5-Aminoimidazole ribotide explained

5′-Phosphoribosyl-5-aminoimidazole (or aminoimidazole ribotide, AIR) is a biochemical intermediate in the formation of purine nucleotides via inosine-5-monophosphate, and hence is a building block for DNA and RNA.[1] The vitamins thiamine[2] [3] and cobalamin[4] also contain fragments derived from AIR.[5] It is an intermediate in the adenine pathway and is synthesized from 5′-phosphoribosylformylglycinamidine by AIR synthetase.[6]

Chemistry

5-aminoimidazole derivatives were considered unstable and therefore difficult to synthesize. The first non-enzymatic synthesis of 5-aminoimidazole ribotide (AIR) was only published in 1988[7] and general methodology for other examples was developed in the 1990s.[8] [9]

Biosynthesis

The furanose (5-carbon) sugar in AIR comes from the pentose phosphate pathway, which converts glucose (as its 6-phosphate derivative) into ribose 5-phosphate (R5P).[10] The subsequent reactions which attach the aminoimidazole portion of the molecule begin when R5P is activated as its pyrophosphate derivative, phosphoribosyl pyrophosphate (PRPP). This reaction is catalysed by ribose-phosphate diphosphokinase.[11]

Five biosynthetic steps complete the transformation.[1] [12] The first enzyme, amidophosphoribosyltransferase, attaches ammonia from glutamine to the ribotide at its anomeric carbon, forming phosphoribosylamine (PRA):

+ → + + PPiNext, PRA is converted to glycineamide ribonucleotide (GAR) by the action of phosphoribosylamine—glycine ligase, forming an amide bond with glycine in a process driven by ATP:

+ + ATP → + ADP + PiA third enzyme, phosphoribosylglycinamide formyltransferase, adds a formyl group from 10-formyltetrahydrofolate to GAR, giving phosphoribosyl-N-formylglycineamide (FGAR):

GAR + 10-formyltetrahydrofolate → FGAR + tetrahydrofolateThe penultimate step converts FGAR to an amidine by the action of phosphoribosylformylglycinamidine synthase, transferring an amino group from glutamine and giving 5′-phosphoribosylformylglycinamidine (FGAM) in a reaction that also requires ATP:

FGAR + ATP + glutamine + H2O → FGAM + ADP + glutamate + PiFGAM is finally converted to AIR by the action of AIR synthetase which uses ATP to activate the terminal carbonyl group to attack by the nitrogen atom at the anomeric centre:

FGAM + ATP → AIR + ADP + Pi + H+

Use as an intermediate in biosynthesis

Purines

The purine ring system of the nucleotide inosine monophosphate is formed in a pathway from AIR[13] that begins when phosphoribosylaminoimidazole carboxylase converts it to the carboxylated derivative in the imidazole ring, 5′-phosphoribosyl-4-carboxy-5-aminoimidazole (CAIR).[14]

AIR + CO2 → CAIR + 2 H+

The same compound can be formed in a two-step pathway when the enzymes involved are 5-(carboxyamino)imidazole ribonucleotide synthase and 5-(carboxyamino)imidazole ribonucleotide mutase.[14]

Radical SAM reactions

Rearrangement reactions starting from AIR incorporate portions of the molecule into additional biochemical pathways. The enzymes involved are in the radical SAM superfamily of iron–sulfur proteins, which use S-adenosyl methionine as a cofactor to initiate the conversions via radical intermediates.[15] [5]

Thiamine

The vitamin thiamine contains a pyrimidine ring system which is formed from AIR in a reaction catalysed by phosphomethylpyrimidine synthase.[2] [16]

This reaction incorporates the blue, green and red fragments shown into the product, 4-amino-5-hydroxymethyl-2-methylpyrimidine phosphate.[3] [17]

5-Hydroxybenzimidazole

In some anaerobes, AIR is a precursor to 5,6-dimethylbenzimidazole, which is incorporated into vitamin B12 in later steps of cobalamin biosynthesis.[5] [18] The initial reaction is catalysed by 5-hydroxybenzimidazole synthase,, and forms 5-hydroxybenzimidazole:

All the carbon atoms of the product are transferred from AIR, as shown.[4] [5]

Notes and References

  1. Web site: Pathway: inosine-5'-phosphate biosynthesis I . R. Caspi . MetaCyc Metabolic Pathway Database . 2009-01-13 . 2022-02-02 .
  2. Web site: Pathway: superpathway of thiamine diphosphate biosynthesis I . R. Caspi . MetaCyc Metabolic Pathway Database . 2011-09-14 . 2022-02-01 .
  3. 10.1002/anie.201003419 . A "Radical Dance" in Thiamin Biosynthesis: Mechanistic Analysis of the Bacterial Hydroxymethylpyrimidine Phosphate Synthase . 2010 . Chatterjee . Abhishek . Hazra . Amrita B. . Abdelwahed . Sameh . Hilmey . David G. . Begley . Tadhg P. . Angewandte Chemie International Edition . 49 . 46 . 8653–8656 . 20886485 . 3147014 .
  4. Web site: Pathway: 5-hydroxybenzimidazole biosynthesis (anaerobic) . R. Caspi . MetaCyc Metabolic Pathway Database . 2019-09-23 . 2022-02-10 .
  5. 10.1021/jacs.5b03576 . Anaerobic 5-Hydroxybenzimidazole Formation from Aminoimidazole Ribotide: An Unanticipated Intersection of Thiamin and Vitamin B12 Biosynthesis . 2015 . Mehta . Angad P. . Abdelwahed . Sameh H. . Fenwick . Michael K. . Hazra . Amrita B. . Taga . Michiko E. . Zhang . Yang . Ealick . Steven E. . Begley . Tadhg P. . Journal of the American Chemical Society . 137 . 33 . 10444–10447 . 26237670 . 4753784 .
  6. 10.1021/ja00168a039. Nonenzymatic synthesis and properties of 5-aminoimidazole ribonucleotide (AIR). Synthesis of specifically 15N-labeled 5-aminoimidazole ribonucleoside (AIRs) derivatives. Journal of the American Chemical Society. 112. 12. 4891–4897. 1990. Bhat. Balkrishen. Groziak. Michael P.. Leonard. Nelson J..
  7. 10.1073/pnas.85.19.7174 . Nonenzymatic synthesis of 5-aminoimidazole ribonucleoside and recognition of its facile rearrangement . 1988 . Groziak . M. P. . Bhat . B. . Leonard . N. J. . Proceedings of the National Academy of Sciences . 85 . 19 . 7174–7176 . 3174626 . 282146 . 1988PNAS...85.7174G . free .
  8. 10.1039/P19920002779 . Preparation, structure and addition reactions of 4- and 5-aminoimidazoles . 1992 . Al-Shaar . Adnan H. M. . Gilmour . David W. . Lythgoe . David J. . McClenaghan . Ian . Ramsden . Christopher A. . Journal of the Chemical Society, Perkin Transactions 1 . 21 . 2779–2788 .
  9. 10.1039/P19920002789 . The synthesis of heterocycles via addition–elimination reactions of 4- and 5-aminoimidazoles . 1992 . Al-Shaar . Adnan H. M. . Chambers . Robert K. . Gilmour . David W. . Lythgoe . David J. . McClenaghan . Ian . Ramsden . Christopher A. . J. Chem. Soc., Perkin Trans. 1 . 21 . 2789–2811 .
  10. Alfarouk . Khalid O. . Ahmed . Samrein B. M. . Elliott . Robert L. . Benoit . Amanda . Alqahtani . Saad S. . Ibrahim . Muntaser E. . Bashir . Adil H. H. . Alhoufie . Sari T. S. . Elhassan . Gamal O. . Wales . Christian C. . Schwartz . Laurent H. . Ali . Heyam S. . Ahmed . Ahmed . Forde . Patrick F. . Devesa . Jesus . Cardone . Rosa A. . Fais . Stefano . Harguindey . Salvador . Reshkin . Stephan J. . The Pentose Phosphate Pathway Dynamics in Cancer and Its Dependency on Intracellular pH . Metabolites . 2020 . 10 . 7 . 285 . 10.3390/metabo10070285 . 32664469 . 7407102 . en. free .
  11. Li . Sheng . Lu . Yongcheng . Peng . Baozhen . Ding . Jianping . Crystal structure of human phosphoribosylpyrophosphate synthetase 1 reveals a novel allosteric site . Biochemical Journal . 401 . 1 . 39–47 . January 2007 . 16939420 . 1698673 . 10.1042/BJ20061066 .
  12. 10.1007/s00018-008-8295-8 . Zhang . Y. . Morar . M. . Ealick . S.E. . Structural biology of the purine biosynthetic pathway . Cellular and Molecular Life Sciences . 65 . 3699–3724 . 2008 . 23 . 18712276 . 2596281 .
  13. Book: 10.1007/978-981-16-0723-3_19 . Nucleotide Biosynthesis and Regulation . Fundamentals of Bacterial Physiology and Metabolism . 2021 . Gupta . Rani . Gupta . Namita . 525–554 . 978-981-16-0722-6 . 234897784 .
  14. 10.1016/S0969-2126(00)80029-5 . Ealick . Steven E. . Stubbe . JoAnne . Kappock . T. Joseph . Mathews . Irimpan I. . Crystal structure of Escherichia coli PurE, an unusual mutase in the purine biosynthetic pathway . Structure . 7 . 11 . 1395–1406 . 1999 . 10574791. free .
  15. Book: 10.1016/bs.mie.2018.06.004 . Atlas of the Radical SAM Superfamily: Divergent Evolution of Function Using a "Plug and Play" Domain . Radical SAM Enzymes . Methods in Enzymology . 2018 . Holliday . Gemma L. . Akiva . Eyal . Meng . Elaine C. . Brown . Shoshana D. . Calhoun . Sara . Pieper . Ursula . Sali . Andrej . Booker . Squire J. . Babbitt . Patricia C. . 606 . 1–71 . 30097089 . 6445391 . 9780128127940 .
  16. 10.1039/C1NP00036E . Radical S-adenosylmethionine enzymes: Mechanism, control and function . 2011 . Challand . Martin R. . Driesener . Rebecca C. . Roach . Peter L. . Natural Product Reports . 28 . 10 . 1709–1710 . 21779595 .
  17. 10.1039/b207131m . Cofactor biosynthesis: An organic chemist's treasure trove . 2006 . Begley . Tadhg P. . Natural Product Reports . 23 . 1 . 15–18 . 16453030 .
  18. 10.1126/science.aba0165 . Sharing vitamins: Cobamides unveil microbial interactions . 2020 . Sokolovskaya . Olga M. . Shelton . Amanda N. . Taga . Michiko E. . Science . 369 . 6499 . 32631870 . 8654454 .

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