Inosine-5′-monophosphate dehydrogenase

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Inosine 5'-monophosphate dehydrogenase
1PVN IMPDH Homotetramer.png
Structure of IMPDH [1]
Identifiers
EC no. 1.1.1.205
CAS no. 9028-93-7
Databases
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BRENDA BRENDA entry
ExPASy NiceZyme view
KEGG KEGG entry
MetaCyc metabolic pathway
PRIAM profile
PDB structures RCSB PDB PDBe PDBsum
Gene Ontology AmiGO / QuickGO
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NCBI proteins

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.

Contents

Structure and function

The canonical monomeric form of IMPDH has a molecular mass 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. Key residues (white) of the protein and the catalytic cysteine (cyan) are shown. Dashed lines represent polar contacts. 1NFB IMPDH Active Site.png
Visual representation of the active site with IMP (green) and NAD (purple) bound. 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

General mechanism used by the enzyme IMPDH to convert IMP to XMP. Only the purine portion of each molecule is shown. IMPDH General Mechanism.png
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
Symbol IMPDH1
Alt. symbolsRP10
NCBI gene 3614
HGNC 6052
OMIM 146690
RefSeq NM_000883
UniProt P20839
Other data
EC number 1.1.1.205
Locus Chr. 7 q31.3-q32
Search for
Structures Swiss-model
Domains InterPro

In humans

IMP dehydrogenase 2
1nf7.jpg
IMP dehydrogenase 2 homotetramer, Human
Identifiers
Symbol IMPDH2
Alt. symbolsIMPD2
NCBI gene 3615
HGNC 6053
OMIM 146691
RefSeq NM_000884
UniProt P12268
Other data
EC number 1.1.1.205
Locus Chr. 3 p21.2
Search for
Structures Swiss-model
Domains InterPro

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

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. Mycophenolate mofetil has been shown to inhibit completely both vaccinia and monkeypox viruses. [36]

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

IMPDH inhibitors have been shown to prevent SARS-CoV-2 replication in cells [37] and are being tested in clinical trials for COVID-19. [38]

See also

Related Research Articles

<span class="mw-page-title-main">Nucleotide</span> Biological molecules constituting nucleic acids

Nucleotides are organic molecules composed of a nitrogenous base, a pentose sugar and a phosphate. They serve as monomeric units of the nucleic acid polymers – deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), both of which are essential biomolecules within all life-forms on Earth. Nucleotides are obtained in the diet and are also synthesized from common nutrients by the liver.

<span class="mw-page-title-main">Inosine</span> Chemical compound

Inosine is a nucleoside that is formed when hypoxanthine is attached to a ribose ring (also known as a ribofuranose) via a β-N9-glycosidic bond. It was discovered in 1965 in analysis of RNA transferase. Inosine is commonly found in tRNAs and is essential for proper translation of the genetic code in wobble base pairs.

<span class="mw-page-title-main">Ribonucleotide</span> Nucleotide containing ribose as its pentose component

In biochemistry, a ribonucleotide is a nucleotide containing ribose as its pentose component. It is considered a molecular precursor of nucleic acids. Nucleotides are the basic building blocks of DNA and RNA. Ribonucleotides themselves are basic monomeric building blocks for RNA. Deoxyribonucleotides, formed by reducing ribonucleotides with the enzyme ribonucleotide reductase (RNR), are essential building blocks for DNA. There are several differences between DNA deoxyribonucleotides and RNA ribonucleotides. Successive nucleotides are linked together via phosphodiester bonds.

<span class="mw-page-title-main">Mycophenolic acid</span> Immunosuppressant medication

Mycophenolic acid is an immunosuppressant medication used to prevent rejection following organ transplantation and to treat autoimmune conditions such as Crohn's disease and lupus. Specifically it is used following kidney, heart, and liver transplantation. It can be given by mouth or by injection into a vein. It comes as mycophenolate sodium and mycophenolate mofetil.

A nucleoside triphosphate is a nucleoside containing a nitrogenous base bound to a 5-carbon sugar, with three phosphate groups bound to the sugar. They are the molecular precursors of both DNA and RNA, which are chains of nucleotides made through the processes of DNA replication and transcription. Nucleoside triphosphates also serve as a source of energy for cellular reactions and are involved in signalling pathways.

<span class="mw-page-title-main">Hypoxanthine-guanine phosphoribosyltransferase</span> Enzyme that converts hypoxanthine to inosine monophosphate

Hypoxanthine-guanine phosphoribosyltransferase (HGPRT) is an enzyme encoded in humans by the HPRT1 gene.

<span class="mw-page-title-main">Inosinic acid</span> Chemical compound

Inosinic acid or inosine monophosphate (IMP) is a nucleotide. Widely used as a flavor enhancer, it is typically obtained from chicken byproducts or other meat industry waste. Inosinic acid is important in metabolism. It is the ribonucleotide of hypoxanthine and the first nucleotide formed during the synthesis of purine nucleotides. It can also be formed by the deamination of adenosine monophosphate by AMP deaminase. It can be hydrolysed to inosine.

<span class="mw-page-title-main">Purine nucleoside phosphorylase</span> Enzyme

Purine nucleoside phosphorylase, PNP, PNPase or inosine phosphorylase is an enzyme that in humans is encoded by the NP gene. It catalyzes the chemical reaction

<span class="mw-page-title-main">Nucleic acid metabolism</span> Process

Nucleic acid metabolism is a collective term that refers to the variety of chemical reactions by which nucleic acids are either synthesized or degraded. Nucleic acids are polymers made up of a variety of monomers called nucleotides. Nucleotide synthesis is an anabolic mechanism generally involving the chemical reaction of phosphate, pentose sugar, and a nitrogenous base. Degradation of nucleic acids is a catabolic reaction and the resulting parts of the nucleotides or nucleobases can be salvaged to recreate new nucleotides. Both synthesis and degradation reactions require multiple enzymes to facilitate the event. Defects or deficiencies in these enzymes can lead to a variety of diseases.

Purine metabolism refers to the metabolic pathways to synthesize and break down purines that are present in many organisms.

<span class="mw-page-title-main">Xanthosine monophosphate</span> Chemical compound

Xanthosine monophosphate (xanthylate) is an intermediate in purine metabolism. It is a ribonucleoside monophosphate. It is formed from IMP via the action of IMP dehydrogenase, and it forms GMP via the action of GMP synthase. Also, XMP can be released from XTP by enzyme deoxyribonucleoside triphosphate pyrophosphohydrolase containing (d)XTPase activity.

<span class="mw-page-title-main">GMP synthase</span> Protein domain

Guanosine monophosphate synthetase, also known as GMPS is an enzyme that converts xanthosine monophosphate to guanosine monophosphate.

<span class="mw-page-title-main">GMP reductase</span> Class of enzymes

GMP reductase EC 1.7.1.7 is an enzyme that catalyzes the irreversible and NADPH-dependent reductive deamination of GMP into IMP.

In enzymology, an adenosine-phosphate deaminase (EC 3.5.4.17) is an enzyme that catalyzes the chemical reaction

<span class="mw-page-title-main">IMPDH1</span> Protein-coding gene in the species Homo sapiens

Inosine-5'-monophosphate dehydrogenase 1, also known as IMP dehydrogenase 1, is an enzyme that in humans is encoded by the IMPDH1 gene.

<span class="mw-page-title-main">Phosphoribosylglycinamide formyltransferase</span>

Phosphoribosylglycinamide formyltransferase (EC 2.1.2.2), also known as glycinamide ribonucleotide transformylase (GAR Tfase), is an enzyme with systematic name 10-formyltetrahydrofolate:5'-phosphoribosylglycinamide N-formyltransferase. This enzyme catalyses the following chemical reaction

<span class="mw-page-title-main">CBS domain</span> Protein domain

In molecular biology, the CBS domain is a protein domain found in a range of proteins in all species from bacteria to humans. It was first identified as a conserved sequence region in 1997 and named after cystathionine beta synthase, one of the proteins it is found in. CBS domains are also found in a wide variety of other proteins such as inosine monophosphate dehydrogenase, voltage gated chloride channels and AMP-activated protein kinase (AMPK). CBS domains regulate the activity of associated enzymatic and transporter domains in response to binding molecules with adenosyl groups such as AMP and ATP, or s-adenosylmethionine.

<span class="mw-page-title-main">IMPDH2</span> Protein-coding gene in the species Homo sapiens

Inosine-5'-monophosphate dehydrogenase 2, also known as IMP dehydrogenase 2, is an enzyme that in humans is encoded by the IMPDH2 gene.

<span class="mw-page-title-main">Purine nucleotide cycle</span> Protein metabolic pathway

The Purine Nucleotide Cycle is a metabolic pathway in protein metabolism requiring the amino acids aspartate and glutamate. The cycle is used to regulate the levels of adenine nucleotides, in which ammonia and fumarate are generated. AMP converts into IMP and the byproduct ammonia. IMP converts to S-AMP (adenylosuccinate), which then converts to AMP and the byproduct fumarate. The fumarate goes on to produce ATP (energy) via oxidative phosphorylation as it enters the Krebs cycle and then the electron transport chain. Lowenstein first described this pathway and outlined its importance in processes including amino acid catabolism and regulation of flux through glycolysis and the Krebs cycle.

The gua operon is responsible for regulating the synthesis of guanosine mono phosphate (GMP), a purine nucleotide, from inosine monophosphate. It consists of two structural genes guaB (encodes for IMP dehydrogenase or and guaA apart from the promoter and operator region.

References

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Further reading

This article incorporates text from the public domain Pfam and InterPro: IPR001093