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Shigi N, Horitani M, Miyauchi K, Suzuki T, Kuroki M. An ancient type of MnmA protein is an iron-sulfur cluster-dependent sulfurtransferase for tRNA anticodons. RNA (NEW YORK, N.Y.) 2020; 26:240-250. [PMID: 31801798 PMCID: PMC7025502 DOI: 10.1261/rna.072066.119] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Accepted: 12/01/2019] [Indexed: 05/27/2023]
Abstract
Transfer RNA (tRNA) is an adaptor molecule indispensable for assigning amino acids to codons on mRNA during protein synthesis. 2-thiouridine (s2U) derivatives in the anticodons (position 34) of tRNAs for glutamate, glutamine, and lysine are post-transcriptional modifications essential for precise and efficient codon recognition in all organisms. s2U34 is introduced either by (i) bacterial MnmA/eukaryote mitochondrial Mtu1 or (ii) eukaryote cytosolic Ncs6/archaeal NcsA, and the latter enzymes possess iron-sulfur (Fe-S) cluster. Here, we report the identification of novel-type MnmA homologs containing three conserved Cys residues, which could support Fe-S cluster binding and catalysis, in a broad range of bacteria, including thermophiles, Cyanobacteria, Mycobacteria, Actinomyces, Clostridium, and Helicobacter Using EPR spectroscopy, we revealed that Thermus thermophilus MnmA (TtMnmA) contains an oxygen-sensitive [4Fe-4S]-type cluster. Efficient in vitro formation of s2U34 in tRNALys and tRNAGln by holo-TtMnmA occurred only under anaerobic conditions. Mutational analysis of TtMnmA suggested that the Fe-S cluster is coordinated by the three conserved Cys residues (Cys105, Cys108, and Cys200), and is essential for its activity. Evolutionary scenarios for the sulfurtransferases, including the Fe-S cluster containing Ncs6/NcsA s2U thiouridylases and several distantly related sulfurtransferases, are proposed.
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Affiliation(s)
- Naoki Shigi
- Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan
| | - Masaki Horitani
- Faculty of Agriculture, Department of Applied Biochemistry and Food Science, Saga University, 1 Honjo-machi, Saga 840-8502, Japan
| | - Kenjyo Miyauchi
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Tsutomu Suzuki
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Misao Kuroki
- Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan
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2
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Coleto I, Trenas AT, Erban A, Kopka J, Pineda M, Alamillo JM. Functional specialization of one copy of glutamine phosphoribosyl pyrophosphate amidotransferase in ureide production from symbiotically fixed nitrogen in Phaseolus vulgaris. PLANT, CELL & ENVIRONMENT 2016; 39:1767-1779. [PMID: 27004600 DOI: 10.1111/pce.12743] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2016] [Revised: 03/09/2016] [Accepted: 03/10/2016] [Indexed: 06/05/2023]
Abstract
Purines are essential molecules formed in a highly regulated pathway in all organisms. In tropical legumes, the nitrogen fixed in the nodules is used to generate ureides through the oxidation of de novo synthesized purines. Glutamine phosphoribosyl pyrophosphate amidotransferase (PRAT) catalyses the first committed step of de novo purine synthesis. In Phaseolus vulgaris there are three genes coding for PRAT. The three full-length sequences, which are intron-less genes, were cloned, and their expression levels were determined under conditions that affect the synthesis of purines. One of the three genes, PvPRAT3, is highly expressed in nodules and protein amount and enzymatic activity in these tissues correlate with nitrogen fixation activity. Inhibition of PvPRAT3 gene expression by RNAi-silencing and subsequent metabolomic analysis of the transformed roots shows that PvPRAT3 is essential for the synthesis of ureides in P. vulgaris nodules.
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Affiliation(s)
- Inmaculada Coleto
- Departamento de Botánica, Ecología y Fisiología Vegetal, Grupo de Fisiología Molecular y Biotecnología de Plantas. Campus de Excelencia Internacional Agroalimentario, CEIA3. Campus de Rabanales, Edif. Severo Ochoa, Universidad de Córdoba, 14071, Córdoba, Spain
| | - Almudena T Trenas
- Departamento de Botánica, Ecología y Fisiología Vegetal, Grupo de Fisiología Molecular y Biotecnología de Plantas. Campus de Excelencia Internacional Agroalimentario, CEIA3. Campus de Rabanales, Edif. Severo Ochoa, Universidad de Córdoba, 14071, Córdoba, Spain
| | - Alexander Erban
- Departamento de Botánica, Ecología y Fisiología Vegetal, Grupo de Fisiología Molecular y Biotecnología de Plantas. Campus de Excelencia Internacional Agroalimentario, CEIA3. Campus de Rabanales, Edif. Severo Ochoa, Universidad de Córdoba, 14071, Córdoba, Spain
| | - Joachim Kopka
- Departamento de Botánica, Ecología y Fisiología Vegetal, Grupo de Fisiología Molecular y Biotecnología de Plantas. Campus de Excelencia Internacional Agroalimentario, CEIA3. Campus de Rabanales, Edif. Severo Ochoa, Universidad de Córdoba, 14071, Córdoba, Spain
| | - Manuel Pineda
- Departamento de Botánica, Ecología y Fisiología Vegetal, Grupo de Fisiología Molecular y Biotecnología de Plantas. Campus de Excelencia Internacional Agroalimentario, CEIA3. Campus de Rabanales, Edif. Severo Ochoa, Universidad de Córdoba, 14071, Córdoba, Spain
| | - Josefa M Alamillo
- Departamento de Botánica, Ecología y Fisiología Vegetal, Grupo de Fisiología Molecular y Biotecnología de Plantas. Campus de Excelencia Internacional Agroalimentario, CEIA3. Campus de Rabanales, Edif. Severo Ochoa, Universidad de Córdoba, 14071, Córdoba, Spain
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3
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Sheftel A, Stehling O, Lill R. Iron-sulfur proteins in health and disease. Trends Endocrinol Metab 2010; 21:302-14. [PMID: 20060739 DOI: 10.1016/j.tem.2009.12.006] [Citation(s) in RCA: 136] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/24/2009] [Revised: 12/11/2009] [Accepted: 12/15/2009] [Indexed: 11/29/2022]
Abstract
Iron-sulfur (Fe/S) proteins are a class of ubiquitous components that assist in vital and diverse biochemical tasks in virtually every living cell. These tasks include respiration, iron homeostasis and gene expression. The past decade has led to the discovery of novel Fe/S proteins and insights into how their Fe/S cofactors are formed and incorporated into apoproteins. This review summarizes our current knowledge of mammalian Fe/S proteins, diseases related to deficiencies in these proteins and on disorders stemming from their defective biogenesis. Understanding both the physiological functions of Fe/S proteins and how Fe/S clusters are formed will undoubtedly enhance our ability to identify and treat known disorders of Fe/S cluster biogenesis and to recognize hitherto undescribed Fe/S cluster-related diseases.
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Affiliation(s)
- Alex Sheftel
- Institut für Zytobiologie, Philipps-Universität Marburg, Robert-Koch-Strasse 6, D-35033 Marburg, Germany
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4
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Affiliation(s)
- Robert L Switzer
- Department of Biochemistry, University of Illinois, Urbana, Illinois 61801, USA.
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5
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Zalkin H. The amidotransferases. ADVANCES IN ENZYMOLOGY AND RELATED AREAS OF MOLECULAR BIOLOGY 2006; 66:203-309. [PMID: 8430515 DOI: 10.1002/9780470123126.ch5] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- H Zalkin
- Department of Biochemistry, Purdue University, West Lafayette, Indiana
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6
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These are the Moments when we Live! From Thunberg Tubes and Manometry to Phone, Fax and Fedex. ACTA ACUST UNITED AC 1995. [DOI: 10.1016/b978-0-444-81942-0.50012-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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7
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Fath MJ, Zhang LH, Rush J, Kolter R. Purification and characterization of colicin V from Escherichia coli culture supernatants. Biochemistry 1994; 33:6911-7. [PMID: 8204625 DOI: 10.1021/bi00188a021] [Citation(s) in RCA: 55] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The peptide antibiotic, colicin V (ColV), has been purified and characterized from Escherichia coli culture supernatants by precipitation with trichloroacetic acid (TCA) and high-performance liquid chromatography (HPLC). Polyacrylamide gel electrophoresis (PAGE) and Western analysis identifies ColV as a polypeptide with an apparent molecular mass of 5.8 kDa. The protein identified remains biologically active after purification and SDS-PAGE. A mutant form of ColV, ColV-1, removes the carboxy-terminal 21 amino acids and replaces them with eight heterologous residues. The ColV-1 mutant is also secreted into the extracellular medium, demonstrating that the carboxy-terminal 21 amino acids are not required for secretion by the dedicated ColV export system, CvaAB/TolC. N-Terminal amino acid sequencing shows that the primary translation product of cvaC, the ColV structural gene, is processed to remove the N-terminal 15 amino acids. The cleavage site is preceded by the sequence Ser-Gly-Gly, making it a potential substrate for leader peptidase. The ColV leader sequence has many characteristics in common with the amino-terminal leader sequences of the lactococcins, lactacins, and pediocins from Gram-positive bacteria. Mass spectroscopy of purified ColV shows that it has a mass of 8741.0 amu, consistent with the mass of the unmodified 88 amino acid polypeptide. The purification scheme provides a rapid and simple way to obtain ColV for further biochemical analysis.
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Affiliation(s)
- M J Fath
- Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, Massachusetts 02115
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8
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Abstract
Most enzymes exist as oligomers or polymers, and a significant subset of these (perhaps 15% of all enzymes) can reversibly dissociate and reassociate in response to an effector ligand. Such a change in subunit assembly usually is accompanied by a change in enzyme activity, providing a mechanism for regulation. Two models are described for a physical mechanism, leading to a change in activity: (1) catalytic activity depends on subunit conformation, which is modulated by subunit dissociation; and (2) catalytic or regulatory sites are located at subunit interfaces and are disrupted by subunit dissociation. Examples of such enzymes show that both catalytic sites and regulatory sites occur at the junction of 2 subunits. In addition, for 9 enzymes, kinetic studies supported the existence of a separate regulatory site with significantly different affinity for the binding of either a substrate or a product of that enzyme. Over 40 dissociating enzymes are described from 3 major metabolic areas: carbohydrate metabolism, nucleotide metabolism, and amino acid metabolism. Important variables that influence enzyme dissociation include: enzyme concentration, ligand concentration, other cellular proteins, pH, and temperature. All these variables can be readily manipulated in vitro, but normally only the first two are physiological variables. Seven of these enzymes are most active as the dissociated monomer, the others as oligomers, emphasizing the importance of a regulated equilibrium between 2 or more conformational states. Experiments to test whether enzyme dissociation occurs in vivo showed this to be the case in 6 out of 7 studies, with 4 different enzymes.
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Affiliation(s)
- T W Traut
- Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill 27599-7260
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9
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Iwahana H, Yamaoka T, Mizutani M, Mizusawa N, Ii S, Yoshimoto K, Itakura M. Molecular cloning of rat amidophosphoribosyltransferase. J Biol Chem 1993. [DOI: 10.1016/s0021-9258(18)53167-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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10
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Zhou G, Broyles S, Dixon J, Zalkin H. Avian glutamine phosphoribosylpyrophosphate amidotransferase propeptide processing and activity are dependent upon essential cysteine residues. J Biol Chem 1992. [DOI: 10.1016/s0021-9258(18)42602-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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11
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Meyer J, Moulis JM, Gaillard J, Lutz M. Replacement Of Sulfur By Selenium In Iron—Sulfur Proteins. ADVANCES IN INORGANIC CHEMISTRY 1992. [DOI: 10.1016/s0898-8838(08)60062-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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12
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Zhou GC, Dixon JE, Zalkin H. Cloning and expression of avian glutamine phosphoribosylpyrophosphate amidotransferase. Conservation of a bacterial propeptide sequence supports a role for posttranslational processing. J Biol Chem 1990. [DOI: 10.1016/s0021-9258(17)45339-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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13
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Zheng L, Andrews PC, Hermodson MA, Dixon JE, Zalkin H. Cloning and structural characterization of porcine heart aconitase. J Biol Chem 1990. [DOI: 10.1016/s0021-9258(19)39874-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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14
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Spectroscopic characterization of the iron-sulfur cluster in Bacillus subtilis glutamine phosphoribosylpyrophosphate amidotransferase. J Biol Chem 1989. [DOI: 10.1016/s0021-9258(18)51476-9] [Citation(s) in RCA: 33] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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15
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Evidence That the Iron-Sulfur Cluster of Bacillus subtilis Glutamine Phosphoribosylpyrophosphate Amidotransferase Determines Stability of the Enzyme to Degradation in Vivo. J Biol Chem 1989. [DOI: 10.1016/s0021-9258(18)83312-9] [Citation(s) in RCA: 56] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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16
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Abstract
Some enzymes are inactivated by their natural substrates during catalytic turnover, limiting the ultimate extent of reaction. These enzymes can be separated into three broad classes, depending on the mechanism of the inactivation process. The first type is enzymes which use molecular oxygen as a substrate. The second type is inactivated by hydrogen peroxide, which is present either as a substrate or a product, and are stabilized by high catalase activity. The oxidation of both types of enzymes shares common features with oxidation of other enzymes and proteins. The third type of enzyme is inactivated by non-oxidative processes, mainly reversible loss of cofactors or attached groups. Sub classes are defined within each broad classification based on kinetics and stoichiometry. Reaction-inactivation is in part a regulatory mechanism in vivo, because specific proteolytic systems give rapid turnover of such labelled enzymes. The methods for enhancing the stability of these enzymes under reaction conditions depends on the enzyme type. The kinetics of these inactivation reactions can be used to optimize bioreactor design and operation.
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Affiliation(s)
- M R Gray
- Department of Chemical Engineering, University of Alberta, Edmonton, Alberta, Canada
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17
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Souciet JL, Hermodson MA, Zalkin H. Mutational analysis of the glutamine phosphoribosylpyrophosphate amidotransferase pro-peptide. J Biol Chem 1988. [DOI: 10.1016/s0021-9258(18)69075-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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18
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Saxild HH, Nygaard P. Gene-enzyme relationships of the purine biosynthetic pathway in Bacillus subtilis. MOLECULAR & GENERAL GENETICS : MGG 1988; 211:160-7. [PMID: 3125411 DOI: 10.1007/bf00338408] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The gene-enzyme relationship has been established for most of the steps of the purine de novo biosynthetic pathway in Bacillus subtilis. The synthesis of inosine monophosphate (IMP) involves ten steps, and the branching from IMP to AMP and to guanosine monophosphate (GMP) synthesis both require two steps. To avoid confusion in the nomenclature of the pur genes we have adopted the Escherichia coli system for B. subtilis. The two genes specifying the enzymes catalysing the conversion of IMP to succinyl-AMP (pur A), and the conversion of IMP to xanthosine monophosphate (guaB), occur as single units whilst the other purine genes are clustered at 55 degrees on the B. subtilis linkage map. Based on transformation and transduction studies, and on complementation studies using B. subtilis pur genes cloned in plasmids, the arrangement of some of the clustered genes has been determined relative to outside markers. The following gene order has been established: pbuG-purB-purF-purM-purH-purD-tre. Three other genes were also found to be located in the cluster, guaA, purL and purE/C. However, we were not able to find their exact location. When the purF, purM, purD and purB genes of B. subtilis are present in plasmids they are capable of directing the synthesis in E. coli of phosphoribosylpyrophosphate amidotransferase (purF), aminoimidazole ribonucleotide synthetase (purM), glycinamide ribonucleotide synthetase (purD) and adenylosuccinate lyase (purB), respectively.
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Affiliation(s)
- H H Saxild
- Enzyme Division, University Institute of Biological Chemistry, Copenhagen K, Denmark
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19
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Traut TW. Enzymes of nucleotide metabolism: the significance of subunit size and polymer size for biological function and regulatory properties. CRC CRITICAL REVIEWS IN BIOCHEMISTRY 1988; 23:121-69. [PMID: 3048887 DOI: 10.3109/10409238809088318] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The 72 enzymes in nucleotide metabolism, from all sources, have a distribution of subunit sizes similar to those from other surveys: an average subunit Mr of 47,900, and a median size of 33,300. The same enzyme, from whatever source, usually has the same subunit size (there are exceptions); enzymes having a similar activity (e.g., kinases, deaminases) usually have a similar subunit size. Most simple enzymes in all EC classes (except class 6, ligases/synthetases) have subunit sizes of less than 30,000. Since structural domains defined in proteins tend to be in the Mr range of 5,000 to 30,000, it may be that most simple enzymes are formed as single domains. Multifunctional proteins and ligases have subunits generally much larger than Mr 40,000. Analyses of several well-characterized ligases suggest that they also have two or more distinct catalytic sites, and that ligases therefore are also multifunctional proteins, containing two or more domains. Cooperative kinetics and evidence for allosteric regulation are much more frequently associated with larger enzymes: such complex functions are associated with only 19% of enzymes having a subunit Mr less than or equal to 29,000, and with 86% of all enzymes having a subunit Mr greater than 50,000. In general, larger enzymes have more functions. Only 20% of these enzymes appear to be monomers; the rest are homopolymers and rarely are they heteropolymers. Evidence for the reversible dissociation of homopolymers has been found for 15% of the enzymes. Such changes in quaternary structure are usually mediated by appropriate physiological effectors, and this may serve as a mechanism for their regulation between active and less active forms. There is considerable structural organization of the various pathways: 19 enzymes are found in various multifunctional proteins, and 13 enzymes are found in different types of multienzyme complexes.
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Affiliation(s)
- T W Traut
- Department of Biochemistry, University of North Carolina School of Medicine, Chapel Hill
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20
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Ebbole DJ, Zalkin H. Cloning and characterization of a 12-gene cluster from Bacillus subtilis encoding nine enzymes for de novo purine nucleotide synthesis. J Biol Chem 1987. [DOI: 10.1016/s0021-9258(18)47560-6] [Citation(s) in RCA: 95] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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21
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Mutagenesis of ligands to the [4 Fe-4S] center of Bacillus subtilis glutamine phosphoribosylpyrophosphate amidotransferase. J Biol Chem 1986. [DOI: 10.1016/s0021-9258(18)67401-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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22
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Switzer RL, Bond RW, Ruppen ME, Rosenzweig S. Involvement of the stringent response in regulation of protein degradation in Bacillus subtilis. CURRENT TOPICS IN CELLULAR REGULATION 1985; 27:373-86. [PMID: 3937667 DOI: 10.1016/b978-0-12-152827-0.50039-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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23
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Glutamine nucleotide sequence of Saccharomyces cerevisiae ADE4 encoding phosphoribosylpyrophosphate amidotransferase. J Biol Chem 1984. [DOI: 10.1016/s0021-9258(17)39755-7] [Citation(s) in RCA: 74] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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24
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Vollmer SJ, Switzer RL, Debrunner PG. Oxidation-reduction properties of the iron-sulfur cluster in Bacillus subtilis glutamine phosphoribosylpyrophosphate amidotransferase. J Biol Chem 1983. [DOI: 10.1016/s0021-9258(17)43858-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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25
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The glutamine-utilizing site of Bacillus subtilis glutamine phosphoribosylpyrophosphate amidotransferase. J Biol Chem 1983. [DOI: 10.1016/s0021-9258(17)44496-6] [Citation(s) in RCA: 31] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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26
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Makaroff CA, Zalkin H, Switzer RL, Vollmer SJ. Cloning of the Bacillus subtilis glutamine phosphoribosylpyrophosphate amidotransferase gene in Escherichia coli. Nucleotide sequence determination and properties of the plasmid-encoded enzyme. J Biol Chem 1983. [DOI: 10.1016/s0021-9258(17)44497-8] [Citation(s) in RCA: 73] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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27
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Ruppen ME, Switzer RL. Degradation of Bacillus subtilis glutamine phosphoribosylpyrophosphate amidotransferase in vivo. J Biol Chem 1983. [DOI: 10.1016/s0021-9258(18)32794-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
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28
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Bernlohr DA, Switzer RL. Regulation of Bacillus subtilis glutamine phosphoribosylpyrophosphate amidotransferase inactivation in vivo. J Bacteriol 1983; 153:937-49. [PMID: 6401710 PMCID: PMC221717 DOI: 10.1128/jb.153.2.937-949.1983] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Glutamine phosphoribosylpyrophosphate amidotransferase is stable in growing cells, but is inactivated in an oxygen-dependent process at various rates in starving or antibiotic-treated cells. On the basis of studies of the purified enzyme, we suggested (D.A. Bernlohr and R.L. Switzer, Biochemistry 20:5675-5681, 1981) that the inactivation in vivo was regulated by substrate stabilization and a competition between stabilizing (AMP) and destabilizing (GMP, GDP, and ADP) nucleotides. This proposal was tested by measuring the intracellular levels of these metabolites under cultural conditions in which the stability of the amidotransferase varied. The results established that the stability of amidotransferase in vivo cannot be explained by the simple interactions observed in vitro. Metabolite levels associated with stability of the enzyme in growing cells did not confer stability under other conditions, such as ammonia starvation or refeeding of glucose-starved cells. The data suggest that a previously unrecognized event, possibly a covalent modification of amidotransferase, is required to mark the enzyme for oxygen-dependent inactivation.
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29
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Zalkin H. Structure, function, and regulation of amidophosphoribosyltransferase from prokaryotes. ADVANCES IN ENZYME REGULATION 1983; 21:225-37. [PMID: 6443594 DOI: 10.1016/0065-2571(83)90016-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Recent studies on the structure, function and regulation of amidophosphoribosyltransferase from E. coli and B. subtilis are reviewed and these properties compared with those of the enzyme from eukaryotes. The availability of large amounts of stable enzyme from the two microbial sources has facilitated the recent studies. The enzyme subunits from E. coli and B. subtilis are of similar size, 56, 395 and approximately 50,000, respectively. Catalytic properties and patterns for allosteric inhibition are similar but not identical. There are two major differences between these enzymes. In contrast to the enzyme from E. coli, B. subtilis amidophosphoribosyltransferase contains an essential Fe-S center. In addition, the enzyme from B. subtilis but not E. coli is inactivated in stationary phase by an oxygen-dependent mechanism which appears to have regulatory significance. As a consequence of the Fe-S center B. subtilis amidophosphoribosyltransferase is oxygen-sensitive in vitro. Amidophosphoribosyltransferase from mammalian sources is similar to the B. subtilis enzyme in its oxygen-sensitivity which may result from an Fe-S center. The amino acid sequence of E. coli amidophosphoribosyltransferase was deduced from the DNA sequence of the purF structural gene. The primary translation product contains 504 amino acid residues. Met-1 is removed by processing leaving an NH2-terminal cysteine residue. The NH2-terminal cysteine was specifically alkylated by the glutamine affinity analog 6-diazo-5-oxonorleucine and is thus identified as the cysteine residue involved in formation of the glutaminyl-enzyme covalent intermediate. The mechanism for glutamine utilization appears identical to other glutamine amido-transferases. Sequence homology was not detected in the glutamine amide transfer domains of E. coli anthranilate synthase and amidophosphoribosyltransferase.
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30
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Tso JY, Hermodson MA, Zalkin H. Glutamine phosphoribosylpyrophosphate amidotransferase from cloned Escherichia coli purF. NH2-terminal amino acid sequence, identification of the glutamine site, and trace metal analysis. J Biol Chem 1982. [DOI: 10.1016/s0021-9258(18)34811-7] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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31
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Nucleotide sequence of Escherichia coli purF and deduced amino acid sequence of glutamine phosphoribosylpyrophosphate amidotransferase. J Biol Chem 1982. [DOI: 10.1016/s0021-9258(18)34810-5] [Citation(s) in RCA: 90] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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de la Torre A, Lara C, Yee BC, Malkin R, Buchanan BB. Physiochemical properties of ferralterin. A regulatory iron-sulfur protein functional in oxygenic photosynthesis. Arch Biochem Biophys 1982; 213:545-50. [PMID: 6280614 DOI: 10.1016/0003-9861(82)90582-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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Buchanan JM. Covalent reaction of substrates and antimetabolites with formylglycinamide ribonucleotide amidotransferase. Methods Enzymol 1982; 87:76-84. [PMID: 7176930 DOI: 10.1016/s0076-6879(82)87009-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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Wong JY, Bernlohr DA, Turnbough CL, Switzer RL. Purification and properties of glutamine phosphoribosylpyrophosphate amidotransferase from Bacillus subtilis. Biochemistry 1981; 20:5669-74. [PMID: 6794613 DOI: 10.1021/bi00523a005] [Citation(s) in RCA: 29] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
A procedure for the rapid and efficient purification of glutamine phosphoribosylpyrophosphate amidotransferase to better than 98% homogeneity from depressed Bacillus subtilis cells is described. The molecular weight of the subunit was estimated to be about 50 000. The purified enzyme exhibits microheterogeneity on electrophoresis on highly resolving polyacrylamide gels; it is suggested that this heterogeneity results from limited proteolytic modification of the native subunit. The native enzyme exists in equilibrium among tetrameric, dimeric, and monomeric forms. The influence of enzyme concentration and the presence of substrates and allosteric inhibitors on this equilibrium are described. There is no simple correlation between allosteric inhibition and stabilization of dimeric or tetrameric states. The amino acid composition of the amidotransferase is reported; presence of a 4Fe-4S center in the enzyme was described previously. Preparation of inactive apoprotein by treatment with 1,10-phenanthroline and general characteristics of the apoprotein are presented.
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Bernlohr DA, Switzer RL. Reaction of Bacillus subtilis glutamine phosphoribosylpyrophosphate amidotransferase with oxygen: chemistry and regulation by ligands. Biochemistry 1981; 20:5675-81. [PMID: 6794614 DOI: 10.1021/bi00523a006] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The inactivation of glutamine phosphoribosylpyrophosphate amidotransferase by reaction of its iron-sulfur center with O2 is believed to be a physiologically important mode of regulation of this enzyme in Bacillus subtilis cells in the stationary phase of growth. Chemical and physical changes accompanying oxidation of the purified enzyme by O2 were studied. The iron of the 4Fe-4S center was oxidized to enzyme-bound high-spin Fe3+; the S2- was oxidized to a mixture of S0 bound as thiocystine and unidentified products. The oxidant appeared to be O2, rather than peroxide, superoxide, hydroxyl radical, or singlet oxygen. Gross physical changes in the oxidized enzyme were shown by its aggregation, decreased solubility, and altered circular dichroic spectrum. Experimental variables affecting the rate of oxidative inactivation were described; the most important of these was modulation of rates of inactivation by the allosteric inhibitors AMP, ADP, GMP, GDP and by the substrate P-Rib-PP. AMP was a potent stabilizer, whose effect was antagonized by P-Rib-PP. The other nucleotides, either acting singly or acting as synergistic pairs, were destabilizers and able to antagonize stabilization by AMP. The results are discussed in terms of the regulation of the stability of amidotransferase and its degradation in vivo.
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Chemical Steps in the Selective Inactivation and Degradation of Glutamine Phosphoribosylpyrophosphate Amidotransferase in Bacillus subtilis. ACTA ACUST UNITED AC 1981. [DOI: 10.1007/978-3-642-68211-7_15] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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Musick WD. Structural features of the phosphoribosyltransferases and their relationship to the human deficiency disorders of purine and pyrimidine metabolism. CRC CRITICAL REVIEWS IN BIOCHEMISTRY 1981; 11:1-34. [PMID: 7030616 DOI: 10.3109/10409238109108698] [Citation(s) in RCA: 94] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Similarities in the physical and chemical properties of the phosphoribosyltransferase family of enzymes suggest that they may share common structural features as observed in other functionally related proteins. The unusually high incidence of structural gene mutations of these enzymes in man are associated with several metabolic diseases of purine and pyrimidine metabolism. It is proposed that these disorders are the consequence of structural mutations to an architectural domain common to all of the phosphoribosyltransferases.
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Holmes EW. Kinetic, physical, and regulatory properties of amidophosphoribosyltransferase. ADVANCES IN ENZYME REGULATION 1981; 19:215-31. [PMID: 6175188 DOI: 10.1016/0065-2571(81)90017-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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Averill B, Dwivedi A, Debrunner P, Vollmer S, Wong J, Switzer R. Evidence for a tetranuclear iron-sulfur center in glutamine phosphoribosylpyrophosphate amidotransferase from Bacillus subtilis. J Biol Chem 1980. [DOI: 10.1016/s0021-9258(18)43687-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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Ruch FE, Lin EC, Kowit JD, Tang CT, Goldberg AL. In vivo inactivation of glycerol dehydrogenase in Klebsiella aerogenes: properties of active and inactivated proteins. J Bacteriol 1980; 141:1077-85. [PMID: 6988402 PMCID: PMC293785 DOI: 10.1128/jb.141.3.1077-1085.1980] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Glycerol:oxidized nicotinamide adenine dinucleotide (NAD+) 2-oxidoreductase (EC 1.1.1.6), an inducible enzyme for anaerobic glycerol catabolism in Klebsiella aerogenes, was purified and found to have a molecular weight of 79,000 by gel electrophoresis. The protein seemed to be enzymatically active either as a dimer of a 40,000-dalton peptide at pH 8.6 or as a tetramer of 160,000 molecular weight at pH 7.0. The enzyme activity was present at high levels in cells growing anaerobically on glycerol, but disappeared with a half-life of about 45 min if molecular oxygen was introduced to the culture. In contrast, no such phenomenon occurred with dihydroxyacetone kinase activity, the second enzyme in the pathway. Immunochemical analysis showed that the inactivation of the oxidoreductase did not involve degradation of the protein. Furthermore, subunits of the active and inactive forms of the enzyme were indistinguishable in size on polyacrylamide gel electrophoresis in the presence of sodium dodecyl sulfate and had similar isoelectric points (pH 4.7). Inactivation did, however, alter the gel filtration properties of the enzyme protein and, more importantly, reduced its affinity for the dye Cibacron F3GA and the coenzyme NAD+.
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Maurizi MR, Switzer RL. Proteolysis in bacterial sporulation. CURRENT TOPICS IN CELLULAR REGULATION 1980; 16:163-224. [PMID: 6772379 DOI: 10.1016/b978-0-12-152816-4.50010-8] [Citation(s) in RCA: 31] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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Wong JY, Switzer RL. Affinity chromatography of Bacillus subtilis glutamine phosphoribosylpyrophosphate amidotransferase. Arch Biochem Biophys 1979; 196:134-7. [PMID: 116595 DOI: 10.1016/0003-9861(79)90559-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Meyer E, Switzer RL. Regulation of Bacillus subtilis glutamine phosphoribosylpyrophosphate amidotransferase activity by end products. J Biol Chem 1979. [DOI: 10.1016/s0021-9258(18)50609-8] [Citation(s) in RCA: 36] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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Messenger LJ, Zalkin H. Glutamine phosphoribosylpyrophosphate amidotransferase from Escherichia coli. Purification and properties. J Biol Chem 1979. [DOI: 10.1016/s0021-9258(18)50771-7] [Citation(s) in RCA: 108] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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