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Thermodynamics of Enzyme-Catalyzed Reactions: Part 4

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Thermodynamics of Enzyme-Catalyzed Reactions: Part 4 Thermodynamics of Enzyme-Catalyzed Reactions: Part 4. Lyases Cite as: Journal of Physical and Chemical Reference Data 24, 1669 (1995); https:// doi.org/10.1063/1.555969 Submitted: 27 January 1995 . Published Online: 15 October 2009 Robert N. Goldberg, and Yadu B. Tewari ARTICLES YOU MAY BE INTERESTED IN Thermodynamics of Enzyme-Catalyzed Reactions: Part 1. Oxidoreductases Journal of Physical and Chemical Reference Data 22, 515 (1993); https:// doi.org/10.1063/1.555939 Thermodynamics of Enzyme-Catalyzed Reactions. Part 3. Hydrolases Journal of Physical and Chemical Reference Data 23, 1035 (1994); https:// doi.org/10.1063/1.555957 Thermodynamics of Enzyme-Catalyzed Reactions: Part 5. Isomerases and Ligases Journal of Physical and Chemical Reference Data 24, 1765 (1995); https:// doi.org/10.1063/1.555970 Journal of Physical and Chemical Reference Data 24, 1669 (1995); https://doi.org/10.1063/1.555969 24, 1669 © 1995 American Institute of Physics for the National Institute of Standards and Technology. Thermodynamics of Enzyme-Catalyzed Reactions: Part 4. Lyases Robert N. Goldberg and Yadu B. Tewari Biotechnology Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899-0001 Received January 27. 1995 Equilibrium constants and enthalpy changes for reactions catalyzed by the lyase class of enzymes have been compiled. For each reaction the following infonnation is given: the reference for the data; the reaction studied; the name of the enzyme used and its Enzyme Commission number; the method of measurement; the conditions of measurement (temperature, pH, ionic strength, and the buffer(s) and cofactor(s) used); the data and an evaluation of it; and, sometimes, commentary on the data and on any corrections which have been applied to it or any calculations for which the data have been used. The data from 106 references have been examined and evaluated. Chemical Abstract Service registry numbers are given for the substances involved in these various reactions. There is a cross reference between the substances and the Enzymc Commission numbcrs of thc enzymes used to catalyze the reactions in which the substances participate. © 1995 American Institute of Physics and American Chemical Society. Key words: apparent equi1ibrium constants; enthalpies of reaction; enzyme-catalyzed reactions; evaluated data; Jyases; transformed thermodynamic properties. Contents 1. Introduction ................................ 1670 5.10. Enzyme: rhamnulose-1-phosphate aldolase 2. Some Aspects and Uses of Thennodynamic Data (EC 4.1.2.19) ......................... 1676 on Biochemical Reactions ................... 1671 5.11. Enzyme: 2-dehydro-3-deoxy-6- 3. Acknowledgments .......................... 1671 phosphogalactonate aldolase (EC 4.1.2.21). 1676 4. References for the Introductory Discussion ...... 1672 5.12. Enzyme: D-arabino-3-hexulose phosphate 5. Table of Equilibrium Constants and Enthalpies fonnaldehyde lyase (EC 4.1.2.a) .......... 1676 of Reaction ............................... 1672 5.13. Enzyme: isocitrate lyase (EC 4.1.3.1) ...... 1676 5.1 Enzyme: phosphoenolpyruvate 5.14. Enzyme: malate synthase (EC 4.1.3.2) ..... 1677 carboxykinase (GTP) (EC 4.1.1.32) ......... 1672 5.15. Enzyme: N-acetylneuraminate lyase 5.2. Enzyme: phosphoenolpyruvate (EC 4.1.3.3) .......................... 1677 carboxykinase (diphosphate) (EC 4.1.1.38) ... 1672 5.16. Enzyme: citrate (pro-3S)-lyase 5.3. Enzyme: ribulose-biphosphate carboxylase (EC 4.1.3.6) .......................... 1677 (EC 4.1.1.39) ........................... 1672 5.17. Enzyme: citrate (sO-synthase (EC 4.1.3.7) .. 1678 5.4. Enzyme: ketotetraose-phosphate aldolase S.lS. Enzyme: ATP citrate (pro-3S)-]yase (EC 4.1.2.2) ............................ 1673 (EC 4.1.3.8) .......................... 1678 5.5. Enzyme: deoxyribose-phosphate aldolase 5.19. Enzyme: 4-hydroxy-2-oxoglutarate (EC 4.1.2.4) ............................ 1673 aldolase (BC 4.1.3.16) .................. 1678 5.6. Enzyme: fructose-biphosphate aldolase 5.20. Enzyme: citramalate lyase (EC 4.1.3.22) ... 1679 (EC 4.1.2.13) ........................... 1673 5.21. Enzyme: malyl-CoA lyase (EC 4.1.3.24) ... 1679 5.7. Enzyme: 5.22. Enzyme: 2,3-dimethylmalate lyase 2-dehydro-3-deoxyphosphogluconate (EC 4.1.3.32) .......................' .. 1679 aldolase (EC 4.1.2.14) .................... 1675 5.23. Enzyme: tryptophanase (EC 4.1.99.1) ...... 1679 5.8. Enzyme: L-fuculose-phosphate aldolase 5.24. Enzyme: fumarate hydratase (EC 4.2.1.2) .. 1680 (EC 4.1.2.17) ........................... 1675 5.25. Enzyme: aconitate hydratase (EC 4.2.1.3) .. 1682 5.9. Enzyme: 2-dehydro-3-deoxY-L-pentonate 5.26. Enzyme: 3-dehydroquinate dehydratase aldolase (Ee 4.1.2.18) .................... 1676 (EC 4.2.1.10) ......................... 1684 5.27. Enzyme: phosphopyruvate hydratase ©1995 by the U. S. Secretary of Commerece on behalf of the United States. (EC 4.2.1.11) ............... -.......... 1685 This copyright is assigned to the American Institute of Physics and the American Chemical Society. 5.28. Enzyme: enoyl-CoA hydratase Reprints available from ACS; see Reprints List at back of issue. (EC 4.2.1.17) ......................... 1686 0047-2689/95/24(5)11669/30/$12.00 1669 J. Phys. Chern. Ref. Data, Vol. 24, No.5, 1995 1670 R. N. GOLDBERG AND Y. B. TEWARI 5.29. Enzyme: tryptophan synthase librium and calorimetric measurements performed on these (EC 4.2.1.20). .. 1686 reactions under in vitro conditions. The thermodynamic 5.30. Enzyme: maleate hydratase (EC 4.2.1.31).. 1687 quantities that are generally given are apparent equilibrium 5.31. Enzyme: (S)-2-methylmalate dehydratase constants K' and calorimetrically determined enthalpies of (EC 4.2.1.34). .. 1688 reaction Ll~(cal). Apparent equilibrium constants calculated 5.32. Enzyme: (R)-2-methylmalate dehydratase from kinetic data are also tabulated. If the change in binding (EC 4.2.1.35). .. 1688 of hydrogen ion Ll~(H+) in a biochemical reaction is 5.33. Enzyme: D-glutamate cyclase known, the standard transformed enthalpy of reaction Ll~' ° (EC 4.2.1.48). .. 1688 can be calculated from the calorimetrically determined en­ 5.34. Enzyme: urocanate hydratase thalpy of reaction.5 Equilibrium constants K and standard (EC 4.2.1.49). .. 1689 molar enthalpies of reaction Ll~o for chemical reference re­ 5.35. Enzyme: crotonoyl-[acyl-carrier-proteinJ actions are also given if they have been reported in the lit­ hydratase (EC 4.2.1.58). .. 1689 erature. The standard transformed enthalpy of reaction Ll~' ° 5.36. Enzyme: dimethylmaleate hydratase can be used to calculate the temperature dependence of ap­ (EC 4.2.1.85). .. 1689 parent equilibrium constants K' in the same way that the 5.37. Enzyme: 3-hydroxybutyryl-CoA dehyratase standard enthalpy ot reaction A/iu is used to calculate the (EC 4.2. La). .. .. 1689 temperature dependence of the equilibrium constant K. 5.38. Enzyme: aspartate ammonia-lyase The data are presented in the same format as in Parts 1 to (EC 4.3.1.1) .......................... 1689 3.1- 3 Thus, the following information is givcn for eaeh entry 5.39. Enzyme: methylaspartate ammonia-lyase in this review: the reference for the data; the biochemical (EC 4.3.1.2). .. 1691 reaction studied; the recommended name4 of the enzyme 5.40. Enzyme: histidine ammonia-lyase used and its Enzyme Commission number: the method of (EC 4.3.1.3). .. 1691 measurement; the conditions of measurement (temperature, 5.41. Enzyme: phenylalanine ammonia-lyase pH, ionic strength, and the buffer(s) and cofactor(s) used); (EC 4.3.1.5).. .. .. .. ... 1692 the data and its evaluation; and, sometimes, commeiItary on 5.42. Enzyme: f3-alanyl-CoA ammonia lyase the data and on any corrections that have been applied or any (EC 4.3.1.6) ........................... 1692 calculations for which the data have been used. The absence 5.43. Enzyme: arginosuccinate lyase of a piece of information indicates that it was not found in (EC 4.3.2.1). .. 1692 the cited paper. The arrangement of the data, its evaluation, 5.44. Enzyme: adenylosuccinate lyase and the thermodynamic conventions have been discussed (EC 4.3.2.2). .. 1692 previously. 1 One should note that equilibrium constants 5.45. Enzyme: ureidoglycolate lyase should be expressed as dimensionless quantities. However, (EC 4.3.2.3). .. 1693 the numerical value obtained for the equilibrium constant of 5.46. Enzyme: lactoylglutathione lyase an unsymmetrical reaction will depend upon the measure of (EC 4.4.1.5). .. 1693 composition and standard concentration selected for the re­ 5.47. Enzyme: adenylate cyclase (EC 4.6.1.1).... 1693 actants and products. Thus, for the chemical reaction 6. List of Substances with Chemical Abstract Service (CAS) Registry Numbers with Cross A( aq) = B (aq) + C( aq) , (1) Reterences to Enzyme Commission Numbers.... 1694 7. Abbreviations.............................. 1696 O Kc= c(B)c(C)/{ c(A)cO}, Km = m(B)m(C)/{ m(A)m }, and 8. Glossary of Symbols. .. 1696 Kx=x(B)x(C)/x(A). Here, c, m, and x are, respectively, con­ 9. Rcfcrcncc Codcs and Rcfcrcnccs in thc Table . .. 1697 centration, molality, and mole fraction, CO 1 mol dm -:}, and m ° = 1 mol kg -1. The equilibrium constant expressed in 1. Introduction terms of mole fractions is automatically dimensionless. Simi­ lat defin.itions and considerations apply to the apparent equi­ This article is a continuation of the first three reviews in librium constant K'. The symbols used in this review are l 3 this series - that dealt, respectively, with the thermodynam­ given in the Glossary (see Section 8). ics of the reactions catalyzed by the oxidoreductases, trans­ The subjective evaluation of the data in this review con­ ferases, and hydrolases. These are the first three classes of sisted of the assignment of a rating: A (high quality), B enzymes classified by the Nomenclature Committee of the (good), C (average), or D (low quality). In making these International Union of Biochemistry.4 In the current review a assignments we considered the. various experimental details critical compilation· of thermodynamic data is provided for which were provided in the study.
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