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Wei L, Li J, Wang Z, Wu J, Wang S, Cai Z, Lu Y, Su C. Evaluating effects of tetrabromobisphenol A and microplastics on anaerobic granular sludge: Physicochemical properties, microbial metabolism, and underlying mechanisms. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 359:121077. [PMID: 38718604 DOI: 10.1016/j.jenvman.2024.121077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 04/07/2024] [Accepted: 04/30/2024] [Indexed: 05/22/2024]
Abstract
Tetrabromobisphenol A (TBBPA) and microplastics are emerging contaminants of widespread concern. However, little is known about the effects of combined exposure to TBBPA and microplastics on the physicochemical properties and microbial metabolism of anaerobic granular sludge. This study investigated the effects of TBBPA, polystyrene microplastics (PS MP) and polybutylene succinate microplastics (PBS MP) on the physicochemical properties, microbial communities and microbial metabolic levels of anaerobic granular sludge. The results showed that chemical oxygen demand (COD) removal of sludge was lowest in the presence of TBBPA alone and PS MP alone with 33.21% and 30.06%, respectively. The microorganisms promoted the secretion of humic substances under the influence of TBBPA, PS MP and PBS MP. The lowest proportion of genes controlling glycolytic metabolism in sludge was 1.52% when both TBBPA and PS MP were added. Microbial reactive oxygen species were increased in anaerobic granular sludge exposed to MPS. In addition, TBBPA treatment decreased electron transfer of the anaerobic granular sludge and disrupted the pathway of anaerobic microorganisms in acquiring adenosine triphosphate, and MPs attenuated the negative effects of TBBPA on the acetate methanogenesis process of the anaerobic granular sludge. This study provides a reference for evaluating the impact of multiple pollutants on anaerobic granular sludge.
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Affiliation(s)
- Lixin Wei
- Guangxi Key Laboratory of Environmental Processes and Remediation in Ecologically Fragile Regions, Guangxi Normal University, 15 Yucai Road, Guilin, 541004, PR China
| | - Junjian Li
- Guangxi Key Laboratory of Environmental Processes and Remediation in Ecologically Fragile Regions, Guangxi Normal University, 15 Yucai Road, Guilin, 541004, PR China
| | - Zi Wang
- Guangxi Key Laboratory of Environmental Processes and Remediation in Ecologically Fragile Regions, Guangxi Normal University, 15 Yucai Road, Guilin, 541004, PR China
| | - Jinyan Wu
- Guangxi Key Laboratory of Environmental Processes and Remediation in Ecologically Fragile Regions, Guangxi Normal University, 15 Yucai Road, Guilin, 541004, PR China
| | - Shuying Wang
- Guangxi Key Laboratory of Environmental Processes and Remediation in Ecologically Fragile Regions, Guangxi Normal University, 15 Yucai Road, Guilin, 541004, PR China
| | - Zhexiang Cai
- Guangxi Key Laboratory of Environmental Processes and Remediation in Ecologically Fragile Regions, Guangxi Normal University, 15 Yucai Road, Guilin, 541004, PR China
| | - Yuxiang Lu
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, 15 Yucai Road, Guilin, 541004, PR China
| | - Chengyuan Su
- Guangxi Key Laboratory of Environmental Processes and Remediation in Ecologically Fragile Regions, Guangxi Normal University, 15 Yucai Road, Guilin, 541004, PR China; Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, 15 Yucai Road, Guilin, 541004, PR China.
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Bachochin MJ, Venegas JC, Singh G, Zhang L, Barber RD. Characterization of a butyrate kinase from Desulfovibrio vulgaris str. Hildenborough. FEMS Microbiol Lett 2020; 367:5804727. [PMID: 32166312 DOI: 10.1093/femsle/fnaa047] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Accepted: 03/10/2020] [Indexed: 11/13/2022] Open
Abstract
Short and branched chain fatty acid kinases participate in both bacterial anabolic and catabolic processes, including fermentation, through the reversible, ATP-dependent synthesis of acyl phosphates. This study reports biochemical properties of a predicted butyrate kinase from Desulfovibrio vulgaris str. Hildenborough (DvBuk) expressed heterologously and purified from Escherichia coli. Gel filtration chromatography indicates purified DvBuk is active as a dimer. The optimum temperature and pH for DvBuk activity is 44°C and 7.5, respectively. The enzyme displays enhanced thermal stability in the presence of substrates as observed for similar enzymes. Measurement of kcat and KM for various substrates reveals DvBuk exhibits the highest catalytic efficiencies for butyrate, valerate and isobutyrate. In particular, these measurements reveal this enzyme's apparent high affinity for C4 fatty acids relative to other butyrate kinases. These results have implications on structure and function relationships within the ASKHA superfamily of phosphotransferases, particularly regarding the acyl binding pocket, as well as potential physiological roles for this enzyme in Desulfovibrio vulgaris str. Hildenborough.
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Affiliation(s)
- Maxwell J Bachochin
- Department of Biological Sciences, College of Natural and Health Sciences, University of Wisconsin-Parkside, Room 355 Greenquist Hall; 900 Wood Rd., Kenosha, WI 53141-2000, USA
| | - Jessica Castillo Venegas
- Department of Biological Sciences, College of Natural and Health Sciences, University of Wisconsin-Parkside, Room 355 Greenquist Hall; 900 Wood Rd., Kenosha, WI 53141-2000, USA
| | - Gundeep Singh
- Department of Biological Sciences, College of Natural and Health Sciences, University of Wisconsin-Parkside, Room 355 Greenquist Hall; 900 Wood Rd., Kenosha, WI 53141-2000, USA
| | - Liyang Zhang
- Department of Biological Sciences, College of Natural and Health Sciences, University of Wisconsin-Parkside, Room 355 Greenquist Hall; 900 Wood Rd., Kenosha, WI 53141-2000, USA
| | - Robert D Barber
- Department of Biological Sciences, College of Natural and Health Sciences, University of Wisconsin-Parkside, Room 355 Greenquist Hall; 900 Wood Rd., Kenosha, WI 53141-2000, USA
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3
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Yoshida Y, Sato M, Nonaka T, Hasegawa Y, Kezuka Y. Characterization of the phosphotransacetylase-acetate kinase pathway for ATP production in Porphyromonas gingivalis. J Oral Microbiol 2019; 11:1588086. [PMID: 31007866 PMCID: PMC6461089 DOI: 10.1080/20002297.2019.1588086] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 02/18/2019] [Accepted: 02/25/2019] [Indexed: 12/19/2022] Open
Abstract
Acetyl phosphate (AcP) is generally produced from acetyl coenzyme A by phosphotransacetylase (Pta), and subsequent reaction with ADP, catalyzed by acetate kinase (Ack), produces ATP. The mechanism of ATP production in Porphyromonas gingivalis is poorly understood. The aim of this study was to explore the molecular basis of the Pta-Ack pathway in this microorganism. Pta and Ack from P. gingivalis ATCC 33277 were enzymatically and structurally characterized. Structural and mutational analyses suggest that Pta is a dimer with two substrate-binding sites in each subunit. Ack is also dimeric, with a catalytic cleft in each subunit, and structural analysis indicates a dramatic domain motion that opens and closes the cleft during catalysis. ATP formation by Ack proceeds via a sequential mechanism. Reverse transcription-PCR analysis demonstrated that the pta (PGN_1179) and ack (PGN_1178) genes, tandemly located in the genome, are cotranscribed as an operon. Inactivation of pta or ack in P. gingivalis by homologous recombination was successful only when the inactivated gene was expressed in trans. Therefore, both pta and ack genes are essential for this microorganism. Insights into the Pta-Ack pathway reported herein would be helpful to understand the energy acquisition in P. gingivalis.
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Affiliation(s)
- Yasuo Yoshida
- Department of Microbiology, School of Dentistry, Aichi Gakuin University, Nagoya, Japan
| | - Mitsunari Sato
- Department of Microbiology, School of Dentistry, Aichi Gakuin University, Nagoya, Japan
| | - Takamasa Nonaka
- Division of Structural Biology, Department of Pharmaceutical Sciences, School of Pharmacy, Iwate Medical University, Yahaba, Japan
| | - Yoshiaki Hasegawa
- Department of Microbiology, School of Dentistry, Aichi Gakuin University, Nagoya, Japan
| | - Yuichiro Kezuka
- Division of Structural Biology, Department of Pharmaceutical Sciences, School of Pharmacy, Iwate Medical University, Yahaba, Japan
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4
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Ferry JG. Acetate Metabolism in Anaerobes from the Domain Archaea. Life (Basel) 2015; 5:1454-71. [PMID: 26068860 PMCID: PMC4500148 DOI: 10.3390/life5021454] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Accepted: 06/01/2015] [Indexed: 01/26/2023] Open
Abstract
Acetate and acetyl-CoA play fundamental roles in all of biology, including anaerobic prokaryotes from the domains Bacteria and Archaea, which compose an estimated quarter of all living protoplasm in Earth's biosphere. Anaerobes from the domain Archaea contribute to the global carbon cycle by metabolizing acetate as a growth substrate or product. They are components of anaerobic microbial food chains converting complex organic matter to methane, and many fix CO2 into cell material via synthesis of acetyl-CoA. They are found in a diversity of ecological habitats ranging from the digestive tracts of insects to deep-sea hydrothermal vents, and synthesize a plethora of novel enzymes with biotechnological potential. Ecological investigations suggest that still more acetate-metabolizing species with novel properties await discovery.
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Affiliation(s)
- James G Ferry
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA.
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Ingram-Smith C, Wharton J, Reinholz C, Doucet T, Hesler R, Smith K. The Role of Active Site Residues in ATP Binding and Catalysis in the Methanosarcina thermophila Acetate Kinase. Life (Basel) 2015; 5:861-71. [PMID: 25775277 PMCID: PMC4390882 DOI: 10.3390/life5010861] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Revised: 03/02/2015] [Accepted: 03/04/2015] [Indexed: 11/16/2022] Open
Abstract
Acetate kinase (ACK), which catalyzes the reversible phosphorylation of acetate by ATP, is a member of the acetate and sugar kinase/heat shock cognate/actin (ASKHA) superfamily. ASKHA family members share a common core fold that includes an ATPase domain with five structural motifs. The PHOSPHATE1 motif has previously been shown to be important for catalysis. We have investigated the role of two of these motifs in the Methanosarcina thermophila ACK (MtACK) and have shown that residues projecting into the ACK active site from the PHOSPHATE2 and ADENOSINE loops and a third highly conserved loop designated here as LOOP3 play key roles in nucleotide triphosphate (NTP) selection and utilization. Alteration of Asn211 of PHOSPHATE2, Gly239 of LOOP3, and Gly331 of ADENOSINE greatly reduced catalysis. In particular, Gly331, which is highly conserved throughout the ASKHA superfamily, has the greatest effect on substrate selection. Alteration at this site strongly skewed MtACK toward utilization of purines over pyrimidines, unlike the wild type enzyme that shows broad NTP utilization. Further investigation into differences between the ATPase domain in MtACK and other acetate kinases that show different substrate preferences will provide us with a better understanding of the diversity of phosphoryl donor selection in this enzyme family.
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Affiliation(s)
- Cheryl Ingram-Smith
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC 29634, USA.
| | - Jeffrey Wharton
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC 29634, USA.
| | - Christian Reinholz
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC 29634, USA.
| | - Tara Doucet
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC 29634, USA.
| | - Rachel Hesler
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC 29634, USA.
| | - Kerry Smith
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC 29634, USA.
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Yoshioka A, Murata K, Kawai S. Structural and mutational analysis of amino acid residues involved in ATP specificity of Escherichia coli acetate kinase. J Biosci Bioeng 2014; 118:502-7. [PMID: 24856051 DOI: 10.1016/j.jbiosc.2014.04.014] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2014] [Revised: 04/21/2014] [Accepted: 04/21/2014] [Indexed: 11/30/2022]
Abstract
Acetate kinase (AK) generally utilizes ATP as a phosphoryl donor, but AK from Entamoeba histolytica (PPi-ehiAK) uses pyrophosphate (PPi), not ATP, and is PPi-specific. The determinants of the phosphoryl donor specificity are unknown. Here, we inferred 5 candidate amino acid residues associated with this specificity, based on structural information. Each candidate residue in Escherichia coli ATP-specific AK (ATP-ecoAK), which is unable to use PPi, was substituted with the respective PPi-ehiAK amino acid residue. Each variant ATP-ecoAK had an increased Km for ATP, indicating that the 5 residues are the determinants for the specificity to ATP in ATP-ecoAK. Moreover, Asn-337 of ATP-ecoAK was shown to be particularly significant for the specificity to ATP. The 5 residues are highly conserved in 2625 PPi-ehiAK homologs, implying that almost all organisms have ATP-dependent, rather than PPi-dependent, AK.
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Affiliation(s)
- Aya Yoshioka
- Laboratory of Basic and Applied Molecular Biotechnology, Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Kousaku Murata
- Laboratory of Basic and Applied Molecular Biotechnology, Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Shigeyuki Kawai
- Laboratory of Basic and Applied Molecular Biotechnology, Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Uji, Kyoto 611-0011, Japan.
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7
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Thaker TM, Tanabe M, Fowler ML, Preininger AM, Ingram-Smith C, Smith KS, Iverson TM. Crystal structures of acetate kinases from the eukaryotic pathogens Entamoeba histolytica and Cryptococcus neoformans. J Struct Biol 2012; 181:185-9. [PMID: 23159802 DOI: 10.1016/j.jsb.2012.11.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2012] [Revised: 11/06/2012] [Accepted: 11/07/2012] [Indexed: 10/27/2022]
Abstract
Acetate kinases (ACKs) are members of the acetate and sugar kinase/hsp70/actin (ASKHA) superfamily and catalyze the reversible phosphorylation of acetate, with ADP/ATP the most common phosphoryl acceptor/donor. While prokaryotic ACKs have been the subject of extensive biochemical and structural characterization, there is a comparative paucity of information on eukaryotic ACKs, and prior to this report, no structure of an ACK of eukaryotic origin was available. We determined the structures of ACKs from the eukaryotic pathogens Entamoeba histolytica and Cryptococcus neoformans. Each active site is located at an interdomain interface, and the acetate and phosphate binding pockets display sequence and structural conservation with their prokaryotic counterparts. Interestingly, the E. histolytica ACK has previously been shown to be pyrophosphate (PP(i))-dependent, and is the first ACK demonstrated to have this property. Examination of its structure demonstrates how subtle amino acid substitutions within the active site have converted cosubstrate specificity from ATP to PP(i) while retaining a similar backbone conformation. Differences in the angle between domains surrounding the active site suggest that interdomain movement may accompany catalysis. Taken together, these structures are consistent with the eukaryotic ACKs following a similar reaction mechanism as is proposed for the prokaryotic homologs.
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Affiliation(s)
- Tarjani M Thaker
- Department of Biochemistry, Vanderbilt University Medical Center, Nashville, TN 37232, USA
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8
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Novel pyrophosphate-forming acetate kinase from the protist Entamoeba histolytica. EUKARYOTIC CELL 2012; 11:1249-56. [PMID: 22903977 DOI: 10.1128/ec.00169-12] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Acetate kinase (ACK) catalyzes the reversible synthesis of acetyl phosphate by transfer of the γ-phosphate of ATP to acetate. Here we report the first biochemical and kinetic characterization of a eukaryotic ACK, that from the protist Entamoeba histolytica. Our characterization revealed that this protist ACK is the only known member of the ASKHA structural superfamily, which includes acetate kinase, hexokinase, and other sugar kinases, to utilize inorganic pyrophosphate (PP(i))/inorganic phosphate (P(i)) as the sole phosphoryl donor/acceptor. Detection of ACK activity in E. histolytica cell extracts in the direction of acetate/PP(i) formation but not in the direction of acetyl phosphate/P(i) formation suggests that the physiological direction of the reaction is toward acetate/PP(i) production. Kinetic parameters determined for each direction of the reaction are consistent with this observation. The E. histolytica PP(i)-forming ACK follows a sequential mechanism, supporting a direct in-line phosphoryl transfer mechanism as previously reported for the well-characterized Methanosarcina thermophila ATP-dependent ACK. Characterizations of enzyme variants altered in the putative acetate/acetyl phosphate binding pocket suggested that acetyl phosphate binding is not mediated solely through a hydrophobic interaction but also through the phosphoryl group, as for the M. thermophila ACK. However, there are key differences in the roles of certain active site residues between the two enzymes. The absence of known ACK partner enzymes raises the possibility that ACK is part of a novel pathway in Entamoeba.
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Abstract
Most of the methane produced in nature derives from the methyl group of acetate, the major end product of anaerobes decomposing complex plant material. The acetate is derived from the metabolic intermediate acetyl-CoA via the combined activities of phosphotransacetylase and acetate kinase. In Methanosarcina species, the enzymes function in the reverse direction to activate acetate to acetyl-CoA prior to cleavage into a methyl and carbonyl group of which the latter is oxidized providing electrons for reduction of the former to methane. Thus, phosphotransacetylase and acetate kinase have a central role in the conversion of complex organic matter to methane by anaerobic microbial food chains. Both enzymes have been purified from Methanosarcina thermophila and characterized. Both enzymes from M. thermophila have also been produced in Escherichia coli permitting crystal structures and amino acid variants, the kinetic and biochemical studies of which have lead to proposals for catalytic mechanisms. The high identity of both enzymes to paralogs in the domain Bacteria suggests ancient origins and common mechanisms.
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Affiliation(s)
- James G Ferry
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, USA
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10
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Structural correlations of activity of Clostridium acetobutylicum ATCC 824 butyrate kinase isozymes. Enzyme Microb Technol 2010. [DOI: 10.1016/j.enzmictec.2009.10.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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López-Canut V, Martí S, Bertrán J, Moliner V, Tuñón I. Theoretical Modeling of the Reaction Mechanism of Phosphate Monoester Hydrolysis in Alkaline Phosphatase. J Phys Chem B 2009; 113:7816-24. [DOI: 10.1021/jp901444g] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Violeta López-Canut
- Departament de Química Física, Universitat de València, València, Spain, Departament de Química Física i Analítica, Universitat Jaume I, Castelló, Spain, and Departament de Química, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Sergio Martí
- Departament de Química Física, Universitat de València, València, Spain, Departament de Química Física i Analítica, Universitat Jaume I, Castelló, Spain, and Departament de Química, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Juan Bertrán
- Departament de Química Física, Universitat de València, València, Spain, Departament de Química Física i Analítica, Universitat Jaume I, Castelló, Spain, and Departament de Química, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Vicente Moliner
- Departament de Química Física, Universitat de València, València, Spain, Departament de Química Física i Analítica, Universitat Jaume I, Castelló, Spain, and Departament de Química, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Iñaki Tuñón
- Departament de Química Física, Universitat de València, València, Spain, Departament de Química Física i Analítica, Universitat Jaume I, Castelló, Spain, and Departament de Química, Universitat Autònoma de Barcelona, Barcelona, Spain
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Gorrell A, Ferry JG. Investigation of the Methanosarcina thermophila acetate kinase mechanism by fluorescence quenching. Biochemistry 2007; 46:14170-6. [PMID: 17999468 DOI: 10.1021/bi701292a] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Acetate kinase, a member of the acetate and sugar kinase/Hsc 70/actin (ASKHA) structural superfamily, catalyzes the reversible transfer of the gamma-phosphoryl group from ATP to acetate, yielding ADP and acetyl phosphate. A catalytic mechanism for the enzyme from Methanosarcina thermophila has been proposed on the basis of the crystal structure and kinetic analyses of amino acid replacement variants. The Gln43Trp variant was generated to further investigate the catalytic mechanism via changes in fluorescence. The dissociation constants for ADP.Mg2+ and ATP.Mg2+ ligands were determined for the Gln43Trp variant and double variants generated by replacing Arg241 and Arg91 with Ala and Lys. The dissociation constants and kinetic analyses indicated roles for the arginines in transition state stabilization for catalysis but not in nucleotide binding. The results also provide the first experimental evidence for domain motion and evidence that catalysis does not occur as two independent active sites of the homodimer but the active site activities are coordinated in a half-the-sites manner.
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Affiliation(s)
- Andrea Gorrell
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
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Ren NQ, Lin HL, Zhang K, Zheng GX, Duan ZJ, Lin M. Cloning, expression, and characterization of an acetate kinase from a high rate of biohydrogen bacterial strain Ethanoligenens sp. hit B49. Curr Microbiol 2007; 55:167-72. [PMID: 17619101 DOI: 10.1007/s00284-007-0172-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2007] [Accepted: 03/28/2007] [Indexed: 10/23/2022]
Abstract
The acetate kinase (ack) gene from Ethanoligenens sp. hit B49, isolated from a biohydrogen production bioreactor, is a key enzyme and responsible for dephosphorylation of acetyl phosphate with the concomitant production of acetate and ATP; it was cloned, sequenced, and functionally expressed in Escherichia coli BL21(DE3). It contained a 1200-bp open reading frame and encoded a 399-amino-acid protein kinase (molecular weight, 43.22 kDa; isoionic point, pH 5.93) sharing 58% similarity with Thermotoga maritima MSB8 ack. Ack was heterologously expressed in E.coli BL21 (DE3). Ack specific activities of the refolded ack inclusion body from Ethanoligenens sp. hit B49 is 42.12 U at 25 degrees C, and the renaturation percent is 14.36%.
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Affiliation(s)
- Nan-qi Ren
- School of Municipal and Environmental Engineering, Harbin Institute of Technology, Harbin, 150090 People's Republic of China
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14
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Ingram-Smith C, Martin SR, Smith KS. Acetate kinase: not just a bacterial enzyme. Trends Microbiol 2006; 14:249-53. [PMID: 16678422 DOI: 10.1016/j.tim.2006.04.001] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2005] [Revised: 03/01/2006] [Accepted: 04/10/2006] [Indexed: 11/23/2022]
Abstract
The bacterial enzymes acetate kinase (AK) and phosphotransacetylase (PTA) form a key pathway for synthesis of the central metabolic intermediate acetyl coenzyme A (acetyl-CoA) from acetate or for generation of ATP from excess acetyl-CoA. Putative AK genes have now been identified in some eukaryotic microbes. In Chlamydomonas reinhardtii and Phytophthora species, AK forms a pathway with PTA. AK has also been identified in non-yeast fungi but these fungi do not have PTA. Instead, AK forms a pathway with D-xylulose 5-phosphate phosphoketolase (XFP), a pathway that was also previously found only in bacteria. In Entamoeba histolytica, neither PTA nor XFP was found as a partner for AK. Thus, eukaryotic microbes seem to have incorporated the 'bacterial' enzyme AK into at least three different metabolic pathways.
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Affiliation(s)
- Cheryl Ingram-Smith
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC 29634-0318, USA
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Simanshu DK, Savithri HS, Murthy MRN. Crystal structures of ADP and AMPPNP-bound propionate kinase (TdcD) from Salmonella typhimurium: comparison with members of acetate and sugar kinase/heat shock cognate 70/actin superfamily. J Mol Biol 2005; 352:876-92. [PMID: 16139298 DOI: 10.1016/j.jmb.2005.07.069] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2005] [Revised: 07/27/2005] [Accepted: 07/28/2005] [Indexed: 10/25/2022]
Abstract
Recently, it has been shown that l-threonine can be catabolized non-oxidatively to propionate via 2-ketobutyrate. Propionate kinase (TdcD; EC 2.7.2.-) catalyses the last step of this metabolic process by enabling the conversion of propionyl phosphate and ADP to propionate and ATP. To provide insights into the substrate-binding pocket and catalytic mechanism of TdcD, the crystal structures of the enzyme from Salmonella typhimurium in complex with ADP and AMPPNP have been determined to resolutions of 2.2A and 2.3A, respectively, by molecular replacement using Methanosarcina thermophila acetate kinase (MAK; EC 2.7.2.1). Propionate kinase, like acetate kinase, contains a fold with the topology betabetabetaalphabetaalphabetaalpha, identical with that of glycerol kinase, hexokinase, heat shock cognaten 70 (Hsc70) and actin, the superfamily of phosphotransferases. The structure consists of two domains with the active site contained in a cleft at the domain interface. Examination of the active site pocket revealed a plausible structural rationale for the greater specificity of the enzyme towards propionate than acetate. This was further confirmed by kinetic studies with the purified enzyme, which showed about ten times lower K(m) for propionate (2.3 mM) than for acetate (26.9 mM). Comparison of TdcD complex structures with those of acetate and sugar kinase/Hsc70/actin obtained with different ligands has permitted the identification of catalytically essential residues involved in substrate binding and catalysis, and points to both structural and mechanistic similarities. In the well-characterized members of this superfamily, ATP phosphoryl transfer or hydrolysis is coupled to a large conformational change in which the two domains close around the active site cleft. The significant amino acid sequence similarity between TdcD and MAK has facilitated study of domain movement, which indicates that the conformation assumed by the two domains in the nucleotide-bound structure of TdcD may represent an intermediate point in the pathway of domain closure.
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Ingram-Smith C, Gorrell A, Lawrence SH, Iyer P, Smith K, Ferry JG. Characterization of the acetate binding pocket in the Methanosarcina thermophila acetate kinase. J Bacteriol 2005; 187:2386-94. [PMID: 15774882 PMCID: PMC1065240 DOI: 10.1128/jb.187.7.2386-2394.2005] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Acetate kinase catalyzes the reversible magnesium-dependent synthesis of acetyl phosphate by transfer of the ATP gamma-phosphoryl group to acetate. Inspection of the crystal structure of the Methanosarcina thermophila enzyme containing only ADP revealed a solvent-accessible hydrophobic pocket formed by residues Val(93), Leu(122), Phe(179), and Pro(232) in the active site cleft, which identified a potential acetate binding site. The hypothesis that this was a binding site was further supported by alignment of all acetate kinase sequences available from databases, which showed strict conservation of all four residues, and the recent crystal structure of the M. thermophila enzyme with acetate bound in this pocket. Replacement of each residue in the pocket produced variants with K(m) values for acetate that were 7- to 26-fold greater than that of the wild type, and perturbations of this binding pocket also altered the specificity for longer-chain carboxylic acids and acetyl phosphate. The kinetic analyses of variants combined with structural modeling indicated that the pocket has roles in binding the methyl group of acetate, influencing substrate specificity, and orienting the carboxyl group. The kinetic analyses also indicated that binding of acetyl phosphate is more dependent on interactions of the phosphate group with an unidentified residue than on interactions between the methyl group and the hydrophobic pocket. The analyses also indicated that Phe(179) is essential for catalysis, possibly for domain closure. Alignments of acetate kinase, propionate kinase, and butyrate kinase sequences obtained from databases suggested that these enzymes have similar catalytic mechanisms and carboxylic acid substrate binding sites.
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Affiliation(s)
- Cheryl Ingram-Smith
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802-4500, USA
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Gorrell A, Lawrence SH, Ferry JG. Structural and kinetic analyses of arginine residues in the active site of the acetate kinase from Methanosarcina thermophila. J Biol Chem 2005; 280:10731-42. [PMID: 15647264 DOI: 10.1074/jbc.m412118200] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Acetate kinase catalyzes transfer of the gamma-phosphate of ATP to acetate. The only crystal structure reported for acetate kinase is the homodimeric enzyme from Methanosarcina thermophila containing ADP and sulfate in the active site (Buss, K. A., Cooper, D. C., Ingram-Smith, C., Ferry, J. G., Sanders, D. A., and Hasson, M. S. (2001) J. Bacteriol. 193, 680-686). Here we report two new crystal structure of the M. thermophila enzyme in the presence of substrate and transition state analogs. The enzyme co-crystallized with the ATP analog adenosine 5'-[gamma-thio]triphosphate contained AMP adjacent to thiopyrophosphate in the active site cleft of monomer B. The enzyme co-crystallized with ADP, acetate, Al(3+), and F(-) contained a linear array of ADP-AlF(3)-acetate in the active site cleft of monomer B. Together, the structures clarify the substrate binding sites and support a direct in-line transfer mechanism in which AlF(3) mimics the meta-phosphate transition state. Monomers A of both structures contained ADP and sulfate, and the active site clefts were closed less than in monomers B, suggesting that domain movement contributes to catalysis. The finding that His(180) was in close proximity to AlF(3) is consistent with a role for stabilization of the meta-phosphate that is in agreement with a previous report indicating that this residue is essential for catalysis. Residue Arg(241) was also found adjacent to AlF(3), consistent with a role for stabilization of the transition state. Kinetic analyses of Arg(241) and Arg(91) replacement variants indicated that these residues are essential for catalysis and also indicated a role in binding acetate.
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Affiliation(s)
- Andrea Gorrell
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
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Gordon PM, Fong R, Deb SK, Li NS, Schwans JP, Ye JD, Piccirilli JA. New strategies for exploring RNA's 2'-OH expose the importance of solvent during group II intron catalysis. ACTA ACUST UNITED AC 2004; 11:237-46. [PMID: 15123285 DOI: 10.1016/j.chembiol.2004.02.011] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2002] [Revised: 10/28/2003] [Accepted: 11/24/2003] [Indexed: 10/21/2022]
Abstract
The 2'-hydroxyl group contributes inextricably to the functional behavior of many RNA molecules, fulfilling numerous essential chemical roles. To assess how hydroxyl groups impart functional behavior to RNA, we developed a series of experimental strategies using an array of nucleoside analogs. These strategies provide the means to investigate whether a hydroxyl group influences function directly (via hydrogen bonding or metal ion coordination), indirectly (via space-filling capacity, inductive effects, and sugar conformation), or through interactions with solvent. The nucleoside analogs span a broad range of chemical diversity, such that quantitative structure activity relationships (QSAR) now become possible in the exploration of RNA biology. We employed these strategies to investigate the spliced exons reopening (SER) reaction of the group II intron. Our results suggest that the cleavage site 2'-hydroxyl may mediate an interaction with a water molecule.
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Affiliation(s)
- Peter M Gordon
- Department of Biochemistry and Molecular Biology, The University of Chicago, 5841 South Maryland Avenue, MC1028, Chicago, IL 60637, USA
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19
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Volz TJ, Kim M, Schenk JO. Covalent and noncovalent chemical modifications of arginine residues decrease dopamine transporter activity. Synapse 2004; 52:272-82. [PMID: 15103693 DOI: 10.1002/syn.20021] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Rotating disk electrode voltammetry was used to measure dopamine (DA) transport in rat striatum and in human embryonic kidney cells expressing the rat dopamine transporter (DAT). The goals of this study were to determine 1) if arginine (Arg) selective agents could alter DA transport, and 2) if DA analogs and DAT inhibitors could attenuate the effects of these agents on the DAT. Phenylglyoxal (PG), Hill coefficient 2.5, and other Arg selective agents decreased DA transport velocities. DA, Hill coefficient 1.0, and its analogs 3-hydroxyphenethylamine and 4-hydroxyphenethylamine attenuated the effects of PG on the DAT while phenethylamine did not. The tropane-based DAT inhibitors cocaine, WIN 35065-2, and WIN 35428 also attenuated the effects of PG. Benztropine, GBR 12935, and GBR 12909 did not. Thus, Arg residues are important for DAT activity and the results suggest that DA and cocaine both interact with Arg residues. Structure-activity studies suggest that DA interacts with Arg through its catechol hydroxyl groups and cocaine through the ester linkage attached to carbon 2 of the tropane ring. The results that 1). DA and cocaine may interact with the same functionally important Arg residue at the DAT, and 2). some members of the tropane and 1,4-dialkylpiperazine classes of DAT inhibitors may interact differently with DAT-derived Arg residue(s) furthers the notion that DAT activity sparing antagonists of cocaine can be designed.
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Affiliation(s)
- Trent J Volz
- Department of Chemistry, Washington State University, Pullman, Washington 99164, USA
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Miles RD, Gorrell A, Ferry JG. Evidence for a transition state analog, MgADP-aluminum fluoride-acetate, in acetate kinase from Methanosarcina thermophila. J Biol Chem 2002; 277:22547-52. [PMID: 11960978 DOI: 10.1074/jbc.m105921200] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Aluminum fluoride has become an important tool for investigating the mechanism of phosphoryl transfer, an essential reaction that controls a host of vital cell functions. Planar AlF(3) or AlF(4)(-) molecules are proposed to mimic the phosphoryl group in the catalytic transition state. Acetate kinase catalyzes phosphoryl transfer of the ATP gamma-phosphate to acetate. Here we describe the inhibition of acetate kinase from Methanosarcina thermophila by preincubation with MgCl(2), ADP, AlCl(3), NaF, and acetate. Preincubation with butyrate in place of acetate did not significantly inhibit the enzyme. Several NTPs can substitute for ATP in the reaction, and the corresponding NDPs, in conjunction with MgCl(2), AlCl(3), NaF, and acetate, inhibit acetate kinase activity. Fluorescence quenching experiments indicated an increase in binding affinity of acetate kinase for MgADP in the presence of AlCl(3), NaF, and acetate. These and other characteristics of the inhibition indicate that the transition state analog, MgADP-aluminum fluoride-acetate, forms an abortive complex in the active site. The protection from inhibition by a non-hydrolyzable ATP analog or acetylphosphate, in conjunction with the strict dependence of inhibition on the presence of both ADP and acetate, supports a direct in-line mechanism for acetate kinase.
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Affiliation(s)
- Rebecca D Miles
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802-4500, USA
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Knorr R, Ehrmann MA, Vogel RF. Cloning, expression, and characterization of acetate kinase from Lactobacillus sanfranciscensis. Microbiol Res 2002; 156:267-77. [PMID: 11716215 DOI: 10.1078/0944-5013-00114] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
In the metabolism of Lactobacillus sanfranciscensis, the acetate kinase (AK) is a key enzyme and responsible for dephosphorylation of acetyl phosphate with the concomitant production of acetate and ATP. The L. sanfranciscensis ack gene was identified by PCR methods. It encodes a 397 amino acid protein sharing 56% similarity with Bacillus subtilis AK. Whereas cotranscription of ack and pta (phosphotransacetylase) is reported in previously characterised organisms, the L. sanfranciscensis ack gene is not located in direct neighbourhood to the encoding gene. AK was heterologously expressed in E. coli and characterised by its v(max) and Km values and by the dependence of enzyme activity on temperature and pH. Based on this data the in vivo role of the enzyme is discussed.
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Affiliation(s)
- R Knorr
- Institut für Technische Mikrobiologie, Technische Universität München, Freising-Weihenstephan, Germany
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22
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Abstract
Escherichia coli alkaline phosphatase (AP) is the prototypical two metal ion catalyst with two divalent zinc ions bound approximately 4 A apart in the active site. Studies spanning half a century have elucidated many structural and mechanistic features of this enzyme, rendering it an attractive model for investigating the potent catalytic power of bimetallic centers. Unfortunately, fundamental mechanistic features have been obscured by limitations with the standard assays. These assays generate concentrations of inorganic phosphate (P(i)) in excess of its inhibition constant (K(i) approximately 1 muM). This tight binding by P(i) has affected the majority of published kinetic constants. Furthermore, binding limits k(cat)/K(m) for reaction of p-nitrophenyl phosphate, the most commonly employed substrate. We describe a sensitive (32)P-based assay for hydrolysis of alkyl phosphates that avoids the complication of product inhibition. We have revisited basic mechanistic features of AP with these alkyl phosphate substrates. The results suggest that the chemical step for phosphorylation of the enzyme limits k(cat)/K(m). The pH-rate profile and additional results suggest that the serine nucleophile is active in its anionic form and has a pK(a) of < or = 5.5 in the free enzyme. An inactivating pK(a) of 8.0 is observed for binding of both substrates and inhibitors, and we suggest that this corresponds to ionization of a zinc-coordinated water molecule. Counter to previous suggestions, inorganic phosphate dianion appears to bind to the highly charged AP active site at least as strongly as the trianion. The dependence of k(cat)/K(m) on the pK(a) of the leaving group follows a Brønsted correlation with a slope of beta(lg) = -0.85 +/- 0.1, differing substantially from the previously reported value of -0.2 obtained from data with a less sensitive assay. This steep leaving group dependence is consistent with a largely dissociative transition state for AP-catalyzed hydrolysis of phosphate monoesters. The new (32)P-based assay employed herein will facilitate continued dissection of the AP reaction by providing a means to readily follow the chemical step for phosphorylation of the enzyme.
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Affiliation(s)
- Patrick J O'Brien
- Department of Biochemistry, Stanford University, Stanford, California 94305-5307, USA
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Miles RD, Iyer PP, Ferry JG. Site-directed mutational analysis of active site residues in the acetate kinase from Methanosarcina thermophila. J Biol Chem 2001; 276:45059-64. [PMID: 11562377 DOI: 10.1074/jbc.m108355200] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Acetate kinase catalyzes the magnesium-dependent transfer of the gamma-phosphate of ATP to acetate. The recently determined crystal structure of the Methanosarcina thermophila enzyme identifies it as a member of the sugar kinase/Hsc70/actin superfamily based on the fold and the presence of five putative nucleotide and metal binding motifs that characterize the superfamily. Residues from four of these motifs in M. thermophila acetate kinase were selected for site-directed replacement and analysis of the variants. Replacement of Asp(148) and Asn(7) resulted in variants with catalytic efficiencies less than 1% of that of the wild-type enzyme, indicating that these residues are essential for activity. Glu(384) was also found to be essential for catalysis. A 30-fold increase in the magnesium concentration required for half-maximal activity of the E384A variant relative to that of the wild type implicated Glu(384) in magnesium binding. The kinetic analysis of variants and structural data is consistent with nonessential roles for active site residues Ser(10), Ser(12), and Lys(14) in catalysis. The results are discussed with respect to the acetate kinase catalytic mechanism and the relationship to other sugar kinase/Hsc70/actin superfamily members.
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Affiliation(s)
- R D Miles
- Department of Biochemistry, The Pennsylvania State University, University Park, Pennsylvania 16802-4500, USA
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Buss KA, Cooper DR, Ingram-Smith C, Ferry JG, Sanders DA, Hasson MS. Urkinase: structure of acetate kinase, a member of the ASKHA superfamily of phosphotransferases. J Bacteriol 2001; 183:680-6. [PMID: 11133963 PMCID: PMC94925 DOI: 10.1128/jb.183.2.680-686.2001] [Citation(s) in RCA: 85] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Acetate kinase, an enzyme widely distributed in the Bacteria and Archaea domains, catalyzes the phosphorylation of acetate. We have determined the three-dimensional structure of Methanosarcina thermophila acetate kinase bound to ADP through crystallography. As we previously predicted, acetate kinase contains a core fold that is topologically identical to that of the ADP-binding domains of glycerol kinase, hexokinase, the 70-kDa heat shock cognate (Hsc70), and actin. Numerous charged active-site residues are conserved within acetate kinases, but few are conserved within the phosphotransferase superfamily. The identity of the points of insertion of polypeptide segments into the core fold of the superfamily members indicates that the insertions existed in the common ancestor of the phosphotransferases. Another remarkable shared feature is the unusual, epsilon conformation of the residue that directly precedes a conserved glycine residue (Gly-331 in acetate kinase) that binds the alpha-phosphate of ADP. Structural, biochemical, and geochemical considerations indicate that an acetate kinase may be the ancestral enzyme of the ASKHA (acetate and sugar kinases/Hsc70/actin) superfamily of phosphotransferases.
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Affiliation(s)
- K A Buss
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907, USA
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Ingram-Smith C, Barber RD, Ferry JG. The role of histidines in the acetate kinase from Methanosarcina thermophila. J Biol Chem 2000; 275:33765-70. [PMID: 10958794 DOI: 10.1074/jbc.m005303200] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The role of histidine in the catalytic mechanism of acetate kinase from Methanosarcina thermophila was investigated by diethylpyrocarbonate inactivation and site-directed mutagenesis. Inactivation was accompanied by an increase in absorbance at 240 nm with no change in absorbance at 280 nm, and treatment of the inactivated enzyme with hydroxylamine restored 95% activity, results that indicated diethylpyrocarbonate inactivates the enzyme by the specific modification of histidine. The substrates ATP, ADP, acetate, and acetyl phosphate protected against inactivation suggesting at least one active site where histidine is modified. Correlation of residual activity with the number of histidines modified, as determined by absorbance at 240 nm, indicated that a maximum of three histidines are modified per subunit, two of which are essential for full inactivation. Comparison of the M. thermophila acetate kinase sequence with 56 putative acetate kinase sequences revealed eight highly conserved histidines, three of which (His-123, His-180, and His-208) are perfectly conserved. Diethylpyrocarbonate inactivation of the eight histidine --> alanine variants indicated that His-180 and His-123 are in the active site and that the modification of both is necessary for full inactivation. Kinetic analyses of the eight variants showed that no other histidines are important for activity. Analysis of additional His-180 variants indicated that phosphorylation of His-180 is not essential for catalysis. Possible functions of His-180 are discussed.
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Affiliation(s)
- C Ingram-Smith
- Department of Biochemistry and Molecular Biology, Eberly College of Science, Pennsylvania State University, University Park, Pennsylvania 16802-4500, USA
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