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Computational evidence for the importance of lysine carboxylation in the reaction catalyzed by carboxyl transferase domain of pyruvate carboxylase: a QM/MM study

  • Xiang Sheng
  • Qianqian Hou
  • Yongjun Liu
Regular Article
  • 49 Downloads

Abstract

Posttranslational modification is a critical process in the cellular regulation, an example of which is the carboxylation of lysine. Pyruvate carboxylase is an enzyme, in which a carboxylated lysine has been found in the metal coordination shell of the active center. In our previous study, the reaction mechanism of the carboxyl transferase domain of the pyruvate carboxylase from Staphylococcus aureus has been investigated by using QM/MM calculations. The suggested mechanism supports the previous proposal, and most of the results are consistent with the experimental data. However, the calculated overall barrier is too high for an enzymatic reaction, which may be the result of the used model failing to take into account the modification of the metal-coordinated lysine. Here, we present a successive study to investigate the importance of lysine carboxylation in the reaction and also to examine if the Zn-coordinated water molecule is required for the catalysis. The reaction mechanism from the new models is consistent with the previous suggestion. More importantly, the energy barriers of all elementary steps are calculated to be much lower than those in our previous work. Notably, the calculated barrier of the overall reaction is ~ 14 kcal/mol, which is in good agreement with the experimental value. Therefore, this study supplies a theoretical evidence for the importance of the modification of Zn-coordinated lysine in the pyruvate carboxylase-catalyzed reaction. In addition, the water molecule in the zinc coordination shell is suggested to contribute to the catalysis.

Keywords

Pyruvate carboxylase Carboxylation of lysine Quantum mechanical/molecular mechanical method (QM/MM) Reaction mechanism 

Abbreviations

PC

Pyruvate carboxylase

PTM

Posttranslational modification

BTI

Biotin

PYR

Pyruvate

BC

Biotin carboxylase

CT

Carboxyl transferase

BCCP

Biotin carboxyl carrier protein

CA-BTI

Carboxybiotin

TC

Transcarboxylase

KCX

Carboxylated lysine

Notes

Acknowledgements

This work was supported by the National Natural Science Foundation of China (21773188).

Supplementary material

214_2018_2408_MOESM1_ESM.docx (5.2 mb)
Supplementary material 1 (DOCX 5344 kb)

References

  1. 1.
    Walsh CT, Garneau-Tsodikova S, Gatto GJ Jr (2005) Protein posttranslational modifications: the chemistry of proteome diversifications. Angew Chem Int Ed 44:7342–7372CrossRefGoogle Scholar
  2. 2.
    Boutureira O, Bernardes GJL (2015) Advances in chemical protein modification. Chem Rev 115:2174–2195PubMedCrossRefGoogle Scholar
  3. 3.
    Mittal S, Saluja D (2015) Protein post-translational modifications: role in protein structure, function and stability. In: Singh LR, Dar TA, Parvaiz A (eds) Proteostasis and chaperone surveillance. Springer, New Delhi, pp 25–37CrossRefGoogle Scholar
  4. 4.
    Jimenez-Morales D, Adamian L, Shi D, Liang J (2014) Lysine carboxylation: unveiling a spontaneous post-translational modification. Acta Crystallogr D 70:48–57PubMedCrossRefGoogle Scholar
  5. 5.
    Che T, Bonomo RA, Shanmugam S, Bethel CR, Pusztai-Carey M, Buynak JD, Carey PR (2012) Carboxylation and decarboxylation of active site Lys 84 controls the activity of OXA-24, and carey, P.Acinetobacter baumannii: Raman crystallographic and solution evidence. J Am Chem Soc 134:11206–11215PubMedPubMedCentralCrossRefGoogle Scholar
  6. 6.
    Stec B (2012) Structural mechanism of RuBisCO activation by carbamylation of the active site lysine. Proc Natl Acad Sci USA 109:18785–18790PubMedCrossRefGoogle Scholar
  7. 7.
    St Maurice M, Reinhardt L, Surinya KH, Attwood PV, Wallace JC, Cleland WW, Rayment I (2007) Domain architecture of pyruvate carboxylase, a biotin-dependent multifunctional enzyme. Science 317:1076–1079PubMedCrossRefGoogle Scholar
  8. 8.
    Ho YY, Huang YH, Huang CY (2013) Chemical rescue of the post-translationally carboxylated lysine mutant of allantoinase and dihydroorotase by metal ions and short-chain carboxylic acids. Amino Acids 44:1181–1191PubMedCrossRefGoogle Scholar
  9. 9.
    Hsieh YC, Chen MC, Hsu CC, Chan SI, Yang YS, Chen CJ (2013) Crystal structures of vertebrate dihydropyrimidinase and complexes from Tetraodon nigroviridis with lysine carbamylation: metal and structural requirements for post-translational modification and function. J Biol Chem 288:30645–30658PubMedPubMedCentralCrossRefGoogle Scholar
  10. 10.
    Jabri E, Carr MB, Hausinger RP, Karplus PA (1995) The crystal structure of urease from Klebsiella aerogenes. Science 268:998–1004PubMedCrossRefGoogle Scholar
  11. 11.
    Lietzan AD, St Maurice M (2014) Functionally diverse biotin-dependent enzymes with oxaloacetate decarboxylase activity. Arch Biochem Biophys 544:75–86PubMedCrossRefGoogle Scholar
  12. 12.
    Tong L (2013) Structure and function of biotin-dependent carboxylases. Cell Mol Life Sci 70:863–891PubMedCrossRefGoogle Scholar
  13. 13.
    Menefee AL, Zeczycki TN (2014) Nearly 50 years in the making: defining the catalytic mechanism of the multifunctional enzyme, pyruvate carboxylase. FEBS J 281:1333–1354PubMedCrossRefGoogle Scholar
  14. 14.
    Jitrapakdee S, Vidal-Puig A, Wallace JC (2006) Anaplerotic roles of pyruvate carboxylase in mammalian tissues. Cell Mol Life Sci 63:843–854PubMedCrossRefGoogle Scholar
  15. 15.
    Marin-Valencia I, Roe CR, Pascual JM (2010) Pyruvate carboxylase deficiency: mechanisms, mimics and anaplerosis. Mol Genet Metab 101:9–17PubMedCrossRefGoogle Scholar
  16. 16.
    Lietzan AD, Lin Y, St Maurice M (2014) The role of biotin and oxamate in the carboxyltransferase reaction of pyruvate carboxylase. Arch Biochem Biophys 562:70–79PubMedPubMedCentralCrossRefGoogle Scholar
  17. 17.
    Lietzan AD, St Maurice M (2013) Insights into the carboxyltransferase reaction of pyruvate carboxylase from the structures of bound product and intermediate analogs. Biochem Biophys Res Commun 441:377–382PubMedPubMedCentralCrossRefGoogle Scholar
  18. 18.
    Lietzan AD, St Maurice M (2013) A substrate-induced biotin binding pocket in the carboxyltransferase domain of pyruvate carboxylase. J Biol Chem 288:19915–19925PubMedPubMedCentralCrossRefGoogle Scholar
  19. 19.
    Lietzan AD, Menefee AL, Zeczycki TN, Kumar S, Attwood PV, Wallace JC, Cleland WW, St Maurice M (2011) Interaction between the biotin carboxyl carrier domain and the biotin carboxylase domain in pyruvate carboxylase from Rhizobium etli. Biochemistry 50:9708–9723PubMedPubMedCentralCrossRefGoogle Scholar
  20. 20.
    Yu LP, Xiang S, Lasso G, Gil D, Valle M, Tong L (2009) A symmetrical tetramer for S. aureus pyruvate carboxylase in complex with coenzyme A. Structure 17:823–832PubMedPubMedCentralCrossRefGoogle Scholar
  21. 21.
    Yu LP, Chou CY, Choi PH, Tong L (2013) Characterizing the importance of the biotin carboxylase domain dimer for Staphylococcus aureus pyruvate carboxylase catalysis. Biochemistry 52:488–496PubMedPubMedCentralCrossRefGoogle Scholar
  22. 22.
    Xiang S, Tong L (2008) Crystal structures of human and Staphylococcus aureus pyruvate carboxylase and molecular insights into the carboxyltransfer reaction. Nat Struct Mol Biol 15:295–302PubMedCrossRefGoogle Scholar
  23. 23.
    Sureka K, Choi PH, Precit M, Delince M, Pensinger DA, Huynh TN, Jurado AR, Goo YA, Sadilek M, Iavarone AT, Sauer JD, Tong L, Woodward JD (2014) The cyclic dinucleotide c-di-AMP is an allosteric regulator of metabolic enzyme function. Cell 158:1389–1401PubMedPubMedCentralCrossRefGoogle Scholar
  24. 24.
    Hall PR, Zheng R, Antony L, Pusztai-Carey M, Carey PR, Yee VC (2004) Transcarboxylase 5S structures: assembly and catalytic mechanism of a multienzyme complex subunit. EMBO J 23:3621–3631PubMedPubMedCentralCrossRefGoogle Scholar
  25. 25.
    Yong-Biao J, Islam MN, Sueda S, Kondo H (2004) Identification of the catalytic residues involved in the carboxyl transfer of pyruvate carboxylase. Biochemistry 43:5912–5920PubMedCrossRefGoogle Scholar
  26. 26.
    Jitrapakdee S, St Maurice M, Rayment I, Cleland WW, Wallace JC, Attwood PV (2008) Structure, mechanism and regulation of pyruvate carboxylase. Biochem J 413:369–387PubMedPubMedCentralCrossRefGoogle Scholar
  27. 27.
    Waldrop GL, Holden HM, St Maurice M (2012) The enzymes of biotin dependent CO2 metabolism: what structures reveal about their reaction mechanisms. Protein Sci 21:1597–1619PubMedPubMedCentralCrossRefGoogle Scholar
  28. 28.
    Phannasil P, Thuwajit C, Warnnissorn M, Wallace JC, MacDonald MJ, Jitrapakdee S (2015) Pyruvate carboxylase is up-regulated in breast cancer and essential to support growth and invasion of MDA-MB-231 cells. PLoS ONE 10:e0129848PubMedPubMedCentralCrossRefGoogle Scholar
  29. 29.
    Cheng T, Sudderth J, Yang C, Mullen AR, Jin ES, Matés JM, DeBerardinis RJ (2011) Pyruvate carboxylase is required for glutamine-independent growth of tumor cells. Proc Natl Acad Sci USA 108:8674–8679PubMedCrossRefGoogle Scholar
  30. 30.
    MacDonald MJ, Longacre MJ, Langberg EC, Tibell A, Kendrick MA, Fukao T, Ostenson CG (2009) Decreased levels of metabolic enzymes in pancreatic islets of patients with type 2 diabetes. Diabetologia 52:1087–1091PubMedPubMedCentralCrossRefGoogle Scholar
  31. 31.
    Xu J, Han J, Long YS, Epstein PN, Liu YQ (2008) The role of pyruvate carboxylase in insulin secretion and proliferation in rat pancreatic beta cells. Diabetologia 51:2022–2030PubMedPubMedCentralCrossRefGoogle Scholar
  32. 32.
    Aresta M, Dibenedetto A (2007) Utilisation of CO2 as a chemical feedstock: opportunities and challenges. Dalton Trans 28:2975–2992CrossRefGoogle Scholar
  33. 33.
    Alissandratos A, Easton CJ (2015) Biocatalysis for the application of CO2 as a chemical feedstock. Beilstein J Org Chem 11:2370–2387PubMedPubMedCentralCrossRefGoogle Scholar
  34. 34.
    Fung CH, Mildvan AS, Allerhand A, Komoroski R, Scrutton MC (1973) Interaction of pyruvate with pyruvate carboxylase and pyruvate kinase as studied by paramagnetic effects on 13C relaxation rates. Biochemistry 12:620–629PubMedCrossRefGoogle Scholar
  35. 35.
    Fung CH, Mildvan AS, Leigh JS Jr (1974) Electron and nuclear magnetic resonance studies of the interaction of pyruvate with transcarboxylase. Biochemistry 13:1160–1169PubMedCrossRefGoogle Scholar
  36. 36.
    Sheng X, Liu YJ (2014) QM/MM study of the reaction mechanism of the carboxyl transferase domain of pyruvate carboxylase from Staphylococcus aureus. Biochemistry 53:4455–4466PubMedCrossRefGoogle Scholar
  37. 37.
    Senn HM, Thiel W (2009) QM/MM methods for biomolecular systems. Angew Chem Int Edit 48:1198–1229CrossRefGoogle Scholar
  38. 38.
    van der Kamp MW, Mulholland AJ (2013) Combined quantum mechanics/molecular mechanics (QM/MM) methods in computational enzymology. Biochemistry 52:2708–2728PubMedCrossRefGoogle Scholar
  39. 39.
    Ranaghan KE, Mulholland AJ (2010) Investigations of enzyme-catalysed reactions with combined quantum mechanics/molecular mechanics (QM/MM) methods. Int Rev Phys Chem 29:65–133CrossRefGoogle Scholar
  40. 40.
    Quesne MG, Borowski T, de Visser SP (2015) Quantum mechanics/molecular mechanics modeling of enzymatic processes: caveats and breakthroughs. Chem A Eur J 22:2562–2581CrossRefGoogle Scholar
  41. 41.
    Sherwood P, de Vries AH, Guest MF, Schreckenbach G, Catlow CRA, French SA, Sokol AA, Bromley ST, Thiel W, Turner AJ, Billeter S, Terstegen F, Thiel S, Kendrick J, Rogers SC, Casci J, Watson M, King F, Karlsen E, Sjovoll M, Fahmi A, Schäfer A, Lennartz C (2003) QUASI: a general purpose implementation of the QM/MM approach and its application to problems in catalysis. J Mol Struct Theochem 632:1–28CrossRefGoogle Scholar
  42. 42.
    Ahlrichs R, Bär M, Häser M, Horn H, Kölmel C (1989) Electronic structure calculations on workstation computers: the program system turbomole. Chem Phys Lett 162:165–169CrossRefGoogle Scholar
  43. 43.
    Smith W, Forester TR (1996) ChemShell—a modular software package for QM/MM simulation. J Mol Graph Model 14:136–141CrossRefGoogle Scholar
  44. 44.
    Field MJ, Bash PA, Karplus M (1990) A combined quantum mechanical and molecular mechanical potential for molecular dynamics simulations. J Comput Chem 11:700–733CrossRefGoogle Scholar
  45. 45.
    de Vries AH, Sherwood P, Collins SJ, Rigby AM, Rigutto M, Kramer GJ (1999) Zeolite structure and reactivity by combined quantum-chemical–classical calculations. J Phys Chem B 103:6133–6141CrossRefGoogle Scholar
  46. 46.
    Becke AD (1993) Density functional thermochemistry. III. The role of exact exchange. J Chem Phys 98:5648–5652CrossRefGoogle Scholar
  47. 47.
    Lee C, Yang W, Parr RG (1988) Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density. Phys Rev B 37:785–789CrossRefGoogle Scholar
  48. 48.
    Dolg M, Wedig U, Stoll H, Preuss H (1987) Energy-adjusted ab initio pseudopotentials for the first row transition elements. J Chem Phys 86:866–872CrossRefGoogle Scholar
  49. 49.
    Becke AD (1988) Density-functional exchange-energy approximation with correct asymptotic behavior. Phys Rev A 38:3098CrossRefGoogle Scholar
  50. 50.
    Perdew JP (1986) Density-functional approximation for the correlation energy of the inhomogeneous electron gas. Phys Rev B 33:8822–8824CrossRefGoogle Scholar
  51. 51.
    Perdew JP (1986) Erratum: density-functional approximation for the correlation energy of the inhomogeneous electron gas. Phys Rev B 34:7406CrossRefGoogle Scholar
  52. 52.
    Tao J, Perdew JP, Staroverov VN, Scuseria GE (2003) Climbing the density functional ladder: nonempirical meta–generalized gradient approximation designed for molecules and solids. Phys Rev Lett 91:146401PubMedCrossRefGoogle Scholar
  53. 53.
    Grimme S, Antony J, Ehrlich S, Krieg H (2010) A consistent and accurate ab initio parametrization of density functional dispersion correction (DFT-D) for the 94 elements H-Pu. J Chem Phys 132:154104PubMedCrossRefGoogle Scholar
  54. 54.
    Grimme S, Ehrlich S, Goerigk L (2011) Effect of the damping function in dispersion corrected density functional theory. J Comput Chem 32:1456–1465PubMedCrossRefGoogle Scholar
  55. 55.
    Laitaoja M, Valjakka J, Jänis J (2013) Zinc coordination spheres in protein structures. Inorg Chem 52:10983–10991PubMedCrossRefGoogle Scholar
  56. 56.
    Zeczycki TN, St. Maurice M, Jitrapakdee S, Wallace JC, Attwood PV, Cleland WW (2009) Insight into the carboxyl transferase domain mechanism of pyruvate carboxylase from Rhizobium etli. Biochemistry 48:4305–4313PubMedPubMedCentralCrossRefGoogle Scholar

Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2019

Authors and Affiliations

  1. 1.School of Chemistry and Chemical EngineeringShandong UniversityJinanChina

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