine/genetics , Medicago truncatula/genetics , Plant Proteins/genetics , Protein Domains , Protein Structure, Secondary
6.
Biochemistry ; 57(29): 4357-4367, 2018 07 24.
Article in English | MEDLINE | ID: mdl-29940105

ABSTRACT

Short-form ATP phosphoribosyltransferase (ATPPRT) is a hetero-octameric allosteric enzyme comprising four catalytic subunits (HisGS) and four regulatory subunits (HisZ). ATPPRT catalyzes the Mg2+-dependent condensation of ATP and 5-phospho-α-d-ribosyl-1-pyrophosphate (PRPP) to generate N1-(5-phospho-ß-d-ribosyl)-ATP (PRATP) and pyrophosphate, the first reaction of histidine biosynthesis. While HisGS is catalytically active on its own, its activity is allosterically enhanced by HisZ in the absence of histidine. In the presence of histidine, HisZ mediates allosteric inhibition of ATPPRT. Here, initial velocity patterns, isothermal titration calorimetry, and differential scanning fluorimetry establish a distinct kinetic mechanism for ATPPRT where PRPP is the first substrate to bind. AMP is an inhibitor of HisGS, but steady-state kinetics and 31P NMR spectroscopy demonstrate that ADP is an alternative substrate. Replacement of Mg2+ by Mn2+ enhances catalysis by HisGS but not by the holoenzyme, suggesting different rate-limiting steps for nonactivated and activated enzyme forms. Density functional theory calculations posit an SN2-like transition state stabilized by two equivalents of the metal ion. Natural bond orbital charge analysis points to Mn2+ increasing HisGS reaction rate via more efficient charge stabilization at the transition state. High solvent viscosity increases HisGS's catalytic rate, but decreases the hetero-octamer's, indicating that chemistry and product release are rate-limiting for HisGS and ATPPRT, respectively. This is confirmed by pre-steady-state kinetics, with a burst in product formation observed with the hetero-octamer but not with HisGS. These results are consistent with an activation mechanism whereby HisZ binding leads to a more active conformation of HisGS, accelerating chemistry beyond the product release rate.


Subject(s)
ATP Phosphoribosyltransferase/metabolism , Psychrobacter/enzymology , ATP Phosphoribosyltransferase/chemistry , Adenosine Diphosphate/metabolism , Adenosine Monophosphate/metabolism , Allosteric Regulation , Binding Sites , Catalytic Domain , Kinetics , Models, Molecular , Moraxellaceae Infections/microbiology , Phosphoribosyl Pyrophosphate/metabolism , Protein Conformation , Protein Multimerization , Psychrobacter/chemistry , Psychrobacter/metabolism , Substrate Specificity
7.
Biochem J ; 475(1): 247-260, 2018 01 05.
Article in English | MEDLINE | ID: mdl-29208762

ABSTRACT

Adenosine triphosphate (ATP) phosphoribosyltransferase (ATP-PRT) catalyses the first committed step of histidine biosynthesis in plants and microorganisms. Two forms of ATP-PRT have been reported, which differ in their molecular architecture and mechanism of allosteric regulation. The short-form ATP-PRT is a hetero-octamer, with four HisG chains that comprise only the catalytic domains and four separate chains of HisZ required for allosteric regulation by histidine. The long-form ATP-PRT is homo-hexameric, with each chain comprising two catalytic domains and a covalently linked regulatory domain that binds histidine as an allosteric inhibitor. Here, we describe a truncated long-form ATP-PRT from Campylobacter jejuni devoid of its regulatory domain (CjeATP-PRTcore). Results showed that CjeATP-PRTcore is dimeric, exhibits attenuated catalytic activity, and is insensitive to histidine, indicating that the covalently linked regulatory domain plays a role in both catalysis and regulation. Crystal structures were obtained for CjeATP-PRTcore in complex with both substrates, and for the first time, the complete product of the reaction. These structures reveal the key features of the active site and provide insights into how substrates move into position during catalysis.


Subject(s)
ATP Phosphoribosyltransferase/chemistry , Adenosine Monophosphate/chemistry , Adenosine Triphosphate/chemistry , Bacterial Proteins/chemistry , Campylobacter jejuni/enzymology , ATP Phosphoribosyltransferase/genetics , ATP Phosphoribosyltransferase/metabolism , Adenosine Monophosphate/metabolism , Adenosine Triphosphate/metabolism , Allosteric Regulation , Amino Acid Motifs , Bacterial Proteins/genetics , Bacterial Proteins/metabolism , Campylobacter jejuni/chemistry , Catalytic Domain , Cloning, Molecular , Crystallography, X-Ray , Escherichia coli/genetics , Escherichia coli/metabolism , Gene Expression , Genetic Vectors/chemistry , Genetic Vectors/metabolism , Histidine/chemistry , Histidine/metabolism , Isoenzymes/chemistry , Isoenzymes/genetics , Isoenzymes/metabolism , Kinetics , Models, Molecular , Protein Binding , Protein Conformation, alpha-Helical , Protein Conformation, beta-Strand , Protein Interaction Domains and Motifs , Protein Multimerization , Recombinant Proteins/chemistry , Recombinant Proteins/genetics , Recombinant Proteins/metabolism , Substrate Specificity
8.
Nat Commun ; 8(1): 203, 2017 08 07.
Article in English | MEDLINE | ID: mdl-28781362

ABSTRACT

ATP-phosphoribosyltransferase (ATP-PRT) is a hexameric enzyme in conformational equilibrium between an open and seemingly active state and a closed and presumably inhibited form. The structure-function relationship of allosteric regulation in this system is still not fully understood. Here, we develop a screening strategy for modulators of ATP-PRT and identify 3-(2-thienyl)-L-alanine (TIH) as an allosteric activator of this enzyme. Kinetic analysis reveals co-occupancy of the allosteric sites by TIH and L-histidine. Crystallographic and native ion-mobility mass spectrometry data show that the TIH-bound activated form of the enzyme closely resembles the inhibited L-histidine-bound closed conformation, revealing the uncoupling between ATP-PRT open and closed conformations and its functional state. These findings suggest that dynamic processes are responsible for ATP-PRT allosteric regulation and that similar mechanisms might also be found in other enzymes bearing a ferredoxin-like allosteric domain.Active and inactive state ATP-phosphoribosyltransferases (ATP-PRTs) are believed to have different conformations. Here the authors show that in both states, ATP-PRT has a similar structural arrangement, suggesting that dynamic alterations are involved in ATP-PRT regulation by allosteric modulators.


Subject(s)
ATP Phosphoribosyltransferase/chemistry , ATP Phosphoribosyltransferase/genetics , ATP Phosphoribosyltransferase/metabolism , Adenosine Triphosphate/chemistry , Adenosine Triphosphate/metabolism , Allosteric Regulation , Allosteric Site , Histidine/chemistry , Histidine/metabolism , Kinetics , Models, Molecular
9.
Structure ; 25(5): 730-738.e4, 2017 05 02.
Article in English | MEDLINE | ID: mdl-28392260

ABSTRACT

MtATP-phosphoribosyltransferase (MtATP-PRT) is an enzyme catalyzing the first step of the biosynthesis of L-histidine in Mycobacterium tuberculosis, and proposed to be regulated via an allosteric mechanism. Native mass spectrometry (MS) reveals MtATP-PRT to exist as a hexamer. Conformational changes induced by L-histidine binding and the influence of buffer pH are determined with ion mobility MS, hydrogen deuterium exchange (HDX) MS, and analytical ultracentrifugation. The experimental collision cross-section (DTCCSHe) decreases from 76.6 to 73.5 nm2 upon ligand binding at pH 6.8, which correlates to the decrease in CCS calculated from crystal structures. No such changes in conformation were found at pH 9.0. Further detail on the regions that exhibit conformational change on L-histidine binding is obtained with HDX-MS experiments. On incubation with L-histidine, rapid changes are observed within domain III, and around the active site at longer times, indicating an allosteric effect.


Subject(s)
ATP Phosphoribosyltransferase/chemistry , Allosteric Site , Bacterial Proteins/chemistry , ATP Phosphoribosyltransferase/metabolism , Allosteric Regulation , Bacterial Proteins/metabolism , Feedback, Physiological , Histidine/chemistry , Histidine/metabolism , Mass Spectrometry/methods , Mycobacterium tuberculosis/enzymology , Protein Binding
10.
Biochemistry ; 56(5): 793-803, 2017 02 07.
Article in English | MEDLINE | ID: mdl-28092443

ABSTRACT

Adenosine 5'-triphosphate phosphoribosyltransferase (ATPPRT) catalyzes the first step in histidine biosynthesis, the condensation of ATP and 5-phospho-α-d-ribosyl-1-pyrophosphate to generate N1-(5-phospho-ß-d-ribosyl)-ATP and inorganic pyrophosphate. The enzyme is allosterically inhibited by histidine. Two forms of ATPPRT, encoded by the hisG gene, exist in nature, depending on the species. The long form, HisGL, is a single polypeptide chain with catalytic and regulatory domains. The short form, HisGS, lacks a regulatory domain and cannot bind histidine. HisGS instead is found in complex with a regulatory protein, HisZ, constituting the ATPPRT holoenzyme. HisZ triggers HisGS catalytic activity while rendering it sensitive to allosteric inhibition by histidine. Until recently, HisGS was thought to be catalytically inactive without HisZ. Here, recombinant HisGS and HisZ from the psychrophilic bacterium Psychrobacter arcticus were independently overexpressed and purified. The crystal structure of P. arcticus ATPPRT was determined at 2.34 Å resolution, revealing an equimolar HisGS-HisZ hetero-octamer. Steady-state kinetics indicate that both the ATPPRT holoenzyme and HisGS are catalytically active. Surprisingly, HisZ confers only a modest 2-4-fold increase in kcat. Reaction profiles for both enzymes cannot be distinguished by 31P nuclear magnetic resonance, indicating that the same reaction is catalyzed. The temperature dependence of kcat shows deviation from Arrhenius behavior at 308 K with the holoenzyme. Interestingly, such deviation is detected only at 313 K with HisGS. Thermal denaturation by CD spectroscopy resulted in Tm's of 312 and 316 K for HisZ and HisGS, respectively, suggesting that HisZ renders the ATPPRT complex more thermolabile. This is the first characterization of a psychrophilic ATPPRT.


Subject(s)
ATP Phosphoribosyltransferase/chemistry , Amino Acyl-tRNA Synthetases/chemistry , Bacterial Proteins/chemistry , Histidine/chemistry , Monosaccharide Transport Proteins/chemistry , Psychrobacter/enzymology , ATP Phosphoribosyltransferase/genetics , ATP Phosphoribosyltransferase/metabolism , Acclimatization , Adenosine Triphosphate/analogs & derivatives , Adenosine Triphosphate/chemistry , Adenosine Triphosphate/metabolism , Allosteric Regulation , Amino Acyl-tRNA Synthetases/genetics , Amino Acyl-tRNA Synthetases/metabolism , Bacterial Proteins/genetics , Bacterial Proteins/metabolism , Cold Temperature , Crystallography, X-Ray , Diphosphates/chemistry , Diphosphates/metabolism , Enzyme Stability , Escherichia coli/genetics , Escherichia coli/metabolism , Gene Expression , Histidine/biosynthesis , Isoenzymes/chemistry , Isoenzymes/genetics , Isoenzymes/metabolism , Kinetics , Models, Molecular , Monosaccharide Transport Proteins/genetics , Monosaccharide Transport Proteins/metabolism , Phosphoribosyl Pyrophosphate/chemistry , Phosphoribosyl Pyrophosphate/metabolism , Protein Domains , Protein Multimerization , Protein Structure, Secondary , Psychrobacter/genetics , Recombinant Proteins/chemistry , Recombinant Proteins/genetics , Recombinant Proteins/metabolism , Thermodynamics
11.
FEBS Lett ; 590(16): 2603-10, 2016 08.
Article in English | MEDLINE | ID: mdl-27393206

ABSTRACT

ATP-phosphoribosyltransferase (ATP-PRT) catalyses the first step of histidine biosynthesis. Two different forms of ATP-PRT have been described; the homo-hexameric long form, and the hetero-octameric short form. Lactococcus lactis possesses the short form ATP-PRT comprising four subunits of HisGS , the catalytic subunit, and four subunits of HisZ, a histidyl-tRNA synthetase paralogue. Previous studies have suggested that HisGS requires HisZ for catalysis. Here, we reveal that the dimeric HisGS does display ATP-PRT activity in the absence of HisZ. This result reflects the evolutionary relationship between the long and short form ATP-PRT, which acquired allosteric inhibition and enhanced catalysis via two divergent strategies.


Subject(s)
ATP Phosphoribosyltransferase/metabolism , Amino Acyl-tRNA Synthetases/metabolism , Bacterial Proteins/metabolism , Monosaccharide Transport Proteins/metabolism , Protein Isoforms/metabolism , ATP Phosphoribosyltransferase/chemistry , ATP Phosphoribosyltransferase/genetics , Amino Acid Sequence , Amino Acyl-tRNA Synthetases/chemistry , Amino Acyl-tRNA Synthetases/genetics , Bacterial Proteins/chemistry , Bacterial Proteins/genetics , Catalysis , Catalytic Domain/genetics , Histidine/chemistry , Histidine/metabolism , Lactococcus lactis/enzymology , Monosaccharide Transport Proteins/chemistry , Monosaccharide Transport Proteins/genetics , Protein Isoforms/chemistry , Protein Isoforms/genetics
12.
Protein Sci ; 25(8): 1492-506, 2016 08.
Article in English | MEDLINE | ID: mdl-27191057

ABSTRACT

Adenosine triphosphate phosphoribosyltransferase (ATP-PRT) catalyzes the first committed step of the histidine biosynthesis in plants and microorganisms. Here, we present the functional and structural characterization of the ATP-PRT from the pathogenic ε-proteobacteria Campylobacter jejuni (CjeATP-PRT). This enzyme is a member of the long form (HisGL ) ATP-PRT and is allosterically inhibited by histidine, which binds to a remote regulatory domain, and competitively inhibited by AMP. In the crystalline form, CjeATP-PRT was found to adopt two distinctly different hexameric conformations, with an open homohexameric structure observed in the presence of substrate ATP, and a more compact closed form present when inhibitor histidine is bound. CjeATP-PRT was observed to adopt only a hexameric quaternary structure in solution, contradicting previous hypotheses favoring an allosteric mechanism driven by an oligomer equilibrium. Instead, this study supports the conclusion that the ATP-PRT long form hexamer is the active species; the tightening of this structure in response to remote histidine binding results in an inhibited enzyme.


Subject(s)
ATP Phosphoribosyltransferase/chemistry , Adenosine Monophosphate/chemistry , Adenosine Triphosphate/chemistry , Bacterial Proteins/chemistry , Campylobacter jejuni/chemistry , Histidine/chemistry , ATP Phosphoribosyltransferase/genetics , ATP Phosphoribosyltransferase/metabolism , Allosteric Regulation , Allosteric Site , Bacterial Proteins/genetics , Bacterial Proteins/metabolism , Binding, Competitive , Campylobacter jejuni/enzymology , Campylobacter jejuni/genetics , Cloning, Molecular , Escherichia coli/genetics , Escherichia coli/metabolism , Gene Expression , Kinetics , Models, Molecular , Mutation , Protein Folding , Protein Interaction Domains and Motifs , Protein Multimerization , Protein Structure, Quaternary , Protein Structure, Secondary , Recombinant Proteins/chemistry , Recombinant Proteins/genetics , Recombinant Proteins/metabolism , Thermodynamics
13.
J Biotechnol ; 206: 26-37, 2015 Jul 20.
Article in English | MEDLINE | ID: mdl-25892668

ABSTRACT

L-Histidine biosynthesis in Corynebacterium glutamicum is mainly regulated by L-histidine feedback inhibition of the ATP-phosphoribosyltransferase HisG that catalyzes the first step of the pathway. The elimination of this feedback inhibition is the first and most important step in the development of an L-histidine production strain. For this purpose, a combined approach of random mutagenesis and rational enzyme redesign was performed. Mutants spontaneously resistant to the toxic L-histidine analog ß-(2-thiazolyl)-DL-alanine (2-TA) revealed novel and unpredicted mutations in the C-terminal regulatory domain of HisG resulting in increased feedback resistance. Moreover, deletion of the entire C-terminal regulatory domain in combination with the gain of function mutation S143F in the catalytic domain resulted in a HisG variant that is still highly active even at L-histidine concentrations close to the solubility limit. Notably, the S143F mutation on its own provokes feedback deregulation, revealing for the first time an amino acid residue in the catalytic domain of HisG that is involved in the feedback regulatory mechanism. In addition, we investigated the effect of hisG mutations for L-histidine production on different levels. This comprised the analysis of different expression systems, including plasmid- and chromosome-based overexpression, as well as the importance of codon choice for HisG mutations. The combination of domain deletions, single amino acid exchanges, codon choice, and chromosome-based overexpression resulted in production strains accumulating around 0.5 g l(-1) L-histidine, demonstrating the added value of the different approaches.


Subject(s)
ATP Phosphoribosyltransferase/metabolism , Corynebacterium glutamicum/genetics , Feedback, Physiological/physiology , Histidine/metabolism , Metabolic Engineering/methods , ATP Phosphoribosyltransferase/chemistry , ATP Phosphoribosyltransferase/genetics , Bacterial Proteins/chemistry , Bacterial Proteins/genetics , Bacterial Proteins/metabolism , Corynebacterium glutamicum/enzymology , Escherichia coli/genetics , Metabolic Networks and Pathways , Recombinant Proteins/chemistry , Recombinant Proteins/genetics , Recombinant Proteins/metabolism , Silent Mutation/genetics , Silent Mutation/physiology
14.
Curr Top Med Chem ; 13(22): 2866-84, 2013.
Article in English | MEDLINE | ID: mdl-24111909

ABSTRACT

Worldwide, tuberculosis is the leading cause of morbidity and mortality due to a single bacterial pathogen, Mycobacterium tuberculosis (Mtb). The increasing prevalence of this disease, the emergence of multi-, extensively, and totally drug-resistant strains, complicated by co-infection with the human immunodeficiency virus, and the length of tuberculosis chemotherapy have led to an urgent and continued need for the development of new and more effective antitubercular drugs. Within this context, the L-histidine biosynthetic pathway, which converts 5-phosphoribosyl 1-pyrophosphate to L-histidine in ten enzymatic steps, has been reported as a promising target of antimicrobial agents. This pathway is found in bacteria, archaebacteria, lower eukaryotes, and plants but is absent in mammals, making these enzymes highly attractive targets for the drug design of new antimycobacterial compounds with selective toxicity. Moreover, the biosynthesis of L-histidine has been described as essential for Mtb growth in vitro. Accordingly, a comprehensive overview of Mycobacterium tuberculosis histidine pathway enzymes as attractive targets for the development of new antimycobacterial agents is provided, mainly summarizing the previously reported inhibition data for Mtb or orthologous proteins.


Subject(s)
Antitubercular Agents/chemistry , Antitubercular Agents/pharmacology , Enzymes/metabolism , Histidine/metabolism , Mycobacterium tuberculosis/drug effects , Mycobacterium tuberculosis/metabolism , ATP Phosphoribosyltransferase/chemistry , ATP Phosphoribosyltransferase/genetics , ATP Phosphoribosyltransferase/metabolism , Aldose-Ketose Isomerases/genetics , Aldose-Ketose Isomerases/metabolism , Aminohydrolases/genetics , Aminohydrolases/metabolism , Drug Design , Enzymes/genetics , Molecular Targeted Therapy , Mycobacterium tuberculosis/genetics
15.
Biochemistry ; 45(50): 14933-43, 2006 Dec 19.
Article in English | MEDLINE | ID: mdl-17154531

ABSTRACT

Two families of ATP phosphoribosyl transferases (ATP-PRT) join ATP and 5-phosphoribosyl-1 pyrophosphate (PRPP) in the first reaction of histidine biosynthesis. These consist of a homohexameric form found in all three kingdoms and a hetero-octameric form largely restricted to bacteria. Hetero-octameric ATP-PRTs consist of four HisGS catalytic subunits related to periplasmic binding proteins and four HisZ regulatory subunits that resemble histidyl-tRNA synthetases. To clarify the relationship between the two families of ATP-PRTs and among phosphoribosyltransferases in general, we determined the steady state kinetics for the hetero-octameric form and characterized the active site by mutagenesis. The KmPRPP (18.4 +/- 3.5 microM) and kcat (2.7 +/- 0.3 s-1) values for the PRPP substrate are similar to those of hexameric ATP-PRTs, but the Km for ATP (2.7 +/- 0.3 mM) is 4-fold higher, suggestive of tighter regulation by energy charge. Histidine and AMP were determined to be noncompetitive (Ki = 81.1 microM) and competitive (Ki = 1.44 mM) inhibitors, respectively, with values that approximate their intracellular concentrations. Mutagenesis experiments aimed at investigating the side chains recognizing PRPP showed that 5'-phosphate contacts (T159A and T162A) had the largest (25- and 155-fold, respectively) decreases in kcat/Km, while smaller decreases were seen with mutants making cross subunit contacts (K50A and K8A) to the pyrophosphate moiety or contacts to the 2'-OH group. Despite their markedly different quaternary structures, hexameric and hetero-octameric ATRP-PRTs exhibit similar functional parameters and employ mechanistic strategies reminiscent of the broader PRT superfamily.


Subject(s)
ATP Phosphoribosyltransferase/chemistry , Bacterial Proteins/chemistry , Lactococcus lactis/enzymology , Multiprotein Complexes/chemistry , ATP Phosphoribosyltransferase/genetics , ATP Phosphoribosyltransferase/metabolism , Adenosine Monophosphate/chemistry , Bacterial Proteins/genetics , Bacterial Proteins/metabolism , Binding Sites , Catalytic Domain/genetics , Histidine/biosynthesis , Histidine/chemistry , Lactococcus lactis/genetics , Multiprotein Complexes/genetics , Multiprotein Complexes/metabolism , Mutagenesis, Site-Directed , Phosphoribosyl Pyrophosphate/chemistry , Phosphoribosyl Pyrophosphate/metabolism , Protein Binding/genetics , Protein Structure, Quaternary/genetics , Protein Subunits/chemistry , Protein Subunits/genetics , Protein Subunits/metabolism , Substrate Specificity/genetics
16.
Mol Microbiol ; 55(3): 675-86, 2005 Feb.
Article in English | MEDLINE | ID: mdl-15660995

ABSTRACT

The molecular structure of the ATP phosphoribosyl transferase from the hyperthermophile Thermotoga maritima is composed of a 220 kDa hetero-octameric complex comprising four catalytic subunits (HisGS) and four regulatory subunits (HisZ). Steady-state kinetics indicate that only the complete octameric complex is active and non-competitively inhibited by the pathway product histidine. The rationale for these findings is provided by the crystal structure revealing a total of eight histidine binding sites that are located within each of the four HisGS-HisZ subunit interfaces formed by the ATP phosphoribosyl transferase complex. While the structure of the catalytic HisGS subunit is related to the catalytic domain of another family of (HisGL)2 ATP phosphoribosyl transferases that is functional in the absence of additional regulatory subunits, the structure of the regulatory HisZ subunit is distantly related to class II aminoacyl-tRNA synthetases. However, neither the mode of the oligomeric subunit arrangement nor the type of histidine binding pockets is found in these structural relatives. Common ancestry of the regulatory HisZ subunit and class II aminoacyl-tRNA synthetase may reflect the balanced need of regulated amounts of a cognate amino acid (histidine) in the translation apparatus, ultimately linking amino acid biosynthesis and protein biosynthesis in terms of function, structure and evolution.


Subject(s)
ATP Phosphoribosyltransferase/genetics , Gene Expression Regulation, Bacterial , Gene Expression Regulation, Enzymologic , Thermotoga maritima/enzymology , ATP Phosphoribosyltransferase/chemistry , ATP Phosphoribosyltransferase/metabolism , Amino Acid Sequence , Amino Acyl-tRNA Synthetases/genetics , Amino Acyl-tRNA Synthetases/metabolism , Binding Sites , Crystallography, X-Ray , Histidine/metabolism , Models, Molecular , Molecular Sequence Data , Structure-Activity Relationship , Thermotoga maritima/genetics
17.
J Mol Biol ; 336(1): 131-44, 2004 Feb 06.
Article in English | MEDLINE | ID: mdl-14741209

ABSTRACT

ATP-phosphoribosyltransferase (ATP-PRT), the first enzyme of the histidine pathway, is a complex allosterically regulated enzyme, which controls the flow of intermediates through this biosynthetic pathway. The crystal structures of Escherichia coli ATP-PRT have been solved in complex with the inhibitor AMP at 2.7A and with product PR-ATP at 2.9A (the ribosyl-triphosphate could not be resolved). On the basis of binding of AMP and PR-ATP and comparison with type I PRTs, the PRPP and parts of the ATP-binding site are identified. These structures clearly identify the AMP as binding in the 5-phosphoribosyl-alpha-1-pyrophosphate (PRPP)-binding site, with the adenosine ring occupying the ATP-binding site. Comparison with the recently solved Mycobacterium tuberculosis ATP-PRT structures indicates that histidine is solely responsible for the large conformational changes observed between the hexameric forms of the enzyme. The role of oligomerisation in inhibition and the structural basis for the synergistic inhibition by histidine and AMP are discussed.


Subject(s)
ATP Phosphoribosyltransferase/chemistry , Adenosine Monophosphate/metabolism , Escherichia coli Proteins/chemistry , Escherichia coli/enzymology , Protein Structure, Tertiary , ATP Phosphoribosyltransferase/antagonists & inhibitors , ATP Phosphoribosyltransferase/genetics , ATP Phosphoribosyltransferase/metabolism , Amino Acid Sequence , Binding Sites , Catalytic Domain , Escherichia coli Proteins/antagonists & inhibitors , Escherichia coli Proteins/genetics , Escherichia coli Proteins/metabolism , Histidine/metabolism , Models, Molecular , Molecular Sequence Data , Molecular Structure , Protein Structure, Quaternary , Sequence Alignment
18.
J Biol Chem ; 278(10): 8333-9, 2003 Mar 07.
Article in English | MEDLINE | ID: mdl-12511575

ABSTRACT

The N-1-(5'-phosphoribosyl)-ATP transferase catalyzes the first step of the histidine biosynthetic pathway and is regulated by a feedback mechanism by the product histidine. The crystal structures of the N-1-(5'-phosphoribosyl)-ATP transferase from Mycobacterium tuberculosis in complex with inhibitor histidine and AMP has been determined to 1.8 A resolution and without ligands to 2.7 A resolution. The active enzyme exists primarily as a dimer, and the histidine-inhibited form is a hexamer. The structure represents a new fold for a phosphoribosyltransferase, consisting of three continuous domains. The inhibitor AMP binds in the active site cavity formed between the two catalytic domains. A model for the mechanism of allosteric inhibition has been derived from conformational differences between the AMP:His-bound and apo structures.


Subject(s)
ATP Phosphoribosyltransferase/chemistry , Mycobacterium tuberculosis/enzymology , ATP Phosphoribosyltransferase/genetics , ATP Phosphoribosyltransferase/metabolism , Adenosine Monophosphate/metabolism , Catalytic Domain , Cloning, Molecular , Models, Molecular , Mycobacterium tuberculosis/genetics , Protein Structure, Quaternary
19.
Curr Opin Struct Biol ; 11(6): 733-9, 2001 Dec.
Article in English | MEDLINE | ID: mdl-11751055

ABSTRACT

Members of the homologous PRT family are catalytic and regulatory proteins involved in nucleotide synthesis and salvage. New crystal structures have revealed key elements of PRT protein function, as well as glimpses of how the fold has evolved to perform both catalytic and regulatory functions.


Subject(s)
ATP Phosphoribosyltransferase/chemistry , Amino Acid Motifs , Catalysis , Magnesium/metabolism , Protein Binding , Protein Folding , Protein Structure, Quaternary , Ribose-Phosphate Pyrophosphokinase/metabolism , Sequence Homology
20.
Acta Crystallogr D Biol Crystallogr ; 56(Pt 11): 1488-91, 2000 Nov.
Article in English | MEDLINE | ID: mdl-11185885

ABSTRACT

ATP-phosphoribosyltransferase (ATP-PRT) from Escherichia coli has been purified and crystals were obtained by the vapour-diffusion method using sodium tartrate as a precipitant. Dynamic light scattering was used to assess conditions for the monodispersity of the enzyme. The crystals are trigonal, space group R32, with unit-cell parameters a = b = 133.6, c= 114.1 A (at 100 K), and diffract to 2.7 A on a synchrotron X-ray source. The asymmetric unit is likely to contain one molecule, corresponding to a packing density of 2.9 A3 Da(-1). A model for the quaternary structure is proposed based on the crystallographic symmetry.


Subject(s)
ATP Phosphoribosyltransferase/isolation & purification , Escherichia coli/enzymology , ATP Phosphoribosyltransferase/chemistry , Crystallization , Crystallography, X-Ray , Light , Models, Molecular , Protein Conformation , Scattering, Radiation
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