Human PAICS is a bifunctional enzyme that is involved in the de novo purine biosynthesis, catalyzing the conversion of aminoimidazole ribonucleotide (AIR) into N-succinylcarboxamide-5-aminoimidazole ribonucleotide (SAICAR). It comprises two distinct active sites, AIR carboxylase (AIRc) where the AIR is initially converted to carboxyaminoimidazole ribonucleotide (CAIR) by reaction with CO2 and SAICAR synthetase (SAICARs) in which CAIR then reacts with an aspartate to form SAICAR, in an ATP-dependent reaction. Human PAICS is a promising target for the treatment of various types of cancer, and it is therefore of high interest to develop a detailed understanding of its reaction mechanism. In the present work, density functional theory calculations are employed to investigate the PAICS reaction mechanism. Starting from the available crystal structures, two large models of the AIRc and SAICARs active sites are built and different mechanistic proposals for the carboxylation and phosphorylation-condensation mechanisms are examined. For the carboxylation reaction, it is demonstrated that it takes place in a two-step mechanism, involving a C-C bond formation followed by a deprotonation of the formed tetrahedral intermediate (known as isoCAIR) assisted by an active site histidine residue. For the phosphorylation-condensation reaction, it is shown that the phosphorylation of CAIR takes place before the condensation reaction with the aspartate. It is further demonstrated that the three active site magnesium ions are involved in binding the substrates and stabilizing the transition states and intermediates of the reaction. The calculated barriers are in good agreement with available experimental data.

Department of Biochemistry and Biophysics Stockholm University SE 10691 Stockholm Sweden

Department of Organic Chemistry Arrhenius Laboratory Stockholm University SE 10691 Stockholm Sweden

Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Flemingovo nam 2 160 00 Prague Czech Republic

See more in PubMed

Hartman S. C.; Buchanan J. M. Biosynthesis of the purines. XXVI. The identification of the formyl donors of the transformylation reactions. J. Biol. Chem. 1959, 234, 1812–1816. 10.1016/S0021-9258(18)69931-4. PubMed DOI

Lukens L. N.; Buchanan J. M. Biosynthesis of the purines. XXIV. The enzymatic synthesis of 5-amino-1-ribosyl-4-imidazolecarboxylic acid 5′-phosphate from 5-amino-1-ribosylimidazole 5′-phosphate and carbon dioxide. J. Biol. Chem. 1959, 234, 1799–1805. 10.1016/S0021-9258(18)69929-6. PubMed DOI

Yin J.; Ren W.; Huang X.; Deng J.; Li T.; Yin Y. Potential mechanisms connecting purine metabolism and cancer therapy. Front. Immunol. 2018, 9, 169710.3389/fimmu.2018.01697. PubMed DOI PMC

Sun W.; Zhang K.; Zhang X.; Lei W.; Xiao T.; Ma J.; Guo S.; Shao S.; Zhang H.; Liu Y.; Yuan J.; Hu Z.; Ma Y.; Feng X.; Hu S.; Zhou J.; Cheng S.; Gao Y. Identification of differentially expressed genes in human lung squamous cell carcinoma using suppression subtractive hybridization. Cancer Lett. 2004, 212, 83–93. 10.1016/j.canlet.2004.03.023. PubMed DOI

Serão N. V.; Delfino K. R.; Southey B. R.; Beever J. E.; Rodriguez-Zas S. L. Cell cycle and aging, morphogenesis, and response to stimuli genes are individualized biomarkers of glioblastoma progression and survival. BMC Med. Genomics 2011, 4, 4910.1186/1755-8794-4-49. PubMed DOI PMC

Cifola I.; Pietrelli A.; Consolandi C.; Severgnini M.; Mangano E.; Russo V.; De Bellis G.; Battaglia C. Comprehensive genomic characterization of cutaneous malignant melanoma cell lines derived from metastatic lesions by whole-exome sequencing and SNP array profiling. PLoS One 2013, 8, e6359710.1371/journal.pone.0063597. PubMed DOI PMC

Eißmann M.; Schwamb B.; Melzer I. M.; Moser J.; Siele D.; Kohl U.; Rieker R. J.; Wachter D. L.; Agaimy A.; Herpel E.; Baumgarten P.; Mittelbronn M.; Rakel S.; Kogel D.; Bohm S.; Gutschner T.; Diederichs S.; Zornig M. A functional yeast survival screen of tumor-derived cDNA libraries designed to identify anti-apoptotic mammalian oncogenes. PLoS One 2013, 8, e6487310.1371/journal.pone.0064873. PubMed DOI PMC

Barfeld S. J.; Fazli L.; Persson M.; Marjavaara L.; Urbanucci A.; Kaukoniemi K. M.; Rennie P. S.; Ceder Y.; Chabes A.; Visakorpi T.; Mills I. G. Myc-dependent purine biosynthesis affects nucleolar stress and therapy response in prostate cancer. Oncotarget 2015, 6, 12587–12602. 10.18632/oncotarget.3494. PubMed DOI PMC

Goswami M. T.; Chen G.; Chakravarthi B. V.; Pathi S. S.; Anand S. K.; Carskadon S. L.; Giordano T. J.; Chinnaiyan A. M.; Thomas D. G.; Palanisamy N.; Beer D. G.; Varambally S. Role and regulation of coordinately expressed de novo purine biosynthetic enzymes PPAT and PAICS in lung cancer. Oncotarget 2015, 6, 23445–23461. 10.18632/oncotarget.4352. PubMed DOI PMC

Chakravarthi B. V. S. K.; Goswami M. T.; Pathi S. S.; Dodson M.; Chandrashekar D. S.; Agarwal S.; Nepal S.; Hodigere Balasubramanya S. A.; Siddiqui J.; Lonigro R. J.; Chinnaiyan A. M.; Kunju L. P.; Palanisamy N.; Varambally S. Expression and role of PAICS, a de novo purine biosynthetic gene in prostate cancer. Prostate 2017, 77, 10–21. 10.1002/pros.23243. PubMed DOI

Meng M.; Chen Y.; Jia J.; Li L.; Yang S. Knockdown of PAICS inhibits malignant proliferation of human breast cancer cell lines. Biol. Res. 2018, 51, 24.10.1186/s40659-018-0172-9. PubMed DOI PMC

Chakravarthi B.; Rodriguez Pena M. D. C.; Agarwal S.; Chandrashekar D. S.; Hodigere Balasubramanya S. A.; Jabboure F. J.; Matoso A.; Bivalacqua T. J.; Rezaei K.; Chaux A.; Grizzle W. E.; Sonpavde G.; Gordetsky J.; Netto G. J.; Varambally S. A. Role for de novo purine metabolic enzyme PAICS in bladder cancer progression. Neoplasia 2018, 20, 894–904. 10.1016/j.neo.2018.07.006. PubMed DOI PMC

Zhou S.; Yan Y.; Chen X.; Wang X.; Zeng S.; Qian L.; Wei J.; Yang X.; Zhou Y.; Gong Z.; Xu Z. Roles of highly expressed PAICS in lung adenocarcinoma. Gene 2019, 692, 1–8. 10.1016/j.gene.2018.12.064. PubMed DOI

Huang Q.; Liu F.; Shen J. Bioinformatic validation identifies candidate key genes in diffuse large-B cell lymphoma. Pers. Med. 2019, 16, 313–323. 10.2217/pme-2018-0068. PubMed DOI

Agarwal S.; Chakravarthi B.; Kim H. G.; Gupta N.; Hale K.; Balasubramanya S. A. H.; Oliver P. G.; Thomas D. G.; Eltoum I. A.; Buchsbaum D. J.; Manne U.; Varambally S. PAICS, a de novo purine biosynthetic enzyme, is overexpressed in pancreatic cancer and is involved in its progression. Transl. Oncol. 2020, 13, 10077610.1016/j.tranon.2020.100776. PubMed DOI PMC

Gallenne T.; Ross K. N.; Visser N. L.; Salony; Desmet C. J.; Wittner B. S.; Wessels L. F. A.; Ramaswamy S.; Peeper D. S. Systematic functional perturbations uncover a prognostic genetic network driving human breast cancer. Oncotarget 2017, 8, 20572–20587. 10.18632/oncotarget.16244. PubMed DOI PMC

Agarwal S.; Chakravarthi B.; Behring M.; Kim H. G.; Chandrashekar D. S.; Gupta N.; Bajpai P.; Elkholy A.; Balasubramanya S. A. H.; Hardy C.; Diffalha S. A.; Varambally S.; Manne U. PAICS, a purine nucleotide metabolic enzyme, is involved in tumor growth and the metastasis of colorectal cancer. Cancers 2020, 12, 77210.3390/cancers12040772. PubMed DOI PMC

Huang N.; Xu C.; Deng L.; Li X.; Bian Z.; Zhang Y.; Long S.; Chen Y.; Zhen N.; Li G.; Sun F. PAICS contributes to gastric carcinogenesis and participates in DNA damage response by interacting with histone deacetylase 1/2. Cell Death Dis. 2020, 11, 50710.1038/s41419-020-2708-5. PubMed DOI PMC

Cheung C. H. Y.; Hsu C. L.; Tsuei C. Y.; Kuo T. T.; Huang C. T.; Hsu W. M.; Chung Y. H.; Wu H. Y.; Hsu C. C.; Huang H. C.; Juan H. F. Combinatorial targeting of MTHFD2 and PAICS in purine synthesis as a novel therapeutic strategy. Cell Death Dis. 2019, 10, 78610.1038/s41419-019-2033-z. PubMed DOI PMC

Yamauchi T.; Miyawaki K.; Semba Y.; Takahashi M.; Izumi Y.; Nogami J.; Nakao F.; Sugio T.; Sasaki K.; Pinello L.; Bauer D. E.; Bamba T.; Akashi K.; Maeda T. Targeting leukemia-specific dependence on the de novo purine synthesis pathway. Leukemia 2022, 36, 383–393. 10.1038/s41375-021-01369-0. PubMed DOI

Mackenzie G.; Shaw G.; Thomas S. E. Synthesis of analogues of 5-aminoimidazole ribonucleotides and their effects as inhibitors and substrates of the enzymes, phosphoribosylaminoimidazole carboxylase and phosphoribosylaminoimidazolesuccinocarboxamide synthetase involved in the biosynthesis of purine nucleotides de novo. J. Chem. Soc., Chem. Commun. 1976, 12, 453–455. 10.1039/C39760000453. DOI

Firestine S. M.; Jo Davisson V. A tight binding inhibitor of 5-aminoimidazole ribonucleotide carboxylase. J. Med. Chem. 1993, 36, 3484–3486. 10.1021/jm00074a033. PubMed DOI

Firestine S. M.; Wu W.; Youn H.; Jo Davisson V. Interrogating the mechanism of a tight binding inhibitor of AIR carboxylase. Bioorg. Med. Chem. 2009, 17, 794–803. 10.1016/j.bmc.2008.11.057. PubMed DOI PMC

Ravi G. R. R.; Biswal J.; Kanagarajan S.; Jeyakanthan J. Exploration of N5-CAIR mutase novel inhibitors from Pyrococcus horikoshii OT3: a computational study. J. Comput. Biol. 2019, 26, 457–472. 10.1089/cmb.2018.0248. PubMed DOI

Streeter C. C.; Lin Q.; Firestine S. M. Isatins inhibit N5-CAIR synthetase by a substrate depletion mechanism. Biochemistry 2019, 58, 2260–2268. 10.1021/acs.biochem.8b00939. PubMed DOI PMC

Charoensutthivarakul S.; Thomas S. E.; Curran A.; Brown K. P.; Belardinelli J. M.; Whitehouse A. J.; Acebrón-García-de-Eulate M.; Sangan J.; Gramani S. G.; Jackson M.; Mendes V.; Andres Floto R.; Blundell T. L.; Coyne A. G.; Abell C. Development of inhibitors of SAICAR synthetase (PurC) from Mycobacterium abscessus using a fragment-based approach. ACS Infect. Dis. 2022, 8, 296–309. 10.1021/acsinfecdis.1c00432. PubMed DOI PMC

Firestine S. M.; Jo Davisson V. Carboxylases in de novo purine biosynthesis. Characterization of the Gallus gallus bifunctional enzyme. Biochemistry 1994, 33, 11917–11926. 10.1021/bi00205a030. PubMed DOI

Firestine S. M.; Poon S. W.; Mueller E. J.; Stubbe J.; Jo Davisson V. Reactions catalyzed by 5-aminoimidazole ribonucleotide carboxylases from Escherichia coli and Gallus gallus: a case for divergent catalytic mechanisms. Biochemistry 1994, 33, 11927–11934. 10.1021/bi00205a031. PubMed DOI

Mueller E. J.; Meyer E.; Rudolph J.; Jo Davisson V.; Stubbe J. N5-carboxyaminoimidazole ribonucleotide: evidence for a new intermediate and two new enzymatic activities in the de novo purine biosynthetic pathway of Escherichia coli. Biochemistry 1994, 33, 2269–2278. 10.1021/bi00174a038. PubMed DOI

Meyer E.; Kappock T. J.; Osuji C.; Stubbe J. Evidence for the direct transfer of the carboxylate of N5-carboxyaminoimidazole ribonucleotide (N5-CAIR) to generate 4-carboxy-5-aminoimidazole ribonucleotide catalyzed by Escherichia coli PurE, an N5-CAIR mutase. Biochemistry 1999, 38, 3012–3018. 10.1021/bi9827159. PubMed DOI

Levdikov V. M.; Barynin V. V.; Grebenko A. I.; Melik-Adamyan W. R.; Lamzin V. S.; Wilson K. S. The structure of SAICAR synthase: an enzyme in the de novo pathway of purine nucleotide biosynthesis. Structure 1998, 6, 363–376. 10.1016/S0969-2126(98)00038-0. PubMed DOI

Mathews I. I.; Kappock T. J.; Stubbe J.; Ealick S. E. Crystal structure of Escherichia coli PurE, an unusual mutase in the purine biosynthetic pathway. Structure 1999, 7, 1395–1406. 10.1016/S0969-2126(00)80029-5. PubMed DOI

Antonyuk S. V.; Grebenko A. I.; Levdikov V. M.; Urusova D. V.; Melik-Adamyan V. R.; Lamzin V. S.; Wilson K. S. X-ray diffraction study of the complexes of SAICAR synthase with adenosinetriphosphate. Crystallogr. Rep. 2001, 46, 620–625. 10.1134/1.1387127. DOI

Urusova D. V.; Antonyuk S. V.; Grebenko A. I.; Lamzin V. S.; Melik-Adamyan V. R. X-ray diffraction study of the complex of the enzyme SAICAR synthase with substrate analogues. Crystallogr. Rep. 2003, 48, 763–767. 10.1134/1.1612597. DOI

Schwarzenbacher R.; Jaroszewski L.; von Delft F.; Abdubek P.; Ambing E.; Biorac T.; Brinen L. S.; Canaves J. M.; Cambell J.; Chiu H. J.; Dai X.; Deacon A. M.; Di Donato M.; Elsliger M. A.; Eshagi S.; Floyd R.; Godzik A.; Grittini C.; Grzechnik S. K.; Hampton E.; Karlak C.; Klock H. E.; Koesema E.; Kovarik J. S.; Kreusch A.; Kuhn P.; Lesley S. A.; Levin I.; McMullan D.; McPhillips T. M.; Miller M. D.; Morse A.; Moy K.; Ouyang J.; Page R.; Quijano K.; Robb A.; Spraggon G.; Stevens R. C.; van den Bedem H.; Velasquez J.; Vincent J.; Wang X.; West B.; Wolf G.; Xu Q.; Hodgson K. O.; Wooley J.; Wilson I. A. Crystal structure of a phosphoribosylaminoimidazole mutase PurE (TM0446) from Thermotoga maritima at 1.77-A resolution. Proteins 2004, 55, 474–478. 10.1002/prot.20023. PubMed DOI

Settembre E. C.; Chittuluru J. R.; Mill C. P.; Kappock T. J.; Ealick S. E. Acidophilic adaptations in the structure of Acetobacter aceti N5-carboxyaminoimidazole ribonucleotide mutase (PurE). Acta Crystallogr., Sect. D: Biol. Crystallogr. 2004, 60, 1753–1760. 10.1107/S090744490401858X. PubMed DOI

Boyle M. P.; Kalliomaa A. K.; Levdikov V.; Blagova E.; Fogg M. J.; Brannigan J. A.; Wilson K. S.; Wilkinson A. J. Crystal structure of PurE (BA0288) from Bacillus anthracis at 1.8 A resolution. Proteins 2005, 61, 674–676. 10.1002/prot.20599. PubMed DOI

Constantine C. Z.; Starks C. M.; Mill C. P.; Ransome A. E.; Karpowicz S. J.; Francois J. A.; Goodman R. A.; Kappock T. J. Biochemical and structural studies of N5-carboxyaminoimidazole ribonucleotide mutase from the acidophilic bacterium Acetobacter aceti. Biochemistry 2006, 45, 8193–8208. 10.1021/bi060465n. PubMed DOI

Zhang R.; Skarina T.; Evdokimova E.; Edwards A.; Savchenko A.; Laskowski R.; Cuff M. E.; Joachimiak A. Structure of SAICAR synthase from Thermotoga maritima at 2.2 angstroms reveals an unusual covalent dimer. Acta Crystallogr., Sect. F: Struct. Biol. Cryst. Commun. 2006, 62, 335–339. 10.1107/S1744309106009651. PubMed DOI PMC

Ginder N. D.; Binkowski D. J.; Fromm H. J.; Honzatko R. B. Nucleotide complexes of Escherichia coli phosphoribosylaminoimidazole succinocarboxamide synthetase. J. Biol. Chem. 2006, 281, 20680–20688. 10.1074/jbc.M602109200. PubMed DOI

Urusova D. V.; Levdikov V. M.; Antonyuk S. V.; Grebenko A. I.; Lamzin V. S.; Melik-Adamyan V. R. X-ray diffraction study of the complex of the enzyme SAICAR synthase with the reaction product. Crystallogr. Rep. 2006, 51, 824–827. 10.1134/S1063774506050129. DOI

Hoskins A. A.; Morar M.; Kappock T. J.; Mathews I. I.; Zaugg J. B.; Barder T. E.; Peng P.; Okamoto A.; Ealick S. E.; Stubbe J. N5-CAIR mutase: role of a CO2 binding site and substrate movement in catalysis. Biochemistry 2007, 46, 2842–2855. 10.1021/bi602436g. PubMed DOI PMC

Li S. X.; Tong Y. P.; Xie X. C.; Wang Q. H.; Zhou H. N.; Han Y.; Zhang Z. Y.; Gao W.; Li S. G.; Zhang X. C.; Bi R. C. Octameric structure of the human bifunctional enzyme PAICS in purine biosynthesis. J. Mol. Biol. 2007, 366, 1603–1614. 10.1016/j.jmb.2006.12.027. PubMed DOI

Brugarolas P.; Duguid E. M.; Zhang W.; Poor C. B.; He C. Structural and biochemical characterization of N5-carboxyaminoimidazole ribonucleotide synthetase and N5-carboxyaminoimidazole ribonucleotide mutase from Staphylococcus aureus. Acta Crystallogr., Sect. D: Biol. Crystallogr. 2011, 67, 707–715. 10.1107/S0907444911023821. PubMed DOI PMC

Tranchimand S.; Starks C. M.; Mathews I. I.; Hockings S. C.; Kappock T. J. Treponema denticola PurE is a bacterial AIR carboxylase. Biochemistry 2011, 50, 4623–4637. 10.1021/bi102033a. PubMed DOI

Oliete R.; Pous J.; Rodriguez-Puente S.; Abad-Zapatero C.; Guasch A. Elastic and inelastic diffraction changes upon variation of the relative humidity environment of PurE crystals. Acta Crystallogr., Sect. D: Biol. Crystallogr. 2013, 69, 194–212. 10.1107/S090744491204454X. PubMed DOI

Taschner M.; Basquin J.; Benda C.; Lorentzen E. Crystal structure of the invertebrate bifunctional purine biosynthesis enzyme PAICS at 2.8 A resolution. Proteins 2013, 81, 1473–1478. 10.1002/prot.24296. PubMed DOI

Manjunath K.; Kanaujia S. P.; Kanagaraj S.; Jeyakanthan J.; Sekar K. Structure of SAICAR synthetase from Pyrococcus horikoshii OT3: insights into thermal stability. Int. J. Biol. Macromol. 2013, 53, 7–19. 10.1016/j.ijbiomac.2012.10.028. PubMed DOI

Wolf N. M.; Abad-Zapatero C.; Johnson M. E.; Fung L. W. Structures of SAICAR synthetase (PurC) from Streptococcus pneumoniae with ADP, Mg2+, AIR and Asp. Acta Crystallogr., Sect. D: Biol. Crystallogr. 2014, 70, 841–850. 10.1107/S139900471303366X. PubMed DOI

Franklin M. C.; Cheung J.; Rudolph M. J.; Burshteyn F.; Cassidy M.; Gary E.; Hillerich B.; Yao Z. K.; Carlier P. R.; Totrov M.; Love J. D. Structural genomics for drug design against the pathogen Coxiella burnetii. Proteins 2015, 83, 2124–2136. 10.1002/prot.24841. PubMed DOI

Škerlová J.; Unterlass J.; Gottmann M.; Marttila P.; Homan E.; Helleday T.; Jemth A. S.; Stenmark P. Crystal structures of human PAICS reveal substrate and product binding of an emerging cancer target. J. Biol. Chem. 2020, 295, 11656–11668. 10.1074/jbc.RA120.013695. PubMed DOI PMC

Firestine S. M.; Wu W.; Youn H.; Jo Davisson V. Interrogating the mechanism of a tight binding inhibitor of AIR carboxylase. Bioorg. Med. Chem. 2009, 17, 794–803. 10.1016/j.bmc.2008.11.057. PubMed DOI PMC

Nelson S. W.; Binkowski D. J.; Honzatko R. B.; Fromm H. J. Mechanism of action of Escherichia coli phosphoribosylaminoimidazolesuccinocarboxamide synthetase. Biochemistry. 2005, 44, 766–774. 10.1021/bi048191w. PubMed DOI

Siegbahn P. E. M.; Himo F. The quantum chemical cluster approach for modeling enzyme reactions. Wiley Interdiscip. Rev.: Comput. Mol. Sci. 2011, 1, 323–336. 10.1002/wcms.13. DOI

Blomberg M. R. A.; Borowski T.; Himo F.; Liao R.-Z.; Siegbahn P. E. M. Quantum chemical studies of mechanisms for metalloenzymes. Chem. Rev. 2014, 114, 3601–3658. 10.1021/cr400388t. PubMed DOI

Himo F. Recent trends in quantum chemical modeling of enzymatic reactions. J. Am. Chem. Soc. 2017, 139, 6780–6786. 10.1021/jacs.7b02671. PubMed DOI

Sheng X.; Kazemi M.; Planas F.; Himo F. Modeling enzymatic enantioselectivity using quantum chemical methodology. ACS Catal. 2020, 10, 6430–6449. 10.1021/acscatal.0c00983. DOI

Sheng X.; Himo F. Mechanisms of metal-dependent non-redox decarboxylases from quantum chemical calculations. Comput. Struct. Biotechnol. J. 2021, 19, 3176–3186. 10.1016/j.csbj.2021.05.044. PubMed DOI PMC

Lee C.; Yang W.; Parr R. G. Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density. Phys. Rev. B: Condens. Matter Mater. Phys. 1988, 37, 785–789. 10.1103/PhysRevB.37.785. PubMed DOI

Becke A. D. Density-functional thermochemistry. III. The role of exact exchange. J. Chem. Phys. 1993, 98, 5648–5652. 10.1063/1.464913. DOI

Grimme S.; Antony J.; Ehrlich S.; Krieg H. A consistent and accurate ab initio parametrization of density functional dispersion correction (DFT-D) for the 94 elements H-Pu. J. Chem. Phys. 2010, 132, 15410410.1063/1.3382344. PubMed DOI

Grimme S.; Ehrlich S.; Goerigk L. Effect of the damping function in dispersion corrected density functional theory. J. Comput. Chem. 2011, 32, 1456–1465. 10.1002/jcc.21759. PubMed DOI

Frisch M. J.; Trucks G. W.; Schlegel H. B.; Scuseria G. E.; Robb M. A.; Cheeseman J. R.; Scalmani G.; Barone V.; Petersson G. A.; Nakatsuji H.; Li X.; Caricato M.; Marenich A. V.; Bloino J.; Janesko B. G.; Gomperts R.; Mennucci B.; Hratchian H. P.; Ortiz J. V.; Izmaylov A. F.; Sonnenberg J. L.; Williams-Young D.; Ding F.; Lipparini F.; Egidi F.; Goings J.; Peng B.; Petrone A.; Henderson T.; Ranasinghe D.; Zakrzewski V. G.; Gao J.; Rega N.; Zheng G.; Liang W.; Hada M.; Ehara M.; Toyota K.; Fukuda R.; Hasegawa J.; Ishida M.; Nakajima T.; Honda Y.; Kitao O.; Nakai H.; Vreven T.; Throssell K.; Montgomery J. A. Jr.; Peralta J. E.; Ogliaro F.; Bearpark M. J.; Heyd J. J.; Brothers E. N.; Kudin K. N.; Staroverov V. N.; Keith T. A.; Kobayashi R.; Normand J.; Raghavachari K.; Rendell A. P.; Burant J. C.; Iyengar S. S.; Tomasi J.; Cossi M.; Millam J. M.; Klene M.; Adamo C.; Cammi R.; Ochterski J. W.; Martin R. L.; Morokuma K.; Farkas O.; Foresman J. B.; Fox D. J.. Gaussian 16, revision 01,C; Gaussian, Inc.: Wallingford CT, 2016.

Wadt W. R.; Hay P. J. Ab initio effective core potentials for molecular calculations–potentials for main group elements Na to Bi. J. Chem. Phys. 1985, 82, 284–298. 10.1063/1.448800. DOI

Marenich A. V.; Cramer C. J.; Truhlar D. G. Universal solvation model based on solute electron density and on a continuum model of the solvent defined by the bulk dielectric constant and atomic surface tensions. J. Phys. Chem. B 2009, 113, 6378–6396. 10.1021/jp810292n. PubMed DOI

Blomberg M. R. A.; Siegbahn P. E. M. Mechanism for N2O generation in bacterial nitric oxide reductase: a quantum chemical study. Biochemistry 2012, 51, 5173–5186. 10.1021/bi300496e. PubMed DOI

Sheng X.; Lind M. E. S.; Himo F. Theoretical study of the reaction mechanism of phenolic acid decarboxylase. FEBS J. 2015, 282, 4703–4713. 10.1111/febs.13525. PubMed DOI

Sheng X.; Zhu W.; Huddleston J. P.; Xiang D. F.; Raushel F. M.; Richards N. G. J.; Himo F. A combined experimental-theoretical study of the LigW-catalyzed decarboxylation of 5-Carboxyvanillate in the metabolic pathway for lignin degradation. ACS Catal. 2017, 7, 4968–4974. 10.1021/acscatal.7b01166. DOI

Planas F.; Sheng X.; McLeish M. J.; Himo F. A theoretical study of the benzoylformate decarboxylase reaction mechanism. Front. Chem. 2018, 6, 20510.3389/fchem.2018.00205. PubMed DOI PMC

Sheng X.; Himo F. Mechanism of 3-methylglutaconyl CoA decarboxylase AibA/AibB: Pericyclic reaction versus direct decarboxylation. Angew. Chem. 2020, 132, 23173–23177. 10.1002/anie.202008919. PubMed DOI PMC

Litchfield G. J.; Shaw G. Purines, pyrimidines, and imidazoles. Part XXXVIII. A kinetics study of the decarboxylation of 5-amino-1-β-D-ribofuranosylimidazole-4-carboxylic acid 5′-phosphate and related compounds. J. Chem. Soc. B 1971, 0, 1474–1484. 10.1039/J29710001474. DOI

Chen Z. D.; Dixon J. E.; Zalkin H. Cloning of a chicken liver cDNA encoding 5-aminoimidazole ribonucleotide carboxylase and 5-aminoimidazole-4-N-succinocarboxamide ribonucleotide synthetase by functional complementation of Escherichia colipur mutants. Proc. Natl. Acad. Sci. U.S.A. 1990, 87, 3097–3101. 10.1073/pnas.87.8.3097. PubMed DOI PMC

Litchfield G. J.; Shaw G. The mechanism of decarboxylation of some 5-aminoimidazole-4-carboxylic acids and the influence of transition metals. Chem. Commun. 1965, 563–565. 10.1039/c19650000563. DOI

Huang X.; Holden H. M.; Raushel F. M. Channeling of substrates and intermediates in enzyme-catalyzed reactions. Annu. Rev. Biochem. 2001, 70, 149–180. 10.1146/annurev.biochem.70.1.149. PubMed DOI

Wang H.; DeRose E. F.; London R. E.; Shears S. B. P6K structure and the molecular determinants of catalytic specificity in an inositol phosphate kinase family. Nat. Commun. 2014, 5, 417810.1038/ncomms5178. PubMed DOI PMC

Wang H.; Shears S. B. Structural features of human inositol phosphate multikinase rationalize its inositol phosphate kinase and phosphoinositide 3-kinase activities. J. Biol. Chem. 2017, 292, 18192–18202. 10.1074/jbc.M117.801845. PubMed DOI PMC

Binkowski D. J.Kinetic studies of Escherichia coli and human SAICAR synthetase. PhD thesis, Iowa State University, Ames, Iowa, USA, 2007.