1
|
Read BJ, Mitchell JBO, da Silva RG. Allosteric activation unveils protein-mass modulation of ATP phosphoribosyltransferase product release. Commun Chem 2024; 7:77. [PMID: 38582930 PMCID: PMC10998830 DOI: 10.1038/s42004-024-01165-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 03/28/2024] [Indexed: 04/08/2024] Open
Abstract
Heavy-isotope substitution into enzymes slows down bond vibrations and may alter transition-state barrier crossing probability if this is coupled to fast protein motions. ATP phosphoribosyltransferase from Acinetobacter baumannii is a multi-protein complex where the regulatory protein HisZ allosterically enhances catalysis by the catalytic protein HisGS. This is accompanied by a shift in rate-limiting step from chemistry to product release. Here we report that isotope-labelling of HisGS has no effect on the nonactivated reaction, which involves negative activation heat capacity, while HisZ-activated HisGS catalytic rate decreases in a strictly mass-dependent fashion across five different HisGS masses, at low temperatures. Surprisingly, the effect is not linked to the chemical step, but to fast motions governing product release in the activated enzyme. Disruption of a specific enzyme-product interaction abolishes the isotope effects. Results highlight how altered protein mass perturbs allosterically modulated thermal motions relevant to the catalytic cycle beyond the chemical step.
Collapse
Affiliation(s)
- Benjamin J Read
- School of Biology, Biomedical Sciences Research Complex, University of St Andrews, St Andrews, UK
| | - John B O Mitchell
- EaStCHEM School of Chemistry, Biomedical Sciences Research Complex, University of St Andrews, St Andrews, UK
| | - Rafael G da Silva
- School of Biology, Biomedical Sciences Research Complex, University of St Andrews, St Andrews, UK.
| |
Collapse
|
2
|
Read B, Cadzow AF, Alphey MS, Mitchell JBO, da Silva RG. Crystal Structure, Steady-State, and Pre-Steady-State Kinetics of Acinetobacter baumannii ATP Phosphoribosyltransferase. Biochemistry 2024; 63:230-240. [PMID: 38150593 PMCID: PMC10795190 DOI: 10.1021/acs.biochem.3c00551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 11/23/2023] [Accepted: 12/11/2023] [Indexed: 12/29/2023]
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-β-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.
Collapse
Affiliation(s)
- Benjamin
J. Read
- School
of Biology, Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST, United Kingdom
| | - Andrew F. Cadzow
- School
of Biology, Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST, United Kingdom
| | - Magnus S. Alphey
- School
of Biology, Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST, United Kingdom
| | - John B. O. Mitchell
- EaStCHEM
School of Chemistry, Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST, United Kingdom
| | - Rafael G. da Silva
- School
of Biology, Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST, United Kingdom
| |
Collapse
|
3
|
Fisher G, Pečaver E, Read BJ, Leese SK, Laing E, Dickson AL, Czekster CM, da Silva RG. Catalytic Cycle of the Bifunctional Enzyme Phosphoribosyl-ATP Pyrophosphohydrolase/Phosphoribosyl-AMP Cyclohydrolase. ACS Catal 2023; 13:7669-7679. [PMID: 37288093 PMCID: PMC10242683 DOI: 10.1021/acscatal.3c01111] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 05/05/2023] [Indexed: 06/09/2023]
Abstract
The bifunctional enzyme phosphoribosyl-ATP pyrophosphohydrolase/phosphoribosyl-AMP cyclohydrolase (HisIE) catalyzes the second and third steps of histidine biosynthesis: pyrophosphohydrolysis of N1-(5-phospho-β-D-ribosyl)-ATP (PRATP) to N1-(5-phospho-β-D-ribosyl)-AMP (PRAMP) and pyrophosphate in the C-terminal HisE-like domain, and cyclohydrolysis of PRAMP to N-(5'-phospho-D-ribosylformimino)-5-amino-1-(5″-phospho-D-ribosyl)-4-imidazolecarboxamide (ProFAR) in the N-terminal HisI-like domain. Here we use UV-VIS spectroscopy and LC-MS to show Acinetobacter baumannii putative HisIE produces ProFAR from PRATP. Employing an assay to detect pyrophosphate and another to detect ProFAR, we established the pyrophosphohydrolase reaction rate is higher than the overall reaction rate. We produced a truncated version of the enzyme-containing only the C-terminal (HisE) domain. This truncated HisIE was catalytically active, which allowed the synthesis of PRAMP, the substrate for the cyclohydrolysis reaction. PRAMP was kinetically competent for HisIE-catalyzed ProFAR production, demonstrating PRAMP can bind the HisI-like domain from bulk water, and suggesting that the cyclohydrolase reaction is rate-limiting for the overall bifunctional enzyme. The overall kcat increased with increasing pH, while the solvent deuterium kinetic isotope effect decreased at more basic pH but was still large at pH 7.5. The lack of solvent viscosity effects on kcat and kcat/KM ruled out diffusional steps limiting the rates of substrate binding and product release. Rapid kinetics with excess PRATP demonstrated a lag time followed by a burst in ProFAR formation. These observations are consistent with a rate-limiting unimolecular step involving a proton transfer following adenine ring opening. We synthesized N1-(5-phospho-β-D-ribosyl)-ADP (PRADP), which could not be processed by HisIE. PRADP inhibited HisIE-catalyzed ProFAR formation from PRATP but not from PRAMP, suggesting that it binds to the phosphohydrolase active site while still permitting unobstructed access of PRAMP to the cyclohydrolase active site. The kinetics data are incompatible with a build-up of PRAMP in bulk solvent, indicating HisIE catalysis involves preferential channeling of PRAMP, albeit not via a protein tunnel.
Collapse
|
4
|
Allosteric rescue of catalytically impaired ATP phosphoribosyltransferase variants links protein dynamics to active-site electrostatic preorganisation. Nat Commun 2022; 13:7607. [PMID: 36494361 PMCID: PMC9734150 DOI: 10.1038/s41467-022-34960-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Accepted: 11/11/2022] [Indexed: 12/13/2022] Open
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.
Collapse
|
5
|
Read BJ, Fisher G, Wissett OLR, Machado TFG, Nicholson J, Mitchell JBO, da Silva RG. Allosteric Inhibition of Acinetobacter baumannii ATP Phosphoribosyltransferase by Protein:Dipeptide and Protein:Protein Interactions. ACS Infect Dis 2022; 8:197-209. [PMID: 34928596 DOI: 10.1021/acsinfecdis.1c00539] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
ATP phosphoribosyltransferase (ATPPRT) catalyzes the first step of histidine biosynthesis in bacteria, namely, the condensation of ATP and 5-phospho-α-d-ribosyl-1-pyrophosphate (PRPP) to generate N1-(5-phospho-β-d-ribosyl)-ATP (PRATP) and pyrophosphate. Catalytic (HisGS) and regulatory (HisZ) subunits assemble in a hetero-octamer where HisZ activates HisGS and mediates allosteric inhibition by histidine. In Acinetobacter baumannnii, HisGS is necessary for the bacterium to persist in the lung during pneumonia. Inhibition of ATPPRT is thus a promising strategy for specific antibiotic development. Here, A. baumannii ATPPRT is shown to follow a rapid equilibrium random kinetic mechanism, unlike any other ATPPRT. Histidine noncompetitively inhibits ATPPRT. Binding kinetics indicates histidine binds to free ATPPRT and to ATPPRT:PRPP and ATPPRT:ATP binary complexes with similar affinity following a two-step binding mechanism, but with distinct kinetic partition of the initial enzyme:inhibitor complex. The dipeptide histidine-proline inhibits ATPPRT competitively and likely uncompetitively, respectively, against PRPP and ATP. Rapid kinetics analysis shows His-Pro binds to the ATPPRT:ATP complex via a two-step binding mechanism. A related HisZ that shares 43% sequence identity with A. baumannii HisZ is a tight-binding allosteric inhibitor of A. baumannii HisGS. These findings lay the foundation for inhibitor design against A. baumannii ATPPRT.
Collapse
Affiliation(s)
- Benjamin J. Read
- School of Biology, Biomedical Sciences Research Complex, University of St Andrews, St Andrews, Fife KY16 9ST, United Kingdom
| | - Gemma Fisher
- School of Biology, Biomedical Sciences Research Complex, University of St Andrews, St Andrews, Fife KY16 9ST, United Kingdom
| | - Oliver L. R. Wissett
- School of Biology, Biomedical Sciences Research Complex, University of St Andrews, St Andrews, Fife KY16 9ST, United Kingdom
| | - Teresa F. G. Machado
- School of Chemistry, Biomedical Sciences Research Complex, University of St Andrews, St Andrews, Fife KY16 9ST, United Kingdom
| | - John Nicholson
- School of Biology, Biomedical Sciences Research Complex, University of St Andrews, St Andrews, Fife KY16 9ST, United Kingdom
| | - John B. O. Mitchell
- School of Chemistry, Biomedical Sciences Research Complex, University of St Andrews, St Andrews, Fife KY16 9ST, United Kingdom
| | - Rafael G. da Silva
- School of Biology, Biomedical Sciences Research Complex, University of St Andrews, St Andrews, Fife KY16 9ST, United Kingdom
| |
Collapse
|
6
|
Zhu Z, Bai Q, Li S, Li S, Liu M, Du F, Sui N, Yu WW. Antibacterial Activity of Graphdiyne and Graphdiyne Oxide. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2020; 16:e2001440. [PMID: 32715643 DOI: 10.1002/smll.202001440] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 06/04/2020] [Indexed: 05/27/2023]
Abstract
From manufacture to disposal, the interaction of graphdiyne based nanomaterials with living organisms is inevitable and crucial. However, the cytotoxic properties of this novel carbon nanomaterial are rarely investigated, and the mechanisms behind their cytotoxicity are totally unknown. In this study, the antibacterial activity of graphdiyne (GDY) and graphdiyne oxide (GDYO) is reported. GDY is capable of inhibiting broad-spectrum bacterial growth while exerting moderate cytotoxicity on mammalian cells. In comparison, GDYO exhibits lower antibacterial activity than that of GDY. Then an alterable, synergetic antibacterial mechanism of GDY, involving wrapping bacterial membrane, membrane insertion and disruption, and reactive oxygen species generation is demonstrated, while the differential gene expression analysis indicates that GDY could only alter the bacterial metabolism slightly and the oxidative stress route may be a minor bactericidal factor. The investigation of the antibacterial behaviors of GDY based nanomaterials may provide useful guidelines for the future design and application of this novel molecular allotrope of carbon.
Collapse
Affiliation(s)
- Zhiling Zhu
- College of Materials Science and Technology, Qingdao University of Science and Technology, Qingdao, Shandong, 266042, China
| | - Qiang Bai
- College of Materials Science and Technology, Qingdao University of Science and Technology, Qingdao, Shandong, 266042, China
| | - Shuo Li
- College of Materials Science and Technology, Qingdao University of Science and Technology, Qingdao, Shandong, 266042, China
| | - Siheng Li
- Department of Chemistry, University of Houston, Houston, TX, 77204, USA
| | - Manhong Liu
- College of Materials Science and Technology, Qingdao University of Science and Technology, Qingdao, Shandong, 266042, China
| | - Fanglin Du
- College of Materials Science and Technology, Qingdao University of Science and Technology, Qingdao, Shandong, 266042, China
| | - Ning Sui
- College of Materials Science and Technology, Qingdao University of Science and Technology, Qingdao, Shandong, 266042, China
| | - William W Yu
- College of Materials Science and Technology, Qingdao University of Science and Technology, Qingdao, Shandong, 266042, China
- Department of Chemistry and Physics, Louisiana State University, Shreveport, LA, 71115, USA
| |
Collapse
|
7
|
Gao S, Radadiya A, Li W, Liu H, Zhu W, de Crécy-Lagard V, Richards NGJ, Naismith JH. Uncovering the chemistry of C-C bond formation in C-nucleoside biosynthesis: crystal structure of a C-glycoside synthase/PRPP complex. Chem Commun (Camb) 2020; 56:7617-7620. [PMID: 32515440 PMCID: PMC8183095 DOI: 10.1039/d0cc02834g] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Accepted: 05/14/2020] [Indexed: 12/19/2022]
Abstract
The enzyme ForT catalyzes C-C bond formation between 5'-phosphoribosyl-1'-pyrophosphate (PRPP) and 4-amino-1H-pyrazole-3,5-dicarboxylate to make a key intermediate in the biosynthesis of formycin A 5'-phosphate by Streptomyces kaniharaensis. We report the 2.5 Å resolution structure of the ForT/PRPP complex and locate active site residues critical for PRPP recognition and catalysis.
Collapse
Affiliation(s)
- Sisi Gao
- Research Complex at Harwell, Didcot, OX11 0FA, UK and BSRC, University of St Andrews, St Andrews, KY16 9ST, UK
| | - Ashish Radadiya
- School of Chemistry, Cardiff University, Cardiff, CF10 3AT, UK
| | - Wenbo Li
- Division of Structural Biology, University of Oxford, Oxford, OX3 7BN, UK.
| | - Huanting Liu
- BSRC, University of St Andrews, St Andrews, KY16 9ST, UK
| | - Wen Zhu
- Department of Chemistry and California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720, USA
| | | | - Nigel G J Richards
- School of Chemistry, Cardiff University, Cardiff, CF10 3AT, UK and Foundation for Applied Molecular Evolution, Alachua, FL 32615, USA
| | - James H Naismith
- Division of Structural Biology, University of Oxford, Oxford, OX3 7BN, UK. and The Rosalind Franklin Institute, Didcot, OX11 0FA, UK
| |
Collapse
|
8
|
Thomson CM, Alphey MS, Fisher G, da Silva RG. Mapping the Structural Path for Allosteric Inhibition of a Short-Form ATP Phosphoribosyltransferase by Histidine. Biochemistry 2019; 58:3078-3086. [PMID: 31251578 PMCID: PMC6685669 DOI: 10.1021/acs.biochem.9b00282] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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.
Collapse
Affiliation(s)
- Catherine M Thomson
- School of Biology, Biomedical Sciences Research Complex , University of St Andrews , St Andrews , Fife KY16 9ST , U.K
| | - Magnus S Alphey
- School of Biology, Biomedical Sciences Research Complex , University of St Andrews , St Andrews , Fife KY16 9ST , U.K
| | - Gemma Fisher
- School of Biology, Biomedical Sciences Research Complex , University of St Andrews , St Andrews , Fife KY16 9ST , U.K
| | - Rafael G da Silva
- School of Biology, Biomedical Sciences Research Complex , University of St Andrews , St Andrews , Fife KY16 9ST , U.K
| |
Collapse
|
9
|
Jiao W, Mittelstädt G, Moggré GJ, Parker EJ. Hinge Twists and Population Shifts Deliver Regulated Catalysis for ATP-PRT in Histidine Biosynthesis. Biophys J 2019; 116:1887-1897. [PMID: 31053263 DOI: 10.1016/j.bpj.2019.03.040] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 03/13/2019] [Accepted: 03/28/2019] [Indexed: 11/30/2022] Open
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.
Collapse
Affiliation(s)
- Wanting Jiao
- Ferrier Research Institute, Victoria University of Wellington, Wellington, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, Auckland, New Zealand; School of Physical and Chemical Sciences, University of Canterbury, Christschurch, New Zealand.
| | - Gerd Mittelstädt
- Ferrier Research Institute, Victoria University of Wellington, Wellington, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, Auckland, New Zealand
| | - Gert-Jan Moggré
- Maurice Wilkins Centre for Molecular Biodiscovery, Auckland, New Zealand; School of Physical and Chemical Sciences, University of Canterbury, Christschurch, New Zealand
| | - Emily J Parker
- Ferrier Research Institute, Victoria University of Wellington, Wellington, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, Auckland, New Zealand; School of Physical and Chemical Sciences, University of Canterbury, Christschurch, New Zealand.
| |
Collapse
|
10
|
Fisher G, Thomson CM, Stroek R, Czekster CM, Hirschi JS, da Silva RG. Allosteric Activation Shifts the Rate-Limiting Step in a Short-Form ATP Phosphoribosyltransferase. Biochemistry 2018; 57:4357-4367. [PMID: 29940105 PMCID: PMC6128619 DOI: 10.1021/acs.biochem.8b00559] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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-β-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.
Collapse
Affiliation(s)
- Gemma Fisher
- School of Biology, Biomedical Sciences Research Complex , University of St Andrews , St Andrews , Fife KY16 9ST , United Kingdom
| | - Catherine M Thomson
- School of Biology, Biomedical Sciences Research Complex , University of St Andrews , St Andrews , Fife KY16 9ST , United Kingdom
| | - Rozanne Stroek
- School of Biology, Biomedical Sciences Research Complex , University of St Andrews , St Andrews , Fife KY16 9ST , United Kingdom
| | - Clarissa M Czekster
- School of Biology, Biomedical Sciences Research Complex , University of St Andrews , St Andrews , Fife KY16 9ST , United Kingdom
| | - Jennifer S Hirschi
- Department of Chemistry , Binghamton University , Binghamton , New York 13902 , United States
| | - Rafael G da Silva
- School of Biology, Biomedical Sciences Research Complex , University of St Andrews , St Andrews , Fife KY16 9ST , United Kingdom
| |
Collapse
|