1
|
Jha JS, Yin J, Haldar T, Wang Y, Gates KS. Reconsidering the Chemical Nature of Strand Breaks Derived from Abasic Sites in Cellular DNA: Evidence for 3'-Glutathionylation. J Am Chem Soc 2022; 144:10471-10482. [PMID: 35612610 DOI: 10.1021/jacs.2c02703] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The hydrolytic loss of coding bases from cellular DNA is a common and unavoidable reaction. The resulting abasic sites can undergo β-elimination of the 3'-phosphoryl group to generate a strand break with an electrophilic α,β-unsaturated aldehyde residue on the 3'-terminus. The work reported here provides evidence that the thiol residue of the cellular tripeptide glutathione rapidly adds to the alkenal group on the 3'-terminus of an AP-derived strand break. The resulting glutathionylated adduct is the only major cleavage product observed when β-elimination occurs at an AP site in the presence of glutathione. Formation of the glutathionylated cleavage product is reversible, but in the presence of physiological concentrations of glutathione, the adduct persists for days. Biochemical experiments provided evidence that the 3'-phosphodiesterase activity of the enzyme apurinic/apyrimidinic endonuclease (APE1) can remove the glutathionylated sugar remnant from an AP-derived strand break to generate the 3'OH residue required for repair via base excision or single-strand break repair pathways. The results suggest that a previously unrecognized 3'glutathionylated sugar remnant─and not the canonical α,β-unsaturated aldehyde end group─may be the true strand cleavage product arising from β-elimination at an abasic site in cellular DNA. This work introduces the 3'glutathionylated cleavage product as the major blocking group that must be trimmed to enable repair of abasic site-derived strand breaks by the base excision repair or single-strand break repair pathways.
Collapse
|
2
|
Watanabe S, Watanabe Y, Nobuchi R, Ono A. Biochemical and Structural Characterization of l-2-Keto-3-deoxyarabinonate Dehydratase: A Unique Catalytic Mechanism in the Class I Aldolase Protein Superfamily. Biochemistry 2020; 59:2962-2973. [DOI: 10.1021/acs.biochem.0c00515] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Seiya Watanabe
- Department of Bioscience, Graduate School of Agriculture, Ehime University, 3-5-7 Tarumi, Matsuyama, Ehime 790-8566, Japan
- Faculty of Agriculture, Ehime University, 3-5-7 Tarumi, Matsuyama, Ehime 790-8566, Japan
- Center for Marine Environmental Studies (CMES), Ehime University, 2-5 Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan
| | - Yasunori Watanabe
- Department of Bioscience, Graduate School of Agriculture, Ehime University, 3-5-7 Tarumi, Matsuyama, Ehime 790-8566, Japan
- Faculty of Agriculture, Ehime University, 3-5-7 Tarumi, Matsuyama, Ehime 790-8566, Japan
| | - Rika Nobuchi
- Faculty of Agriculture, Ehime University, 3-5-7 Tarumi, Matsuyama, Ehime 790-8566, Japan
| | - Akari Ono
- Faculty of Agriculture, Ehime University, 3-5-7 Tarumi, Matsuyama, Ehime 790-8566, Japan
| |
Collapse
|
3
|
|
4
|
Brouns SJJ, Barends TRM, Worm P, Akerboom J, Turnbull AP, Salmon L, van der Oost J. Structural insight into substrate binding and catalysis of a novel 2-keto-3-deoxy-D-arabinonate dehydratase illustrates common mechanistic features of the FAH superfamily. J Mol Biol 2008; 379:357-71. [PMID: 18448118 DOI: 10.1016/j.jmb.2008.03.064] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2007] [Revised: 03/22/2008] [Accepted: 03/25/2008] [Indexed: 11/29/2022]
Abstract
The archaeon Sulfolobus solfataricus converts d-arabinose to 2-oxoglutarate by an enzyme set consisting of two dehydrogenases and two dehydratases. The third step of the pathway is catalyzed by a novel 2-keto-3-deoxy-D-arabinonate dehydratase (KdaD). In this study, the crystal structure of the enzyme has been solved to 2.1 A resolution. The enzyme forms an oval-shaped ring of four subunits, each consisting of an N-terminal domain with a four-stranded beta-sheet flanked by two alpha-helices, and a C-terminal catalytic domain with a fumarylacetoacetate hydrolase (FAH) fold. Crystal structures of complexes of the enzyme with magnesium or calcium ions and either a substrate analog 2-oxobutyrate, or the aldehyde enzyme product 2,5-dioxopentanoate revealed that the divalent metal ion in the active site is coordinated octahedrally by three conserved carboxylate residues, a water molecule, and both the carboxylate and the oxo groups of the substrate molecule. An enzymatic mechanism for base-catalyzed dehydration is proposed on the basis of the binding mode of the substrate to the metal ion, which suggests that the enzyme enhances the acidity of the protons alpha to the carbonyl group, facilitating their abstraction by glutamate 114. A comprehensive structural comparison of members of the FAH superfamily is presented and their evolution is discussed, providing a basis for functional investigations of this largely unexplored protein superfamily.
Collapse
Affiliation(s)
- Stan J J Brouns
- Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, Dreienplein 10, 6703 HB Wageningen, Netherlands.
| | | | | | | | | | | | | |
Collapse
|
5
|
Barbas C. Organocatalysis Lost: Modern Chemistry, Ancient Chemistry, and an Unseen Biosynthetic Apparatus. Angew Chem Int Ed Engl 2008; 47:42-7. [DOI: 10.1002/anie.200702210] [Citation(s) in RCA: 474] [Impact Index Per Article: 29.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
|
6
|
Barbas C. Die verlorene Organokatalyse: moderne Chemie, klassische Chemie und ein unbemerkter Biosynthesemechanismus. Angew Chem Int Ed Engl 2008. [DOI: 10.1002/ange.200702210] [Citation(s) in RCA: 223] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
|
7
|
Arigoni D, Eliel EL. Chirality Due to the Presence of Hydrogen Isotopes at Noncyclic Positions. TOPICS IN STEREOCHEMISTRY 2007. [DOI: 10.1002/9780470147139.ch4] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
|
8
|
Watanabe S, Shimada N, Tajima K, Kodaki T, Makino K. Identification and Characterization of l-Arabonate Dehydratase, l-2-Keto-3-deoxyarabonate Dehydratase, and l-Arabinolactonase Involved in an Alternative Pathway of l-Arabinose Metabolism. J Biol Chem 2006; 281:33521-36. [PMID: 16950779 DOI: 10.1074/jbc.m606727200] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Azospirillum brasiliense possesses an alternative pathway of L-arabinose metabolism, different from the known bacterial and fungal pathways. In the preceding articles, we identified and characterized L-arabinose-1-dehydrogenase and alpha-ketoglutaric semialdehyde dehydrogenase, which catalyzes the first and final reaction steps in this pathway, respectively (Watanabe, S., Kodaki, T., and Makino, K. (2006) J. Biol. Chem. 281, 2612-2623 and Watanabe, S., Kodaki, T., and Makino, K. (2006) J. Biol. Chem. 281, 28876-28888). We here report the remaining three enzymes, L-arabonate dehydratase, L-2-keto-3-deoxyarabonate (L-KDA) dehydratase, and L-arabinolactonase. N-terminal amino acid sequences of L-arabonate dehydratase and L-KDA dehydratase purified from A. brasiliense cells corresponded to those of AraC and AraD genes, which form a single transcriptional unit together with the L-arabinose-1-dehydrogenase gene. Furthermore, the L-arabinolactonase gene (AraB) was also identified as a component of the gene cluster. Genetic characterization of the alternative L-arabinose pathway suggested a significant evolutional relationship with the known sugar metabolic pathways, including the Entner-Doudoroff (ED) pathway and the several modified versions. L-arabonate dehydratase belongs to the ILVD/EDD family and spectrophotometric and electron paramagnetic resonance analysis revealed it to contain a [4Fe-4S](2+) cluster. Site-directed mutagenesis identified three cysteine ligands essential for cluster coordination. L-KDA dehydratase was sequentially similar to DHDPS/NAL family proteins. D-2-Keto-3-deoxygluconate aldolase, a member of the DHDPS/NAL family, catalyzes the equivalent reaction to L-KDA aldolase involved in another alternative L-arabinose pathway, probably associating a unique evolutional event between the two alternative L-arabinose pathways by mutation(s) of a common ancestral enzyme. Site-directed mutagenesis revealed a unique catalytic amino acid residue in L-KDA dehydratase, which may be a candidate for such a natural mutation.
Collapse
Affiliation(s)
- Seiya Watanabe
- Faculty of Engineering, Kyoto University, Kyotodaigaku-katsura, Saikyo-ku, Kyoto 615-8530, Japan
| | | | | | | | | |
Collapse
|
9
|
Brouns SJJ, Walther J, Snijders APL, van de Werken HJG, Willemen HLDM, Worm P, de Vos MGJ, Andersson A, Lundgren M, Mazon HFM, van den Heuvel RHH, Nilsson P, Salmon L, de Vos WM, Wright PC, Bernander R, van der Oost J. Identification of the Missing Links in Prokaryotic Pentose Oxidation Pathways. J Biol Chem 2006; 281:27378-88. [PMID: 16849334 DOI: 10.1074/jbc.m605549200] [Citation(s) in RCA: 94] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The pentose metabolism of Archaea is largely unknown. Here, we have employed an integrated genomics approach including DNA microarray and proteomics analyses to elucidate the catabolic pathway for D-arabinose in Sulfolobus solfataricus. During growth on this sugar, a small set of genes appeared to be differentially expressed compared with growth on D-glucose. These genes were heterologously overexpressed in Escherichia coli, and the recombinant proteins were purified and biochemically studied. This showed that D-arabinose is oxidized to 2-oxoglutarate by the consecutive action of a number of previously uncharacterized enzymes, including a D-arabinose dehydrogenase, a D-arabinonate dehydratase, a novel 2-keto-3-deoxy-D-arabinonate dehydratase, and a 2,5-dioxopentanoate dehydrogenase. Promoter analysis of these genes revealed a palindromic sequence upstream of the TATA box, which is likely to be involved in their concerted transcriptional control. Integration of the obtained biochemical data with genomic context analysis strongly suggests the occurrence of pentose oxidation pathways in both Archaea and Bacteria, and predicts the involvement of additional enzyme components. Moreover, it revealed striking genetic similarities between the catabolic pathways for pentoses, hexaric acids, and hydroxyproline degradation, which support the theory of metabolic pathway genesis by enzyme recruitment.
Collapse
Affiliation(s)
- Stan J J Brouns
- Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, Hesselink van Suchtelenweg 4, 6703 CT Wageningen, the Netherlands.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
10
|
Bouř P, Tam CN, Shaharuzzaman M, Chickos JS, Keiderling TA. Vibrational Optical Activity Study of trans-Succinic-d2 Anhydride. ACTA ACUST UNITED AC 1996. [DOI: 10.1021/jp961217b] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Petr Bouř
- Department of Chemistry (M/C 111), University of Illinois at Chicago, 845 W. Taylor Street, Chicago, Illinois 60607-7061, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, 16610 Prague 6, Czech Republic, and Department of Chemistry, University of Missouri St. Louis, 8001 Natural Bridge Road, St. Louis, Missouri 63121
| | - Cheok N. Tam
- Department of Chemistry (M/C 111), University of Illinois at Chicago, 845 W. Taylor Street, Chicago, Illinois 60607-7061, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, 16610 Prague 6, Czech Republic, and Department of Chemistry, University of Missouri St. Louis, 8001 Natural Bridge Road, St. Louis, Missouri 63121
| | - Mohammad Shaharuzzaman
- Department of Chemistry (M/C 111), University of Illinois at Chicago, 845 W. Taylor Street, Chicago, Illinois 60607-7061, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, 16610 Prague 6, Czech Republic, and Department of Chemistry, University of Missouri St. Louis, 8001 Natural Bridge Road, St. Louis, Missouri 63121
| | - James. S. Chickos
- Department of Chemistry (M/C 111), University of Illinois at Chicago, 845 W. Taylor Street, Chicago, Illinois 60607-7061, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, 16610 Prague 6, Czech Republic, and Department of Chemistry, University of Missouri St. Louis, 8001 Natural Bridge Road, St. Louis, Missouri 63121
| | - Timothy A. Keiderling
- Department of Chemistry (M/C 111), University of Illinois at Chicago, 845 W. Taylor Street, Chicago, Illinois 60607-7061, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, 16610 Prague 6, Czech Republic, and Department of Chemistry, University of Missouri St. Louis, 8001 Natural Bridge Road, St. Louis, Missouri 63121
| |
Collapse
|
11
|
Shaharuzzaman M, Chickos J, Tam CN, Keiderling TA. A convenient synthesis of chiral succinic acid-d2 by catalytic asymmetric reduction using a ruthenium BINAP catalyst. ACTA ACUST UNITED AC 1995. [DOI: 10.1016/0957-4166(95)00389-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
|
12
|
|
13
|
Ducrocq C, Fraisse D, Tabet JC, Azerad R. An enzymatic method for the determination of enantiomeric composition and absolute configuration of deuterated or tritiated succinic acid. Anal Biochem 1984; 141:418-22. [PMID: 6149705 DOI: 10.1016/0003-2697(84)90064-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The distribution of hydrogen isotope between pro-R and pro-S positions of succinic acid has been determined by comparison of its isotopic content before and after incubation with isocitrate lyase. This enzyme, in the presence of glyoxylate, exchanges exclusively the pro-S protons of succinate with water (M. Sprecher, R. Berger, and D. B. Sprinson (1964) J. Biol. Chem. 239, 4268-4271). With [1-14C,2(R,S)-3H]succinate as substrate, the exchange was easily followed by the decrease of 3H/14C ratio (dried aliquots), which accounted for the high isotopic effect of this reaction. The final ratio was within +/- 5% of the theoretical one. The evolution of the exchange of deuterated succinate added with [1-14C,2(R,S)-3H]succinate acid was again followed by 3H/14C ratio. The deuterium content of [2,3-2H2]succinic acid, [2-2H2]succinic acid (derived from L-[4-2H2]glutamic acid by oxidation) and of the corresponding succinates isolated after incubation with isocitrate lyase was determined by gas chromatography-mass spectroscopy of their dimethylester under NH4+ chemical ionization. This method provides the basis for a quantitative measurement of the distribution of hydrogen isotopes in unsymmetrically 2-labeled succinate or 4-labeled glutamate.
Collapse
|
14
|
Chapter 8 Enzyme reactions involving imine formation. ACTA ACUST UNITED AC 1984. [DOI: 10.1016/s0167-7306(08)60379-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
|
15
|
Helmreich EJ, Klein HW. The role of pyridoxal phosphate in the catalysis of glycogen phosphorylases. Angew Chem Int Ed Engl 1980; 19:441-5. [PMID: 6773443 DOI: 10.1002/anie.198004411] [Citation(s) in RCA: 53] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
|
16
|
Helmreich EJM, Klein HW. Die Rolle von Pyridoxalphosphat bei der Katalyse der Glykogen-Phosphorylasen. Angew Chem Int Ed Engl 1980. [DOI: 10.1002/ange.19800920605] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
|
17
|
|
18
|
|
19
|
Kaeppeli F, Rétey J. Studies on the mechanism and stereospecificity of the urocanase reaction. EUROPEAN JOURNAL OF BIOCHEMISTRY 1971; 23:198-202. [PMID: 5127386 DOI: 10.1111/j.1432-1033.1971.tb01609.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
|
20
|
Walsh CT, Schonbrunn A, Abeles RH. Studies on the Mechanism of Action of d-Amino Acid Oxidase. J Biol Chem 1971. [DOI: 10.1016/s0021-9258(19)45925-5] [Citation(s) in RCA: 120] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
|
21
|
Abstract
A literature search reveals 60 cases in which there is strong evidence for covalent enzyme-substrate intermediates.
Collapse
|
22
|
Rétey J, Seibl J, Arigoni D, Cornforth JW, Ryback G, Zeylemaker WP, Veeger C. Stereochemical studies of the exchange and abstraction of succinate hydrogen on succinate dehydrogenase. EUROPEAN JOURNAL OF BIOCHEMISTRY 1970; 14:232-42. [PMID: 5506168 DOI: 10.1111/j.1432-1033.1970.tb00282.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
|
23
|
|
24
|
|
25
|
|
26
|
Krongelb M, Smith TA, Abeles RH. The formation of an enzyme-bound beta-carbanion in the enzymic conversion of L-homoserine to alpha-ketobutyrate. BIOCHIMICA ET BIOPHYSICA ACTA 1968; 167:473-5. [PMID: 5729963 DOI: 10.1016/0005-2744(68)90231-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
|
27
|
Huüfner M, Hollocher TC. Studies on the Mechanism of Hydrogen Exchange between Succinate and Water Catalyzed by the Soluble Succinic Dehydrogenase of Singer from Bovine Heart. J Biol Chem 1968. [DOI: 10.1016/s0021-9258(18)93333-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
|