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Inosine-5′-monophosphate dehydrogenase

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Inosine 5'-monophosphate dehydrogenase
Structure of IMPDH[1]
Identifiers
EC no.1.1.1.205
CAS no.9028-93-7
Databases
IntEnzIntEnz view
BRENDABRENDA entry
ExPASyNiceZyme view
KEGGKEGG entry
MetaCycmetabolic pathway
PRIAMprofile
PDB structuresRCSB PDB PDBe PDBsum
Gene OntologyAmiGO / QuickGO
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NCBIproteins

Inosine 5′-monophosphate dehydrogenase (IMPDH) is a purine biosynthetic enzyme that catalyzes the nicotinamide adenine dinucleotide (NAD+)-dependent oxidation of inosine monophosphate (IMP) to xanthosine monophosphate (XMP), the first committed and rate-limiting step towards the de novo biosynthesis of guanine nucleotides from IMP.[2][3] IMPDH is a regulator of the intracellular guanine nucleotide pool, and is therefore important for DNA and RNA synthesis, signal transduction, energy transfer, glycoprotein synthesis, as well as other process that are involved in cellular proliferation.

Structure and function

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The canonic monomeric form of IMPDH has a molecular masse of approximately 55 kDa[4] and generally consists of 400-500 residues.[5] IMPDHs have been described as tetrameric,[6][7][8] although further data validated the existence of octameric forms.[9]

Visual representation of the active site with IMP (green) and NAD (purple) bound.[10] Key residues (white) of the protein and the catalytic cysteine (cyan) are shown. Dashed lines represent polar contacts.

Most IMPDH monomers contain two domains: a catalytic (β/α)8 barrel domain with an active site located in the loops at the C-terminal end of the barrel, and a subdomain, named the Bateman domain, and consisting of two, repeated cystathionine beta synthetase (CBS) domains that are inserted within the dehydrogenase sequence.[5][11] Monovalent cations have been shown to activate most IMPDH enzymes and may serve to stabilize the conformation of the active-site loop.[12]

The Bateman domain is not required for catalytic activity. Mutations within the Bateman domain or a complete deletion of the domain do not impair the in vitro catalytic activity of some IMPDH .[13][14][15][16] Other deletion examples of the Bateman domain in IMPDH have shown an enhanced in vitro catalytic activity in comparison with the corresponding wild-type counterpart.[17] An in vivo deletion of the Bateman domain in E. coli suggests that the domain can act as a negative transregulator of adenine nucleotide synthesis.[18][19] IMPDH has also been shown to bind nucleic acids,[20][21] and this function can be impaired by mutations that are located in the Bateman domain.[22] The Bateman domain has also been implicated in mediating IMPDH association with polyribosomes,[23] which suggests a potential moonlighting role for IMPDH as a translational regulatory protein. In Staphylococcus aureus, IMPDH have been identified as a plasminogen-binding protein.[24] Drosophila IMPDH has been demonstrated to act as a sequence-specific transcriptional repressor that can reduce the expression of histone genes and E2F.[25] IMPDH localizes to the nucleus at the end of the S phase and nuclear accumulation is mostly restricted to the G2 phase. In addition, metabolic stress has been shown to induce the nuclear localization of IMPDH.[25]

Mechanism

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General mechanism used by the enzyme IMPDH to convert IMP to XMP. Only the purine portion of each molecule is shown.

The overall reaction catalyzed by IMPDH is:[26]

inosine 5'-phosphate + NAD+ + H2O xanthosine 5'-phosphate + NADH + H+

The mechanism of IMPDH involves a sequence of two different chemical reactions: (1) a fast redox reaction involving a hydride transfer to NAD+ which generates NADH and an enzyme-bound XMP intermediate (E-XMP*) and (2) a hydrolysis step that releases XMP from the enzyme. IMP binds to the active site and a conserved cysteine residue attacks the 2-position of the purine ring. A hydride ion is then transferred from the C2 position to NAD+ and the E-XMP* intermediate is formed. NADH dissociates from the enzyme and a mobile active-site flap element moves a conserved catalytic dyad of arginine and threonine into the newly unoccupied NAD binding site. The arginine residue is thought to act as the general base that activates a water molecule for the hydrolysis reaction.[5] Alternatively, molecular mechanics simulations suggest that in conditions where the arginine residue is protonated, the threonine residue is also capable of activating water by accepting a proton from water while transferring its own proton to a nearby residue.[27]

IMP dehydrogenase 1
Identifiers
SymbolIMPDH1
Alt. symbolsRP10
NCBI gene3614
HGNC6052
OMIM146690
RefSeqNM_000883
UniProtP20839
Other data
EC number1.1.1.205
LocusChr. 7 q31.3-q32
Search for
StructuresSwiss-model
DomainsInterPro

In humans

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IMP dehydrogenase 2
IMP dehydrogenase 2 homotetramer, Human
Identifiers
SymbolIMPDH2
Alt. symbolsIMPD2
NCBI gene3615
HGNC6053
OMIM146691
RefSeqNM_000884
UniProtP12268
Other data
EC number1.1.1.205
LocusChr. 3 p21.2
Search for
StructuresSwiss-model
DomainsInterPro

Humans express two distinct isozymes of IMPDH encoded by two distinct genes, IMPDH1 and IMPDH2.

Both isozymes contain 514 residues, have an 84% similarity in peptide sequence, and have similar kinetic properties.[28] Both isozymes are constitutively expressed in most tissues, but IMPDH1 is predominately expressed in the spleen, retina, and peripheral blood leukocytes.[5] IMPDH1 is generally expressed constitutively at low levels, and IMPDH2 is generally upregulated in proliferating cells and neoplastic tissues.[29][30][31] Homozygous IMPDH1 knockout mice demonstrate a mild retinopathy in which a slow, progressive form of retinal degeneration gradually weakens visual transduction,[32] while homozygous IMPDH2 knockout mice display embryonic lethality.[33]

Clinical significance

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Guanine nucleotide synthesis is essential for maintaining normal cell function and growth, and is also important for the maintenance of cell proliferation and immune responses. IMPDH expression is found to be upregulated in some tumor tissues and cell lines.[30] B and T lymphocytes display a dependence on IMPDH for normal activation and function,[34][35] and demonstrate upregulated IMPDH expression.[31] Therefore, IMPDH has been addressed as a drug target for immunosuppressive and cancer chemotherapy.

Mycophenolate is an immunosuppressant that is used to prevent transplant rejection and acts through inhibition of IMPDH.

Mutations in the Bateman domain of IMPDH1 are associated with the RP10 form of autosomal dominant retinitis pigmentosa and dominant Leber's congenital amaurosis.[22]

Research

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IMPDH inhibitors have been shown to prevent SARS-CoV-2 replication in cells[36] and are being tested in clinical trials for COVID-19.[37]

See also

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References

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  1. ^ Gan L, Seyedsayamdost MR, Shuto S, Matsuda A, Petsko GA, Hedstrom L (February 2003). "The immunosuppressive agent mizoribine monophosphate forms a transition state analogue complex with inosine monophosphate dehydrogenase". Biochemistry. 42 (4): 857–63. doi:10.1021/bi0271401. PMID 12549902.
  2. ^ Hedstrom, Lizbeth (2009-07-08). "IMP Dehydrogenase: Structure, Mechanism, and Inhibition". Chemical Reviews. 109 (7): 2903–2928. doi:10.1021/cr900021w. ISSN 0009-2665. PMC 2737513. PMID 19480389.
  3. ^ Ayoub, Nour; Gedeon, Antoine; Munier-Lehmann, Hélène (2024-02-20). "A journey into the regulatory secrets of the de novo purine nucleotide biosynthesis". Frontiers in Pharmacology. 15. doi:10.3389/fphar.2024.1329011. ISSN 1663-9812. PMC 10912719. PMID 38444943.
  4. ^ Sintchak MD, Nimmesgern E (May 2000). "The structure of inosine 5'-monophosphate dehydrogenase and the design of novel inhibitors". Immunopharmacology. 47 (2–3): 163–84. doi:10.1016/S0162-3109(00)00193-4. PMID 10878288.
  5. ^ a b c d Hedstrom L (July 2009). "IMP dehydrogenase: structure, mechanism, and inhibition". Chemical Reviews. 109 (7): 2903–28. doi:10.1021/cr900021w. PMC 2737513. PMID 19480389.
  6. ^ Zhang R, Evans G, Rotella FJ, Westbrook EM, Beno D, Huberman E, Joachimiak A, Collart FR (April 1999). "Characteristics and crystal structure of bacterial inosine-5'-monophosphate dehydrogenase". Biochemistry. 38 (15): 4691–700. CiteSeerX 10.1.1.488.2542. doi:10.1021/bi982858v. PMID 10200156.
  7. ^ Whitby FG, Luecke H, Kuhn P, Somoza JR, Huete-Perez JA, Phillips JD, Hill CP, Fletterick RJ, Wang CC (September 1997). "Crystal structure of Tritrichomonas foetus inosine-5'-monophosphate dehydrogenase and the enzyme-product complex". Biochemistry. 36 (35): 10666–74. doi:10.1021/bi9708850. PMID 9271497.
  8. ^ Prosise GL, Luecke H (February 2003). "Crystal structures of Tritrichomonasfoetus inosine monophosphate dehydrogenase in complex with substrate, cofactor and analogs: a structural basis for the random-in ordered-out kinetic mechanism". Journal of Molecular Biology. 326 (2): 517–27. doi:10.1016/S0022-2836(02)01383-9. PMID 12559919.
  9. ^ Labesse, Gilles; Alexandre, Thomas; Vaupré, Laurène; Salard-Arnaud, Isabelle; Him, Joséphine Lai Kee; Raynal, Bertrand; Bron, Patrick; Munier-Lehmann, Hélène (2013-06-04). "MgATP regulates allostery and fiber formation in IMPDHs". Structure. 21 (6): 975–985. doi:10.1016/j.str.2013.03.011. ISSN 1878-4186. PMID 23643948.
  10. ^ PDB ID: 1NFB, Risal, D., Strickler M,D., Goldstein, B.M.,The Conformation of NAD Bound to Human Inosine Monophosphate Dehydrogenase Type II.
  11. ^ Magasanik B, Moyed HS, Gehring LB (May 1957). "Enzymes essential for the biosynthesis of nucleic acid guanine; inosine 5'-phosphate dehydrogenase of Aerobacter aerogenes". J. Biol. Chem. 226 (1): 339–50. doi:10.1016/S0021-9258(18)64835-5. PMID 13428767.
  12. ^ Xiang B, Taylor JC, Markham GD (January 1996). "Monovalent cation activation and kinetic mechanism of inosine 5'-monophosphate dehydrogenase". The Journal of Biological Chemistry. 271 (3): 1435–40. doi:10.1074/jbc.271.3.1435. PMID 8576135.
  13. ^ Mortimer SE, Hedstrom L (August 2005). "Autosomal dominant retinitis pigmentosa mutations in inosine 5'-monophosphate dehydrogenase type I disrupt nucleic acid binding". The Biochemical Journal. 390 (Pt 1): 41–7. doi:10.1042/BJ20042051. PMC 1184561. PMID 15882147.
  14. ^ Nimmesgern E, Black J, Futer O, Fulghum JR, Chambers SP, Brummel CL, Raybuck SA, Sintchak MD (November 1999). "Biochemical analysis of the modular enzyme inosine 5'-monophosphate dehydrogenase". Protein Expression and Purification. 17 (2): 282–9. doi:10.1006/prep.1999.1136. PMID 10545277.
  15. ^ Buey, Rubén M.; Ledesma-Amaro, Rodrigo; Velázquez-Campoy, Adrián; Balsera, Mónica; Chagoyen, Mónica; de Pereda, José M.; Revuelta, José L. (2015-11-12). "Guanine nucleotide binding to the Bateman domain mediates the allosteric inhibition of eukaryotic IMP dehydrogenases". Nature Communications. 6 (1): 8923. Bibcode:2015NatCo...6.8923B. doi:10.1038/ncomms9923. ISSN 2041-1723. PMC 4660370. PMID 26558346.
  16. ^ Nimmesgern, E.; Black, J.; Futer, O.; Fulghum, J. R.; Chambers, S. P.; Brummel, C. L.; Raybuck, S. A.; Sintchak, M. D. (November 1999). "Biochemical analysis of the modular enzyme inosine 5'-monophosphate dehydrogenase". Protein Expression and Purification. 17 (2): 282–289. doi:10.1006/prep.1999.1136. ISSN 1046-5928. PMID 10545277.
  17. ^ Gedeon, Antoine; Ayoub, Nour; Brûlé, Sébastien; Raynal, Bertrand; Karimova, Gouzel; Gelin, Muriel; Mechaly, Ariel; Haouz, Ahmed; Labesse, Gilles; Munier-Lehmann, Hélène (August 2023). "Insight into the role of the Bateman domain at the molecular and physiological levels through engineered IMP dehydrogenases". Protein Science. 32 (8): e4703. doi:10.1002/pro.4703. ISSN 0961-8368. PMC 10357500. PMID 37338125.
  18. ^ Pimkin M, Pimkina J, Markham GD (March 2009). "A regulatory role of the Bateman domain of IMP dehydrogenase in adenylate nucleotide biosynthesis". The Journal of Biological Chemistry. 284 (12): 7960–9. doi:10.1074/jbc.M808541200. PMC 2658089. PMID 19153081.
  19. ^ Pimkin, Maxim; Markham, George D. (April 2008). "The CBS subdomain of inosine 5'-monophosphate dehydrogenase regulates purine nucleotide turnover". Molecular Microbiology. 68 (2): 342–359. doi:10.1111/j.1365-2958.2008.06153.x. ISSN 1365-2958. PMC 2279236. PMID 18312263.
  20. ^ McLean JE, Hamaguchi N, Belenky P, Mortimer SE, Stanton M, Hedstrom L (April 2004). "Inosine 5'-monophosphate dehydrogenase binds nucleic acids in vitro and in vivo". The Biochemical Journal. 379 (Pt 2): 243–51. doi:10.1042/BJ20031585. PMC 1224093. PMID 14766016.
  21. ^ Cornuel, Jean-François; Moraillon, Anne; Guéron, Maurice (April 2002). "Participation of yeast inosine 5′-monophosphate dehydrogenase in an in vitro complex with a fragment of the C-rich telomeric strand". Biochimie. 84 (4): 279–289. doi:10.1016/s0300-9084(02)01400-1. ISSN 0300-9084. PMID 12106905.
  22. ^ a b Bowne SJ, Sullivan LS, Mortimer SE, Hedstrom L, Zhu J, Spellicy CJ, Gire AI, Hughbanks-Wheaton D, Birch DG, Lewis RA, Heckenlively JR, Daiger SP (January 2006). "Spectrum and frequency of mutations in IMPDH1 associated with autosomal dominant retinitis pigmentosa and leber congenital amaurosis". Investigative Ophthalmology & Visual Science. 47 (1): 34–42. doi:10.1167/iovs.05-0868. PMC 2581444. PMID 16384941.
  23. ^ Mortimer SE, Xu D, McGrew D, Hamaguchi N, Lim HC, Bowne SJ, Daiger SP, Hedstrom L (December 2008). "IMP dehydrogenase type 1 associates with polyribosomes translating rhodopsin mRNA". The Journal of Biological Chemistry. 283 (52): 36354–60. doi:10.1074/jbc.M806143200. PMC 2605994. PMID 18974094.
  24. ^ Mölkänen, Tomi; Tyynelä, Jaana; Helin, Jari; Kalkkinen, Nisse; Kuusela, Pentti (2002-04-24). "Enhanced activation of bound plasminogen on Staphylococcus aureus by staphylokinase". FEBS Letters. 517 (1–3): 72–78. Bibcode:2002FEBSL.517...72M. doi:10.1016/S0014-5793(02)02580-2. ISSN 0014-5793. PMID 12062412.
  25. ^ a b Kozhevnikova EN, van der Knaap JA, Pindyurin AV, Ozgur Z, van Ijcken WF, Moshkin YM, Verrijzer CP (July 2012). "Metabolic enzyme IMPDH is also a transcription factor regulated by cellular state". Molecular Cell. 47 (1): 133–9. doi:10.1016/j.molcel.2012.04.030. PMID 22658723.
  26. ^ Collart FR, Huberman E (October 1988). "Cloning and sequence analysis of the human and Chinese hamster inosine-5'-monophosphate dehydrogenase cDNAs". J. Biol. Chem. 263 (30): 15769–72. doi:10.1016/S0021-9258(19)37654-9. PMID 2902093.
  27. ^ Min D, Josephine HR, Li H, Lakner C, MacPherson IS, Naylor GJ, Swofford D, Hedstrom L, Yang W (August 2008). "An enzymatic atavist revealed in dual pathways for water activation". PLOS Biology. 6 (8): e206. doi:10.1371/journal.pbio.0060206. PMC 2525682. PMID 18752347.
  28. ^ Natsumeda Y, Ohno S, Kawasaki H, Konno Y, Weber G, Suzuki K (March 1990). "Two distinct cDNAs for human IMP dehydrogenase". The Journal of Biological Chemistry. 265 (9): 5292–5. doi:10.1016/S0021-9258(19)34120-1. PMID 1969416.
  29. ^ Senda M, Natsumeda Y (1994). "Tissue-differential expression of two distinct genes for human IMP dehydrogenase (E.C.1.1.1.205)". Life Sciences. 54 (24): 1917–26. doi:10.1016/0024-3205(94)90150-3. PMID 7910933.
  30. ^ a b Collart FR, Chubb CB, Mirkin BL, Huberman E (October 1992). "Increased inosine-5'-phosphate dehydrogenase gene expression in solid tumor tissues and tumor cell lines". Cancer Research. 52 (20): 5826–8. doi:10.2172/10148922. PMID 1356621.
  31. ^ a b Zimmermann AG, Gu JJ, Laliberté J, Mitchell BS (1998). Inosine-5'-monophosphate dehydrogenase: regulation of expression and role in cellular proliferation and T lymphocyte activation. Progress in Nucleic Acid Research and Molecular Biology. Vol. 61. pp. 181–209. doi:10.1016/S0079-6603(08)60827-2. ISBN 978-0-12-540061-9. PMID 9752721.
  32. ^ Aherne A, Kennan A, Kenna PF, McNally N, Lloyd DG, Alberts IL, Kiang AS, Humphries MM, Ayuso C, Engel PC, Gu JJ, Mitchell BS, Farrar GJ, Humphries P (March 2004). "On the molecular pathology of neurodegeneration in IMPDH1-based retinitis pigmentosa". Human Molecular Genetics. 13 (6): 641–50. doi:10.1093/hmg/ddh061. PMID 14981049.
  33. ^ Gu JJ, Tolin AK, Jain J, Huang H, Santiago L, Mitchell BS (September 2003). "Targeted disruption of the inosine 5'-monophosphate dehydrogenase type I gene in mice". Molecular and Cellular Biology. 23 (18): 6702–12. doi:10.1128/MCB.23.18.6702-6712.2003. PMC 193693. PMID 12944494.
  34. ^ Jonsson CA, Carlsten H (January 2003). "Mycophenolic acid inhibits inosine 5'-monophosphate dehydrogenase and suppresses immunoglobulin and cytokine production of B cells". International Immunopharmacology. 3 (1): 31–7. doi:10.1016/s1567-5769(02)00210-2. PMID 12538032.
  35. ^ Gu JJ, Stegmann S, Gathy K, Murray R, Laliberte J, Ayscue L, Mitchell BS (August 2000). "Inhibition of T lymphocyte activation in mice heterozygous for loss of the IMPDH II gene". The Journal of Clinical Investigation. 106 (4): 599–606. doi:10.1172/JCI8669. PMC 380246. PMID 10953035.
  36. ^ Bojkova, Denisa; Klann, Kevin; Koch, Benjamin; Widera, Marek; Krause, David; Ciesek, Sandra; Cinatl, Jindrich; Münch, Christian (2020-05-14). "Proteomics of SARS-CoV-2-infected host cells reveals therapy targets". Nature. 583 (7816): 469–472. Bibcode:2020Natur.583..469B. doi:10.1038/s41586-020-2332-7. ISSN 1476-4687. PMID 32408336.
  37. ^ Clinical trial number NCT04356677 for "Study to Evaluate the Safety and Efficacy of VIRAZOLE® in Hospitalized Adult Participants With Respiratory Distress Due to COVID-19" at ClinicalTrials.gov

Further reading

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  • Wang J, Yang JW, Zeevi A, Webber SA, Girnita DM, Selby R, Fu J, Shah T, Pravica V, Hutchinson IV, Burckart GJ (May 2008). "IMPDH1 gene polymorphisms and association with acute rejection in renal transplant patients". Clin. Pharmacol. Ther. 83 (5): 711–7. doi:10.1038/sj.clpt.6100347. PMID 17851563. S2CID 12718828.
This article incorporates text from the public domain Pfam and InterPro: IPR001093
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