Methionine synthase

Last updated

MTR
2o2k.jpg
Available structures
PDB Ortholog search: PDBe RCSB
Identifiers
Aliases MTR , HMAG, MS, cblG, 5-methyltetrahydrofolate-homocysteine methyltransferase
External IDs OMIM: 156570 MGI: 894292 HomoloGene: 37280 GeneCards: MTR
EC number 2.1.1.13
Orthologs
SpeciesHumanMouse
Entrez
Ensembl
UniProt
RefSeq (mRNA)

NM_000254
NM_001291939
NM_001291940

NM_001081128

RefSeq (protein)

NP_000245
NP_001278868
NP_001278869

NP_001074597

Location (UCSC) Chr 1: 236.8 – 236.92 Mb Chr 13: 12.2 – 12.27 Mb
PubMed search [3] [4]
Wikidata
View/Edit Human View/Edit Mouse

Methionine synthase (MS, MeSe, MTR) is responsible for the regeneration of methionine from homocysteine. In humans it is encoded by the MTR gene (5-methyltetrahydrofolate-homocysteine methyltransferase). [5] [6] Methionine synthase forms part of the S-adenosylmethionine (SAMe) biosynthesis and regeneration cycle, [7] and is the enzyme responsible for linking the cycle to one-carbon metabolism via the folate cycle. There are two primary forms of this enzyme, the Vitamin B12 (cobalamin)-dependent (MetH) and independent (MetE) forms, [8] although minimal core methionine synthases that do not fit cleanly into either category have also been described in some anaerobic bacteria. [9] The two dominant forms of the enzymes appear to be evolutionary independent and rely on considerably different chemical mechanisms. [10] Mammals and other higher eukaryotes express only the cobalamin-dependent form. In contrast, the distribution of the two forms in Archaeplastida (plants and algae) is more complex. Plants exclusively possess the cobalamin-independent form, [11] while algae have either one of the two, depending on species. [12] Many different microorganisms express both the cobalamin-dependent and cobalamin-independent forms. [13]

Contents

Mechanism

The reaction catalyzed by methionine synthase (click to enlarge) VitaminB12 2.png
The reaction catalyzed by methionine synthase (click to enlarge)

Methionine synthase catalyzes the final step in the regeneration of methionine (Met) from homocysteine (Hcy). Both the cobalamin-dependent and cobalamin-independent forms of the enzyme carry out the same overall chemical reaction, the transfer of a methyl group from 5-methyltetrahydrofolate (N5-MeTHF) to homocysteine, yielding tetrahydrofolate (THF) and methionine. [8] Methionine synthase is the only mammalian enzyme that metabolizes N5-MeTHF to regenerate the active cofactor THF. In the cobalamin-dependent (MetH) form of the enzyme, the reaction proceeds by two steps in a preferred ordered sequential mechanism. [14] The physiological resting state of the enzyme is thought to contain the enzyme-bound(Cob) cofactor in the methylcobalamin form, with the cobalt atom in the formal +3 valence state (Cob(III)-Me). The cobalamin is then demethylated by zinc-activated thiolate homocysteine, generating methionine and reducing the cofactor to a Cob(I) state. When in the Cob(I) form, the enzyme-bound cofactor is now able to abstract a methyl group from activated 5-methyltetrahydrofolate (N5-MeTHF), yielding tetrahydrofolate (THF) and regenerating the methylcoalamin form of the enzyme. [15]

Scavenger Pathway of Methionine Synthase Reductase to Recover Inactivated Methionine Synthase Methionine Synthase Reductase Pathway.png
Scavenger Pathway of Methionine Synthase Reductase to Recover Inactivated Methionine Synthase

Under physiological conditions, approximately once every 2000 catalytic turnovers the Co(I) may be oxidized into inactive Co(II) in cob-dependent MetH. To account for this effect, the protein contains a self-reactivation mechanism, a reductive methylation process that uses S-adenosylmethionine as a distinct methyl donor. In humans, the enzyme is reduced in this process by methionine synthase reductase (MTRR), which consists of flavodoxin-like and ferrodoxin-NADP+ oxidoreductase (FNR)-like domains. [16] In many bacteria, the reduction is carried out by a single domain flavodoxin protein. [17] The reductase protein is responsible for transfer of an electron from a reduced FMN cofactor to the inactive Cob(II), which enables regeneration of the active methylcobalamin enzyme via methyl transfer from S-adenosylmethionine to the reduced Cob(I) intermediate. [18] This process is known as the reactivation cycle, and is thought to be gated from the normal catalytic cycle by large-scale conformational rearrangements within the enzyme. [19] Because the oxidation of Cob(I) inevitably shuts down cob-dependent methionine synthase activity, defects or deficiencies in methionine synthase reductase have been implicated in some of the disease associations for methionine synthase deficiency. [20]

The mechanism of the cobalamin-independent (MetE) form, by contrast, proceeds through a direct methyl transfer from the activated N5-MeTHF to zinc thiolate homocysteine. Although the mechanism is considerably simpler, the direct transfer reaction is much less favorable than the cobalamin-mediated reactions and as a result the turnover rate for MetE is ~100x slower than that of MetH. As it does not contain the cobalamin cofactor, the cobalamin-independent enzyme is not prone to oxidative inactivation [21] [8] [22] [23]

Structure

Homocysteine Binding Domain in Methionine Synthase. His 618, Cys 620, and Cys704 bind Zn(purple) which binds to Homocysteine(Red) Homocysteine Binding Site.png
Homocysteine Binding Domain in Methionine Synthase. His 618, Cys 620, and Cys704 bind Zn(purple) which binds to Homocysteine(Red)

High-resolution structures have been solved by X-ray crystallography for intact MetE both in the absence and presence of substrates [23] [22] and for fragments of MetH, [24] [25] [26] [27] although no structural description exists of a fully intact MetH enzyme. The available structures and accompanying bioinformatic analysis indicate minimal similarity in the overall structure, although there are similarities within the substrate-binding sites themselves. [28] Cob-dependent MetH is divided into 4 separate domains. The domains, from N- to C-terminus, are denoted homocysteine binding (Hcy domain), N5-methylTHF binding (MTHF domain) Cobalamin-binding (Cob domain) and the S-adenosymethionine-binding or reactivation domain. The reactivation domain binds SAM and is the site of interaction with flavodoxin or Methionine Synthase Reductase during the reactivation cycle of the enzyme. [17] [16] [20] The cobalamin-binding domain contains two subdomains, with the cofactor bound to the Rossman-fold B12-binding subdomain, which is in turn capped by the other subdomain, the four-helix bundle cap subdomain. [25] The four-helix bundle serves to protect the cobalamin cofactor from unwanted reactivity, but can significantly change conformations to expose the cofactor allow it access to the other substrates during turnover. [26] Both the Hcy and N5-MeTHF domains adopt a TIM barrel architecture; the Hcy domain contains the zinc-binding site, which in MetH consists of three cysteine residues coordinated to a zinc ion which in turn binds and activates Hcy. The N5-MeTHF binding domain binds and activates N5-MeTHF via a hydrogen bonding network with several asparagine, arginine, and aspartic acid residues. During turnover, the enzyme undergoes significant conformational changes that involve moving the Cob-domain back and forth from the Hcy domain to the N5-MeTHF domain in order for the two methyl transfer reactions to proceed. [24]

The cob-independent MetE consists of two TIM-barrel domains that bind homocysteine and N5-MeTHF individually. The two domains adopt a face-to-face double barrel architecture, which requires a "closing" of the structure upon binding of both substrates to enable the direct methyl transfer. [22] Substrate-binding strategies are similar to MetH, although in the case of MetE the zinc atom is instead coordinated to two cysteines, a histidine and a glutamate, [23] for which an example is shown on the right.

Biochemical function

Methionine synthase is enzyme 4 Met pathway.svg
Methionine synthase is enzyme 4

In humans the enzyme's main purpose is to regenerate Met in the S-adenosylmethionine (SAM) cycle. The SAM cycle in a single turnover consumes Met and ATP and generates Hcy, and can involve any of a number of critical enzymatic reactions that use S-adenosylmethionine as the source of an active methyl group for methylation of nucleic acids, histones, phospholipids and various proteins. [29] [30] As such, methionine synthase serves an essential function by allowing the SAM cycle to perpetuate without a constant influx of Met. As a secondary effect, methionine synthase also serves to maintain low levels of Hcy and, because methionine synthase is one of the few enzymes that used N5-MeTHF as a substrate, to indirectly maintain THF levels. [31] [32]

In bacteria and plants, methionine synthase serves a dual purpose of both perpetuating the SAM cycle and catalyzing the final synthetic step in the de novo synthesis of Met, which is one of the 20 canonical amino acids. [33] [11] While the chemical reaction is exactly the same for both processes, the overall function is distinct from methionine synthase in humans because Met is an essential amino acid that is not synthesized de novo in the body. [34]

Clinical significance

Mutations in the MTR gene have been identified as the underlying cause of methylcobalamin deficiency complementation group G, or methylcobalamin deficiency cblG-type. [5] Deficiency or deregulation of the enzyme due to deficient methionine synthase reductase can directly result in elevated levels of homocysteine (hyperhomocysteinemia), which is associated with blindness, neurological symptoms, and birth defects. [35] [36] Methionine synthase reductase (MTRR) or methylene-tetrahydrofolate reductase (MTHFR) deficiencies can also result in the condition. Most cases of methionine synthase deficiency are symptomatic within 2 years of birth with many patients rapidly developing severe encephalopathy. [37] One consequence of reduced methionine synthase activity that is measurable by routine clinical blood tests is megaloblastic anemia.

Genetics

Several cblG-associated polymorphisms in the MTR gene have been identified. [38]

See also

Related Research Articles

<span class="mw-page-title-main">Methionine</span> Sulfur-containing amino acid

Methionine is an essential amino acid in humans.

Methylation, in the chemical sciences, is the addition of a methyl group on a substrate, or the substitution of an atom by a methyl group. Methylation is a form of alkylation, with a methyl group replacing a hydrogen atom. These terms are commonly used in chemistry, biochemistry, soil science, and biology.

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

Homocysteine or Hcy: is a non-proteinogenic α-amino acid. It is a homologue of the amino acid cysteine, differing by an additional methylene bridge (-CH2-). It is biosynthesized from methionine by the removal of its terminal Cε methyl group. In the body, homocysteine can be recycled into methionine or converted into cysteine with the aid of vitamin B6, B9, and B12.

<i>S</i>-Adenosyl methionine Chemical compound found in all domains of life with largely unexplored effects

S-Adenosyl methionine (SAM), also known under the commercial names of SAMe, SAM-e, or AdoMet, is a common cosubstrate involved in methyl group transfers, transsulfuration, and aminopropylation. Although these anabolic reactions occur throughout the body, most SAM is produced and consumed in the liver. More than 40 methyl transfers from SAM are known, to various substrates such as nucleic acids, proteins, lipids and secondary metabolites. It is made from adenosine triphosphate (ATP) and methionine by methionine adenosyltransferase. SAM was first discovered by Giulio Cantoni in 1952.

<span class="mw-page-title-main">Homocystinuria</span> Medical condition

Homocystinuria or HCU is an inherited disorder of the metabolism of the amino acid methionine due to a deficiency of cystathionine beta synthase or methionine synthase. It is an inherited autosomal recessive trait, which means a child needs to inherit a copy of the defective gene from both parents to be affected. Symptoms of homocystinuria can also be caused by a deficiency of vitamins B6, B12, or folate.

<span class="mw-page-title-main">Methylenetetrahydrofolate reductase</span> Rate-limiting enzyme in the methyl cycle

Methylenetetrahydrofolate reductase (MTHFR) is the rate-limiting enzyme in the methyl cycle, and it is encoded by the MTHFR gene. Methylenetetrahydrofolate reductase catalyzes the conversion of 5,10-methylenetetrahydrofolate to 5-methyltetrahydrofolate, a cosubstrate for homocysteine remethylation to methionine. Natural variation in this gene is common in otherwise healthy people. Although some variants have been reported to influence susceptibility to occlusive vascular disease, neural tube defects, Alzheimer's disease and other forms of dementia, colon cancer, and acute leukemia, findings from small early studies have not been reproduced. Some mutations in this gene are associated with methylenetetrahydrofolate reductase deficiency. Complex I deficiency with recessive spastic paraparesis has also been linked to MTHFR variants. In addition, the aberrant promoter hypermethylation of this gene is associated with male infertility and recurrent spontaneous abortion.

<span class="mw-page-title-main">Methyltransferase</span> Group of methylating enzymes

Methyltransferases are a large group of enzymes that all methylate their substrates but can be split into several subclasses based on their structural features. The most common class of methyltransferases is class I, all of which contain a Rossmann fold for binding S-Adenosyl methionine (SAM). Class II methyltransferases contain a SET domain, which are exemplified by SET domain histone methyltransferases, and class III methyltransferases, which are membrane associated. Methyltransferases can also be grouped as different types utilizing different substrates in methyl transfer reactions. These types include protein methyltransferases, DNA/RNA methyltransferases, natural product methyltransferases, and non-SAM dependent methyltransferases. SAM is the classical methyl donor for methyltransferases, however, examples of other methyl donors are seen in nature. The general mechanism for methyl transfer is a SN2-like nucleophilic attack where the methionine sulfur serves as the leaving group and the methyl group attached to it acts as the electrophile that transfers the methyl group to the enzyme substrate. SAM is converted to S-Adenosyl homocysteine (SAH) during this process. The breaking of the SAM-methyl bond and the formation of the substrate-methyl bond happen nearly simultaneously. These enzymatic reactions are found in many pathways and are implicated in genetic diseases, cancer, and metabolic diseases. Another type of methyl transfer is the radical S-Adenosyl methionine (SAM) which is the methylation of unactivated carbon atoms in primary metabolites, proteins, lipids, and RNA.

<span class="mw-page-title-main">Methylcobalamin</span> Form of vitamin B12

Methylcobalamin (mecobalamin, MeCbl, or MeB12) is a cobalamin, a form of vitamin B12. It differs from cyanocobalamin in that the cyano group at the cobalt is replaced with a methyl group. Methylcobalamin features an octahedral cobalt(III) centre and can be obtained as bright red crystals. From the perspective of coordination chemistry, methylcobalamin is notable as a rare example of a compound that contains metal–alkyl bonds. Nickel–methyl intermediates have been proposed for the final step of methanogenesis.

<span class="mw-page-title-main">Cystathionine beta synthase</span> Mammalian protein found in humans

Cystathionine-β-synthase, also known as CBS, is an enzyme (EC 4.2.1.22) that in humans is encoded by the CBS gene. It catalyzes the first step of the transsulfuration pathway, from homocysteine to cystathionine:

In enzymology, a 5-methyltetrahydropteroyltriglutamate—homocysteine S-methyltransferase is an enzyme that catalyzes the chemical reaction

<span class="mw-page-title-main">(Methionine synthase) reductase</span> Class of enzymes

[Methionine synthase] reductase, or Methionine synthase reductase, encoded by the gene MTRR, is an enzyme that is responsible for the reduction of methionine synthase inside human body. This enzyme is crucial for maintaining the one carbon metabolism, specifically the folate cycle. The enzyme employs one coenzyme, flavoprotein.

<span class="mw-page-title-main">Cyanocobalamin</span> Form of vitamin B-12

Cyanocobalamin is a form of vitamin B
12
used to treat and prevent vitamin B
12
deficiency
except in the presence of cyanide toxicity. The deficiency may occur in pernicious anemia, following surgical removal of the stomach, with fish tapeworm, or due to bowel cancer. It is used by mouth, by injection into a muscle, or as a nasal spray.

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

Methionine synthase reductase, also known as MSR, is an enzyme that in humans is encoded by the MTRR gene.

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

Cob(I)yrinic acid a,c-diamide adenosyltransferase, mitochondrial is an enzyme that in humans is encoded by the MMAB gene.

<span class="mw-page-title-main">Imerslund–Gräsbeck syndrome</span> Medical condition

Imerslund–Gräsbeck syndrome is a rare autosomal recessive, familial form of vitamin B12 deficiency caused by malfunction of the "Cubam" receptor located in the terminal ileum. This receptor is composed of two proteins, amnionless (AMN), and cubilin. A defect in either of these protein components can cause this syndrome. This is a rare disease, with a prevalence about 1 in 200,000, and is usually seen in patients of European ancestry.

<span class="mw-page-title-main">Vitamin B12-binding domain</span> Type of protein domain

In molecular biology, the vitamin B12-binding domain is a protein domain which binds to cobalamin. It can bind two different forms of the cobalamin cofactor, with cobalt bonded either to a methyl group (methylcobalamin) or to 5'-deoxyadenosine (adenosylcobalamin). Cobalamin-binding domains are mainly found in two families of enzymes present in animals and prokaryotes, which perform distinct kinds of reactions at the cobalt-carbon bond. Enzymes that require methylcobalamin carry out methyl transfer reactions. Enzymes that require adenosylcobalamin catalyse reactions in which the first step is the cleavage of adenosylcobalamin to form cob(II)alamin and the 5'-deoxyadenosyl radical, and thus act as radical generators. In both types of enzymes the B12-binding domain uses a histidine to bind the cobalt atom of cobalamin cofactors. This histidine is embedded in a DXHXXG sequence, the most conserved primary sequence motif of the domain. Proteins containing the cobalamin-binding domain include:

<span class="mw-page-title-main">Cobalamin biosynthesis</span>

Cobalamin biosynthesis is the process by which bacteria and archea make cobalamin, vitamin B12. Many steps are involved in converting aminolevulinic acid via uroporphyrinogen III and adenosylcobyric acid to the final forms in which it is used by enzymes in both the producing organisms and other species, including humans who acquire it through their diet.

Radical SAMenzymes is a superfamily of enzymes that use a [4Fe-4S]+ cluster to reductively cleave S-adenosyl-L-methionine (SAM) to generate a radical, usually a 5′-deoxyadenosyl radical (5'-dAdo), as a critical intermediate. These enzymes utilize this radical intermediate to perform diverse transformations, often to functionalize unactivated C-H bonds. Radical SAM enzymes are involved in cofactor biosynthesis, enzyme activation, peptide modification, post-transcriptional and post-translational modifications, metalloprotein cluster formation, tRNA modification, lipid metabolism, biosynthesis of antibiotics and natural products etc. The vast majority of known radical SAM enzymes belong to the radical SAM superfamily, and have a cysteine-rich motif that matches or resembles CxxxCxxC. Radical SAM enzymes comprise the largest superfamily of metal-containing enzymes.

<span class="mw-page-title-main">Uroporphyrinogen-III C-methyltransferase</span> Class of enzymes

Uroporphyrinogen-III C-methyltransferase, uroporphyrinogen methyltransferase, uroporphyrinogen-III methyltransferase, adenosylmethionine-uroporphyrinogen III methyltransferase, S-adenosyl-L-methionine-dependent uroporphyrinogen III methylase, uroporphyrinogen-III methylase, SirA, CysG, CobA, uroporphyrin-III C-methyltransferase, S-adenosyl-L-methionine:uroporphyrin-III C-methyltransferase) is an enzyme with systematic name S-adenosyl-L-methionine:uroporphyrinogen-III C-methyltransferase. This enzyme catalyses the following chemical reaction

Rowena Green Matthews, born in 1938, is the G. Robert Greenberg Distinguished University professor emeritus at the University of Michigan, Ann Arbor. Her research focuses on the role of organic cofactors as partners of enzymes catalyzing difficult biochemical reactions, especially folic acid and cobalamin. Among other honors, she was elected to the National Academy of Sciences in 2002 and the Institute of Medicine in 2004.

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Further reading