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Buckel W, Beatrix B, Zelder O. Glutamate mutase and 2-methyleneglutarate mutase. Methods Enzymol 2022; 668:285-307. [PMID: 35589197 DOI: 10.1016/bs.mie.2021.12.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Affiliation(s)
- Wolfgang Buckel
- Department of Biology, Philipps University, Marburg, Germany.
| | - Birgitta Beatrix
- Gene Center, Department of Biochemistry, Ludwig Maximilian University, München, Germany
| | - Oskar Zelder
- Department of Biology, Philipps University, Marburg, Germany; Industrial Biotechnology I, BASF SE, Ludwigshafen am Rhein, Germany
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Rommel JB, Liu Y, Werner HJ, Kästner J. Role of tunneling in the enzyme glutamate mutase. J Phys Chem B 2012; 116:13682-9. [PMID: 23127187 DOI: 10.1021/jp308526t] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The role of quantum mechanical atom tunneling during the conversion of glutamate to methylaspartate catalyzed by glutamate mutase is investigated by quantum mechanical/molecular mechanical (QM/MM) simulations based on coupled cluster and density functional calculations. The use of instanton theory allows us to calculate the tunneling contributions of up to 78 atoms in the active site. We calculate kinetic isotope effects (KIEs) and compare them to experimental data. The simulations lead to deuterium KIEs of 10 for the hydrogen abstraction from glutamate substrate and 16 for the hydrogen abstraction from methylaspartate substrate, which are consistent with the experimental results. The hydrogen abstraction from methylaspartate has higher primary deuterium and tritium (46.1) KIEs than the abstraction from glutamate. The tunneling effect increases the reaction rate by a factor of 12.3 for the hydrogen abstraction from methylaspartate at 0. Tunneling is supported by the environment by preparing the enzyme through classical motions. Consideraton of the tunneling contributions of more and more atoms around the active center shows that the motions at the ribose ring play a central role during the tunneling enhancement of the hydrogen transfers. Our simulations give new insight into the catalytic process in glutamate mutase and the way enzymes use tunneling effects for a successful catalysis.
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Affiliation(s)
- Judith B Rommel
- Institute of Theoretical Chemistry, University of Stuttgart, Pfaffenwaldring 55, D-70569 Stuttgart, Germany
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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]
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Ducrocq C, Maréchal PDL, Azerad R. Synthesis of L-glutamic acid stereospecifically labeled at C-4 with deuterium. J Labelled Comp Radiopharm 2006. [DOI: 10.1002/jlcr.2580220109] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Kunz F, Rétey J, Arigoni D, Tsai L, Stadtman TC. Die absolute Konfiguration der 3,5-Diaminohexansäure aus der β-Lysin-Mutase-Reaktion. Helv Chim Acta 2004. [DOI: 10.1002/hlca.19780610328] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Flohr H, Pannhorst W, Rétey J. Ein synthetisches Modell für die Aktivstelle der Coenzym-B12-abhängigen Methylmalonyl-CoA-Mutase. Helv Chim Acta 2004. [DOI: 10.1002/hlca.19780610509] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Beatrix B, Zelder O, Kroll FK, Örlygsson G, Golding BT, Buckel W. Hinweise auf einen Fragmentierungsmechanismus bei Coenzym-B12-abhängigen Umlagerungen des Kohlenstoffgerüsts. Angew Chem Int Ed Engl 1995. [DOI: 10.1002/ange.19951072113] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Hartzoulakis B, Gani D. The mechanism of glutamate mutase: An unusually substrate-specific enzyme. J CHEM SCI 1994. [DOI: 10.1007/bf02841924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Igbavboa U, Leistner E. Sequence of proton abstraction and stereochemistry of the reaction catalyzed by naphthoate synthase, an enzyme involved in menaquinone (vitamin K2) biosynthesis. EUROPEAN JOURNAL OF BIOCHEMISTRY 1990; 192:441-9. [PMID: 2209599 DOI: 10.1111/j.1432-1033.1990.tb19246.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The enzymic conversion of the coenzyme A ester of 4-(2'-carboxyphenyl)-4-oxobutyric acid (i.e. o-succinylbenzoic acid) to 1,4-dihydroxy-2-naphthoic acid is a cyclization reaction which is part of menaquinone (vitamin K2) biosynthesis. This conversion, which is probably a two-step process, was investigated using chirally labelled samples of the coenzyme A ester of 4-(2'-carboxyphenyl)-4-oxobutyric acid. To synthesize these, the following enzymes were employed: isocitrate: NADP+ oxidoreductase (EC 1.1.1.42), isocitrate glyoxylate-lyase (EC 4.1.3.1), 2-oxoglutarate dehydrogenase complex (which includes EC 1.2.4.2), 4-(2'-carboxyphenyl)-4-oxobutyrate synthase system and 4-(2'-carboxyphenyl)-4-oxobutyrate: CoA ligase. Isocitrate: NADP+ oxidoreductase was employed to generate the two enantiomeric samples of 2-oxoglutarate enantiotopically labelled at C-3. These samples were converted enzymically to succinate with retention of configuration at C-2 and C-3, and to 4-(2'-carboxyphenyl)-4-oxobutyric acid with retention of configuration at C-3. Isocitrate glyoxylate-lyase and isocitrate NADP+ oxidoreductase were employed to generate samples of 2-oxoglutarate enantiotopically tritiated at C-4 or at C-3 and C-4. The four variously labelled samples of 2-oxoglutarate were enzymically converted to the coenzyme A ester of 4-(2'-carboxyphenyl)-4-oxobutyric acid. The resulting variously labelled coenzyme A esters were incubated with naphthoate synthase to investigate the ring closure reaction. In the first step the 2HRe atom of the oxobutyric moiety of the coenzyme A ester is equilibrated with solvent protons in a fast and reversible reaction. Subsequently the 2HSi and 3HSi atoms are removed whereas the 3HRe atom becomes the proton at C-3 of 1,4-dihydroxy-2-naphthoic acid. The second step in this ring closure reaction is the rate-limiting step.
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Affiliation(s)
- U Igbavboa
- Institut für Pharmazeutische Biologie, Rheinische Friedrich-Wilhelms-Universität Bonn, Federal Republic Germany
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Murakami Y, Hisaeda Y, Ohno T. Artificial Glutamate Mutase Composed of Hydrophobic Vitamin B12and Synthetic Bilayer Membrane. CHEM LETT 1987. [DOI: 10.1246/cl.1987.1357] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Hartrampf G, Buckel W. On the steric course of the adenosylcobalamin-dependent 2-methyleneglutarate mutase reaction in Clostridium barkeri. EUROPEAN JOURNAL OF BIOCHEMISTRY 1986; 156:301-4. [PMID: 3699016 DOI: 10.1111/j.1432-1033.1986.tb09582.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The enzymatically active enantiomer of 3-methylitaconate in Clostridium barkeri has (R)-configuration. This was checked by fermentation of the racemate and reisolation of the (S)-enantiomer. In addition (R)-3-methylitaconate was synthesized by enzymatic isomerisation of 2,3-dimethylmaleate which was protonated at the Si-face. 2-Methylene[2-2H1]glutarate was synthesized via (R)-3-methyl[3-2H1]itaconate by brief incubation of 2,3-dimethylmaleate with a cell-free extract of Clostridium barkeri in 2H2O. The predominantly monodeuterated compound was oxidized to (S)-[2-2H1]succinate as analysed by circular dichroism. The results demonstrate that 2-methyleneglutarate mutase catalyses the reversible migration of an acryloyl residue from the alpha-carbon to the beta-carbon of propionate with inversion of configuration at the alpha-carbon.
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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.
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Finke RG, Schiraldi DA, Mayer BJ. Towards the unification of coenzyme B12-dependent diol dehydratase stereochemical and model studies: The bound radical mechanism. Coord Chem Rev 1984. [DOI: 10.1016/0010-8545(84)85016-x] [Citation(s) in RCA: 64] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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Zagalak B. [Vitamin B12 as a biologically active model compound]. THE SCIENCE OF NATURE - NATURWISSENSCHAFTEN 1982; 69:63-74. [PMID: 7070534 DOI: 10.1007/bf00441225] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
A critical review on corrinoid biochemistry and physiology is presented. This includes: chemical synthesis of biologically important organocorrinoids and the correlation between their structures and coenzymatic activity; forms, distribution and transport of physiologically active corrinoids; methylcobalamin- and adenosylcobalamin-dependent enzymatic reactions and their physiological functions; and steric course of the adenosylcobalamin-dependent enzymatic rearrangements. Special attention is paid to the mechanisms of adenosylcobalamin-dependent enzymatic reactions.
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Chapter 2 Chemical methods for the investigation of stereochemical problems in biology. ACTA ACUST UNITED AC 1982. [DOI: 10.1016/s0167-7306(08)60393-2] [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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Rétey J. Chapter 6 Vitamin B12: Stereochemical aspects of its biological functions and of its biosynthesis. ACTA ACUST UNITED AC 1982. [DOI: 10.1016/s0167-7306(08)60397-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2023]
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Diziol P, Haas H, Rétey J, Graves SW, Babior BM. The substrate-dependent steric course of the ethanolamine ammonia-lyase reaction. EUROPEAN JOURNAL OF BIOCHEMISTRY 1980; 106:211-24. [PMID: 7341225 DOI: 10.1111/j.1432-1033.1980.tb06012.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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Babior BM, Krouwer JS. The mechanism of adenosylcobalamin-dependent reactions. CRC CRITICAL REVIEWS IN BIOCHEMISTRY 1979; 6:35-102. [PMID: 222536 DOI: 10.3109/10409237909105424] [Citation(s) in RCA: 49] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Rétey J, Smith EH, Zagalak B. Investigation of the mechanism of the methylmalonyl-CoA mutase reaction with the substrate analogue: ethylmalonyl-CoA. EUROPEAN JOURNAL OF BIOCHEMISTRY 1978; 83:437-51. [PMID: 24538 DOI: 10.1111/j.1432-1033.1978.tb12110.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
1. Ethylmalonyl-CoA was found to be a substrate for methylmalonyl-CoA mutase from Propionibacterium shermanii, the product being mainly (2R)-methylsuccinyl-CoA along with some (2S)-diastereoisomer. 2. The relevant 1H-nuclear magnetic resonance signals of methylsuccinic acid and of its dimethyl ester were assigned to the diastereotopic methylene hydrogens using sterospecifically dideuterated specimens of known configuration. 3. [2(-2)H1]Ethylmalonyl-CoA was converted by methylmalonyl-CoA mutase in 2H2O mainly to (2R, 3S)-[3(-2)H1]methylsuccinyl-CoA. No dideuterated product was observed. 4. Starting from (1R)-[1(-2)H1]-ethathanol, (1S)-[1(-2)H1]ethanol and [2H6] ethanol the following deuterated specimens of ethylmalonic acid were synthesised and characterised: (3S)-[3(-2)H1], (3R)-[3(-2)H1] and [3(-2)H2, 4(-2)H3], respectively. 5. Conversion of (3S)-[3(-2)H1]-ethylmalonyl-CoA (70% 2H1 and 2% 2H2 species) on the mutase in water afforded mainly (2R)-[2(-2)H1]methylsuccinyl-CoA along with some (2S)-diastereoisomer. No deuterium loss was observed. 6. Methylmalonyl-CoA mutase converted (3R)-[3(-2)H1]ethylmalonyl-CoA (81% 2H1 and 2% 2H2 species) to the following methylsuccinyl-CoA species: 33% [3(-2)H1], the deuterium being in the threo position with respect to the methyl group; 21% [2(-2)H1]; 46% unlabelled. The ratio of the species with (2R) and (2S) configuration was about 60:40. 7. Reaction of [3(-2)H2, 4(-2)H3]ethylmalonyl-CoA (94.5% [2H5] species) with the mutase gave the following labelled methylsuccinyl-CoA species:53.4% [methyl-2H3, 2(-2)H1, 3(-2)H1], the 3-deuterium being in the threo position with respect to the methyl group; 37.6% [methyl-2H3, 2(-2)H1]; 5% [methyl(-2)H3, 2(-2)H1, 2(-2)H1, 3(-2)H1] the 3-deuterium being in erythro position with respect to the methyl group; 4% [methyl(-2)H3, 3(-2)H1]. The ratio of the species with (2R) and (2S) configuration was about 70:30. 8. Implications of these findings for the mechanism of the rearrangements catalysed by coenzyme B12 are discussed.
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Abstract
Adenosylcobalamin-dependent rearrangements are enzyme catalyzed reactions in which a hydrogen atom is transfered from one carbon atom to an adjacent one in exchange for a group X which migrates in the opposite direction. In the hydrogen transfer step, the mechanism of which is reasonably well understood, the cofactor serves as an intermediate hydrogen carrier. The transfer of hydrogen to the cofactor involves homolysis of the carbon-cobalt bond to generate cob(II) alamin and the 5'-deoxyadenos-5'-yl radical, followed by abstraction of a hydrogen atom from the substrate to form 5'-deoxyadenosine and the substrate radical. After migration of group X, the hydrogen atom is returned to the product radical by the reverse of the above reactions to generate the final product and reconstitute the cofactor. In contrast to the transfer of hydrogen, the mechanism of group X migration is poorly understood. Many reactions mechanisms have been proposed on chemical grounds, but there is insufficient biochemical evidence to permit a choice among these propsals. A quantity of negative evidence has accumulated suggesting that group X migration does not involve alkylation of the cobalt of cobalamin by the substrate, but in the absence of firm data supporting an alternative mechanism, even this weak conclusion must be regarded as provisional.
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Thauer RK, Jungermann K, Decker K. Energy conservation in chemotrophic anaerobic bacteria. BACTERIOLOGICAL REVIEWS 1977; 41:100-80. [PMID: 860983 PMCID: PMC413997 DOI: 10.1128/br.41.1.100-180.1977] [Citation(s) in RCA: 1319] [Impact Index Per Article: 28.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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The Stereochemistry of the Reaction Catalyzed by Ethanolamine AmmoniaLyase, an Adenosylcobalamindependent Enzyme. J Biol Chem 1974. [DOI: 10.1016/s0021-9258(19)42263-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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Rétey J, Zagalak B. Stereochemistry of the coenzyme-B12-dependent methylamalonyl-CoA-mutase reaction. Investigation with ethylmalonyl-CoA. Angew Chem Int Ed Engl 1973; 12:671-2. [PMID: 4202104 DOI: 10.1002/anie.197306712] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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Rétey J, Zagalak B. Stereochemie der coenzym -B12-abhängigen Methylmalonyl-CoA-Mutase-Reaktion. Untersuchung mit Äthylmalonyl-CoA. Angew Chem Int Ed Engl 1973. [DOI: 10.1002/ange.19730851606] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Hydrogen Transfer between Substrates and Deoxyadenosylcobalamin in the Glutamate Mutase Reaction. J Biol Chem 1969. [DOI: 10.1016/s0021-9258(18)63655-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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Englard S, Britten JS, Listowsky I. Stereochemical Course of the Maleate Hydratase Reaction. J Biol Chem 1967. [DOI: 10.1016/s0021-9258(18)96042-4] [Citation(s) in RCA: 37] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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Frank L. Proline metabolism in Escherichia coli. IV. Preparation of proline-2- and proline-5- 3H and location of 3H in proline. Anal Biochem 1966; 17:423-33. [PMID: 5338482 DOI: 10.1016/0003-2697(66)90178-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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Sprecher M, Clark M, Sprinson DB. The Absolute Configuration of Methylmalonyl Coenzyme A and Stereochemistry of the Methylmalonyl Coenzyme A Mutase Reaction. J Biol Chem 1966. [DOI: 10.1016/s0021-9258(18)96846-8] [Citation(s) in RCA: 23] [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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