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Bauwe H. Photorespiration - Rubisco's repair crew. JOURNAL OF PLANT PHYSIOLOGY 2023; 280:153899. [PMID: 36566670 DOI: 10.1016/j.jplph.2022.153899] [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: 11/15/2022] [Revised: 12/11/2022] [Accepted: 12/11/2022] [Indexed: 06/17/2023]
Abstract
The photorespiratory repair pathway (photorespiration in short) was set up from ancient metabolic modules about three billion years ago in cyanobacteria, the later ancestors of chloroplasts. These prokaryotes developed the capacity for oxygenic photosynthesis, i.e. the use of water as a source of electrons and protons (with O2 as a by-product) for the sunlight-driven synthesis of ATP and NADPH for CO2 fixation in the Calvin cycle. However, the CO2-binding enzyme, ribulose 1,5-bisphosphate carboxylase (known under the acronym Rubisco), is not absolutely selective for CO2 and can also use O2 in a side reaction. It then produces 2-phosphoglycolate (2PG), the accumulation of which would inhibit and potentially stop the Calvin cycle and subsequently photosynthetic electron transport. Photorespiration removes the 2-PG and in this way prevents oxygenic photosynthesis from poisoning itself. In plants, the core of photorespiration consists of ten enzymes distributed over three different types of organelles, requiring interorganellar transport and interaction with several auxiliary enzymes. It goes together with the release and to some extent loss of freshly fixed CO2. This disadvantageous feature can be suppressed by CO2-concentrating mechanisms, such as those that evolved in C4 plants thirty million years ago, which enhance CO2 fixation and reduce 2PG synthesis. Photorespiration itself provided a pioneer variant of such mechanisms in the predecessors of C4 plants, C3-C4 intermediate plants. This article is a review and update particularly on the enzyme components of plant photorespiration and their catalytic mechanisms, on the interaction of photorespiration with other metabolism and on its impact on the evolution of photosynthesis. This focus was chosen because a better knowledge of the enzymes involved and how they are embedded in overall plant metabolism can facilitate the targeted use of the now highly advanced methods of metabolic network modelling and flux analysis. Understanding photorespiration more than before as a process that enables, rather than reduces, plant photosynthesis, will help develop rational strategies for crop improvement.
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Affiliation(s)
- Hermann Bauwe
- University of Rostock, Plant Physiology, Albert-Einstein-Straße 3, D-18051, Rostock, Germany.
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Lanz ND, Pandelia ME, Kakar ES, Lee KH, Krebs C, Booker SJ. Evidence for a catalytically and kinetically competent enzyme-substrate cross-linked intermediate in catalysis by lipoyl synthase. Biochemistry 2014; 53:4557-72. [PMID: 24901788 PMCID: PMC4216189 DOI: 10.1021/bi500432r] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Lipoyl synthase (LS) catalyzes the final step in lipoyl cofactor biosynthesis: the insertion of two sulfur atoms at C6 and C8 of an (N(6)-octanoyl)-lysyl residue on a lipoyl carrier protein (LCP). LS is a member of the radical SAM superfamily, enzymes that use a [4Fe-4S] cluster to effect the reductive cleavage of S-adenosyl-l-methionine (SAM) to l-methionine and a 5'-deoxyadenosyl 5'-radical (5'-dA(•)). In the LS reaction, two equivalents of 5'-dA(•) are generated sequentially to abstract hydrogen atoms from C6 and C8 of the appended octanoyl group, initiating sulfur insertion at these positions. The second [4Fe-4S] cluster on LS, termed the auxiliary cluster, is proposed to be the source of the inserted sulfur atoms. Herein, we provide evidence for the formation of a covalent cross-link between LS and an LCP or synthetic peptide substrate in reactions in which insertion of the second sulfur atom is slowed significantly by deuterium substitution at C8 or by inclusion of limiting concentrations of SAM. The observation that the proteins elute simultaneously by anion-exchange chromatography but are separated by aerobic SDS-PAGE is consistent with their linkage through the auxiliary cluster that is sacrificed during turnover. Generation of the cross-linked species with a small, unlabeled (N(6)-octanoyl)-lysyl-containing peptide substrate allowed demonstration of both its chemical and kinetic competence, providing strong evidence that it is an intermediate in the LS reaction. Mössbauer spectroscopy of the cross-linked intermediate reveals that one of the [4Fe-4S] clusters, presumably the auxiliary cluster, is partially disassembled to a 3Fe-cluster with spectroscopic properties similar to those of reduced [3Fe-4S](0) clusters.
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Affiliation(s)
- Nicholas D Lanz
- Department of Biochemistry and Molecular Biology and ‡Department of Chemistry, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
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Self WT, Tsai L, Stadtman TC. Synthesis and characterization of selenotrisulfide-derivatives of lipoic acid and lipoamide. Proc Natl Acad Sci U S A 2000; 97:12481-6. [PMID: 11050172 PMCID: PMC18789 DOI: 10.1073/pnas.220426897] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Thiol-containing compounds, such as glutathione and cysteine, react with selenite under specific conditions to form selenotrisulfides. Previous studies have focused on isolation and characterization of intermolecular selenotrisulfides. This study describes the preparation and characterization of intramolecular selenotrisulfide derivatives of lipoic acid and lipoamide. These derivatives, after separation from other reaction products by reverse-phase HPLC, exhibit an absorbance maximum at 288 nm with an extinction coefficient of 1,500 M(-1) small middle dotcm(-1). The selenotrisulfide derivative of lipoic acid was significantly stable at or below pH 8.0 in contrast to several other previously studied selenotrisulfides. Mass spectral analysis of the lipoic acid and lipoamide derivatives confirmed both the expected molecular weights and also the presence of a single atom of selenium as revealed by its isotopic distribution. The selenotrisulfide derivative of lipoic acid was found to serve as an effective substrate for recombinant human thioredoxin reductase as well as native rat thioredoxin reductase in the presence of NADPH. Likewise, the lipoamide derivative was efficiently reduced by NADH-dependent bovine lipoamide dehydrogenase. The significant in vitro stability of these intramolecular selenotrisulfide derivatives of lipoic acid can serve as an important asset in the study of such selenium adducts as model selenium donor compounds for selenophosphate biosynthesis and as rate enhancement effectors in various redox reactions.
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Affiliation(s)
- W T Self
- Laboratory of Biochemistry, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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Haj-Yehia AI, Assaf P, Nassar T, Katzhendler J. Determination of lipoic acid and dihydrolipoic acid in human plasma and urine by high-performance liquid chromatography with fluorimetric detection. J Chromatogr A 2000; 870:381-8. [PMID: 10722093 DOI: 10.1016/s0021-9673(99)00857-2] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
A highly sensitive method for the determination of alpha-lipoic acid (LA) and dihydrolipoic acid (DHLA) in human plasma and urine has been developed. Samples were acidified and extracted with organic solvent, and the free sulfhydryls of DHLA protected as the dicarboxyethylate by treatment with ethylchloroformate. The free carboxylic function of LA and the SH-protected DHLA were converted into their amide derivatives with the strong fluorophore 2-(4-aminophenyl)-6-methylbenzothiazole in the presence of a coupling agent and a base catalyst. The resulting fluorescent amides of both LA and DHLA were separated on a reversed-phase column (Ultrasphere C8) using simple isocratic elution with acetonitrile-water (80:20) and detected fluorimetrically (excitation 343, emission 423 nm). The method is highly sensitive, reproducible, and is easily applied for the simultaneous determination of LA and DHLA in biological samples.
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Affiliation(s)
- A I Haj-Yehia
- Department of Pharmaceutics, The David R. Bloom Center for Pharmacy, School of Pharmacy, Hebrew University of Jerusalem, Israel.
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Abstract
Some strict anaerobic bacteria catalyze with glycine as substrate an internal Stickland reaction by which glycine serves as electron donor being oxidized by glycine-cleavage system or as electron acceptor being reduced by glycine reductase. In both cases, energy is conserved by substrate level phosphorylation. Except for the different substrate-activating proteins PB, reduction of sarcosine or betaine to acetyl phosphate involves in Eubacterium acidaminophilum the same set of proteins as observed for glycine, e.g. a unique thioredoxin system as electron donor and an acetyl phosphate-forming protein PC interacting with the intermediarily formed Secarboxymethylselenoether bound to protein PA.
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Affiliation(s)
- J R Andreesen
- Institute of Microbiology, University of Halle, Germany
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The glycine cleavage system. Occurrence of two types of chicken H-protein mRNAs presumably formed by the alternative use of the polyadenylation consensus sequences in a single exon. J Biol Chem 1991. [DOI: 10.1016/s0021-9258(18)49990-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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Teuber L. Naturally Occurring 1,2-Dithiolanes and 1,2,3-Trithianes. Chemical and Biological Properties. ACTA ACUST UNITED AC 1990. [DOI: 10.1080/01961779008048732] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Kim Y, Oliver DJ. Molecular cloning, transcriptional characterization, and sequencing of cDNA encoding the H-protein of the mitochondrial glycine decarboxylase complex in peas. J Biol Chem 1990. [DOI: 10.1016/s0021-9258(19)40127-0] [Citation(s) in RCA: 57] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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Kochi H, Seino H, Ono K. Inhibition of glycine oxidation by pyruvate, alpha-ketoglutarate, and branched-chain alpha-keto acids in rat liver mitochondria: presence of interaction between the glycine cleavage system and alpha-keto acid dehydrogenase complexes. Arch Biochem Biophys 1986; 249:263-72. [PMID: 3753002 DOI: 10.1016/0003-9861(86)90002-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Pyruvate, alpha-ketoglutarate, and branched-chain alpha-keto acids which were transaminated products of valine, leucine, and isoleucine inhibited glycine decarboxylation by rat liver mitochondria. However, glycine synthesis (the reverse reaction of glycine decarboxylation) was stimulated by those alpha-keto acids with the concomitant decarboxylation of alpha-keto acid added in the absence of NADH. Both the decarboxylation and the synthesis of glycine by mitochondrial extract were affected similarly by alpha-ketoglutarate and branched-chain alpha-keto acids in the absence of pyridine nucleotide, but not by pyruvate. This failure of pyruvate to have an effect was due to the lack of pyruvate oxidation activity in the mitochondrial extract employed. It indicated that those alpha-keto acids exerted their effects by providing reducing equivalents to the glycine cleavage system, possibly through lipoamide dehydrogenase, a component shared by the glycine cleavage system and alpha-keto acid dehydrogenase complexes. On the decarboxylation of pyruvate, alpha-ketoglutarate, and branched-chain alpha-keto acids in intact mitochondria, those alpha-keto acids inhibited one another. In similar experiments with mitochondrial extract, decarboxylations of alpha-ketoglutarate and branched-chain alpha-keto acid were inhibited by branched-chain alpha-keto acid and alpha-ketoglutarate, respectively, but not by pyruvate. NADH was unlikely to account for the inhibition. We suggest that the lipoamide dehydrogenase component is an indistinguishable constituent among alpha-keto acid dehydrogenase complexes and the glycine cleavage system in mitochondria in nature, and that lipoamide dehydrogenase-mediated transfer of reducing equivalents might regulate alpha-keto acid oxidation as well as glycine oxidation.
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Fujiwara K, Okamura-Ikeda K, Motokawa Y. Chicken liver H-protein, a component of the glycine cleavage system. Amino acid sequence and identification of the N epsilon-lipoyllysine residue. J Biol Chem 1986. [DOI: 10.1016/s0021-9258(19)84457-5] [Citation(s) in RCA: 56] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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13
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Walker JL, Oliver DJ. Glycine decarboxylase multienzyme complex. Purification and partial characterization from pea leaf mitochondria. J Biol Chem 1986. [DOI: 10.1016/s0021-9258(17)35920-3] [Citation(s) in RCA: 95] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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Wood HG, Ragsdale SW, Pezacka E. The acetyl-CoA pathway: a newly discovered pathway of autotrophic growth. Trends Biochem Sci 1986. [DOI: 10.1016/0968-0004(86)90223-9] [Citation(s) in RCA: 88] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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15
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Gariboldi RT, Drake HL. Glycine synthase of the purinolytic bacterium, Clostridium acidiurici. Purification of the glycine-CO2 exchange system. J Biol Chem 1984. [DOI: 10.1016/s0021-9258(20)82108-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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16
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Sokatch JR, Burns G. Oxidation of glycine by Pseudomonas putida requires a specific lipoamide dehydrogenase. Arch Biochem Biophys 1984; 228:660-6. [PMID: 6546487 DOI: 10.1016/0003-9861(84)90036-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Pseudomonas putida produces two lipoamide dehydrogenases with molecular weights of 49,000 and 56,000 designated LPD-val and LPD-glc, respectively. LPD-val is required for oxidation of valine, since it is specifically utilized as the E3 component of branched-chain keto acid dehydrogenase. Since glycine oxidation by bacteria and mammals also requires lipoamide dehydrogenase, we desired to determine which lipoamide dehydrogenase would be used by the P. putida glycine oxidation system. When grown in a medium with glycine as the sole nitrogen source, P. putida produced a single lipoamide dehydrogenase with a molecular weight of 56,000 and which reacted with antiserum to LPD-glc. The partially purified glycine oxidation system from P. putida was stimulated by LPD-glc but not by LPD-val and was inhibited by anti-LPD-glc, but not by anti-LPD-val. It was not possible to detect LPD-val in extracts of cells grown in glucose-glycine medium by the use of anti-LPD-val. LPD-glc was five times as active as LPD-val in catalyzing the oxidation of purified protein H, the heat-stable, lipoic acid-containing protein of the glycine oxidation system. These results indicate that LPD-glc is specifically utilized for glycine oxidation in P. putida.
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Fujiwara K, Motokawa Y. Mechanism of the glycine cleavage reaction. Steady state kinetic studies of the P-protein-catalyzed reaction. J Biol Chem 1983. [DOI: 10.1016/s0021-9258(20)82042-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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18
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D�rre P, Spahr R, Andreesen JR. Glycine fermentation via a glycine reductase in Peptococcus glycinophilus and Peptococcus magnus. Arch Microbiol 1983. [DOI: 10.1007/bf00407945] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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19
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Okamura-Ikeda K, Fujiwara K, Motokawa Y. Purification and characterization of chicken liver T-protein, a component of the glycine cleavage system. J Biol Chem 1982. [DOI: 10.1016/s0021-9258(19)68336-5] [Citation(s) in RCA: 23] [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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20
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Chapter 4 Stereochemistry of pyridoxal phosphate-catalyzed reactions. ACTA ACUST UNITED AC 1982. [DOI: 10.1016/s0167-7306(08)60395-6] [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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Shih JC, Steinsberger SC. Determination of lipoic acid in chick livers and chicken eggs during incubation. Anal Biochem 1981; 116:65-8. [PMID: 6795967 DOI: 10.1016/0003-2697(81)90322-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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22
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23
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The mitochondrial glycine cleavage system. Purification and properties of glycine decarboxylase from chicken liver mitochondria. J Biol Chem 1980. [DOI: 10.1016/s0021-9258(19)70183-5] [Citation(s) in RCA: 58] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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24
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Matuda S, Obo F. Isolation and characterization of a protein having lipoic acid as prosthetic group from Ascaris muscle microsomes. Biochem Biophys Res Commun 1980; 92:775-80. [PMID: 6767475 DOI: 10.1016/0006-291x(80)90770-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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25
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Fujiwara K, Okamura K, Motokawa Y. Hydrogen carrier protein from chicken liver: purification, characterization, and role of its prosthetic group, lipolic acid, in the glycine cleavage reaction. Arch Biochem Biophys 1979; 197:454-62. [PMID: 389161 DOI: 10.1016/0003-9861(79)90267-4] [Citation(s) in RCA: 67] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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26
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O'Brien WE. Inhibition of glycine synthase by branched-chain alpha-keto acids. A possible mechanism for abnormal glycine metabolism in ketotic hyperglycinemia. Arch Biochem Biophys 1978; 189:291-7. [PMID: 708054 DOI: 10.1016/0003-9861(78)90215-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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27
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Kochi H, Kikuchi G. Mechanism of reversible glycine cleavage reaction in Arthrobacter globiformis. Function of lipoic acid in the cleavage and synthesis of blycine. Arch Biochem Biophys 1976; 173:71-81. [PMID: 1259444 DOI: 10.1016/0003-9861(76)90236-8] [Citation(s) in RCA: 48] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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28
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Motokawa Y, Kikuchi G. Glycine metabolism by rat liver mitochondria. Isolation and some properties of the protein-bound intermediate of the reversible glycine cleavage reaction. Arch Biochem Biophys 1974; 164:634-40. [PMID: 4460883 DOI: 10.1016/0003-9861(74)90075-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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