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    MTR 5-methyltetrahydrofolate-homocysteine methyltransferase [ Homo sapiens (human) ]

    Gene ID: 4548, updated on 7-Oct-2018

    Summary

    Official Symbol
    MTRprovided by HGNC
    Official Full Name
    5-methyltetrahydrofolate-homocysteine methyltransferaseprovided by HGNC
    Primary source
    HGNC:HGNC:7468
    See related
    Ensembl:ENSG00000116984 MIM:156570; Vega:OTTHUMG00000040060
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    MS; HMAG; cblG
    Summary
    This gene encodes the 5-methyltetrahydrofolate-homocysteine methyltransferase. This enzyme, also known as cobalamin-dependent methionine synthase, catalyzes the final step in methionine biosynthesis. Mutations in MTR have been identified as the underlying cause of methylcobalamin deficiency complementation group G. Alternatively spliced transcript variants encoding distinct isoforms have been found for this gene. [provided by RefSeq, May 2014]
    Expression
    Ubiquitous expression in kidney (RPKM 5.8), thyroid (RPKM 4.9) and 25 other tissues See more
    Orthologs

    Genomic context

    See MTR in Genome Data Viewer
    Location:
    1q43
    Exon count:
    33
    Annotation release Status Assembly Chr Location
    109 current GRCh38.p12 (GCF_000001405.38) 1 NC_000001.11 (236794304..236903981)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (236958581..237067281)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene control region 3 heart enhancer Neighboring gene VISTA enhancer hs2135 Neighboring gene actinin alpha 2 Neighboring gene ribosomal protein SA pseudogene 21 Neighboring gene uncharacterized LOC105373218 Neighboring gene uncharacterized LOC107985368 Neighboring gene ribosomal protein L35 pseudogene 1

    Genomic regions, transcripts, and products

    Expression

    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Jun 15 11:32:44 2016

    Bibliography

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    Phenotypes

    NHGRI GWAS Catalog

    Description
    Common genetic loci influencing plasma homocysteine concentrations and their effect on risk of coronary artery disease.
    NHGRI GWA Catalog

    HIV-1 interactions

    Protein interactions

    Protein Gene Interaction Pubs
    Vif vif HIV-1 Vif interacts with MTR; interaction predicted to be relevant to purine pyrimidine biosynthesis PubMed

    Go to the HIV-1, Human Interaction Database

    Pathways from BioSystems

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Homology

    Clone Names

    • FLJ33168, FLJ43216, FLJ45386

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    cobalamin binding IEA
    Inferred from Electronic Annotation
    more info
     
    methionine synthase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    methionine synthase activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    methionine synthase activity IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    zinc ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    Process Evidence Code Pubs
    axon regeneration ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    cellular response to nitric oxide ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    cobalamin metabolic process IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    cobalamin metabolic process TAS
    Traceable Author Statement
    more info
     
    methionine biosynthetic process IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    methylation IEA
    Inferred from Electronic Annotation
    more info
     
    nervous system development TAS
    Traceable Author Statement
    more info
    PubMed 
    pteridine-containing compound metabolic process IEA
    Inferred from Electronic Annotation
    more info
     
    response to axon injury ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    Component Evidence Code Pubs
    cytosol IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    cytosol IDA
    Inferred from Direct Assay
    more info
     
    cytosol TAS
    Traceable Author Statement
    more info
     

    General protein information

    Preferred Names
    methionine synthase
    Names
    5-methyltetrahydrofolate-homocysteine methyltransferase 1
    cobalamin-dependent methionine synthase
    vitamin-B12 dependent methionine synthase
    NP_000245.2
    NP_001278868.1
    NP_001278869.1
    XP_005273198.1
    XP_006711833.1
    XP_011542496.1
    XP_016856818.1
    XP_016856819.1

    NCBI Reference Sequences (RefSeq)

    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    Genomic

    1. NG_008959.1 RefSeqGene

      Range
      5001..113701
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_000254.2NP_000245.2  methionine synthase isoform 1

      See identical proteins and their annotated locations for NP_000245.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      AL359259, DC377743, U73338, U75743
      Consensus CDS
      CCDS1614.1
      UniProtKB/Swiss-Prot
      Q99707
      Related
      ENSP00000355536.5, OTTHUMP00000037964, ENST00000366577.9, OTTHUMT00000096632
      Conserved Domains (5) summary
      COG0646
      Location:21340
      MetH1; Methionine synthase I (cobalamin-dependent), methyltransferase domain [Amino acid transport and metabolism]
      PRK09490
      Location:191261
      metH; B12-dependent methionine synthase; Provisional
      cd00740
      Location:371627
      MeTr; MeTr subgroup of pterin binding enzymes. This family includes cobalamin-dependent methyltransferases such as methyltetrahydrofolate, corrinoid iron-sulfur protein methyltransferase (MeTr) and methionine synthase (MetH). Cobalamin-dependent ...
      cd02069
      Location:671897
      methionine_synthase_B12_BD; B12 binding domain of methionine synthase. This domain binds methylcobalamin, which it uses as an intermediate methyl carrier from methyltetrahydrofolate (CH3H4folate) to homocysteine (Hcy).
      pfam02965
      Location:9651246
      Met_synt_B12; Vitamin B12 dependent methionine synthase, activation domain
    2. NM_001291939.1NP_001278868.1  methionine synthase isoform 2

      See identical proteins and their annotated locations for NP_001278868.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an in-frame exon in the central coding region, compared to variant 1. The resulting isoform (2) lacks an internal segment, compared to isoform 1.
      Source sequence(s)
      AL359259, BC144095, CB241165, DC377743
      Consensus CDS
      CCDS73054.1
      UniProtKB/Swiss-Prot
      Q99707
      Related
      ENSP00000441845.1, ENST00000535889.5
      Conserved Domains (5) summary
      COG0646
      Location:21340
      MetH1; Methionine synthase I (cobalamin-dependent), methyltransferase domain [Amino acid transport and metabolism]
      PRK09490
      Location:191210
      metH; B12-dependent methionine synthase; Provisional
      cd00740
      Location:371627
      MeTr; MeTr subgroup of pterin binding enzymes. This family includes cobalamin-dependent methyltransferases such as methyltetrahydrofolate, corrinoid iron-sulfur protein methyltransferase (MeTr) and methionine synthase (MetH). Cobalamin-dependent ...
      pfam02965
      Location:9141195
      Met_synt_B12; Vitamin B12 dependent methionine synthase, activation domain
      cl00293
      Location:679846
      B12-binding_like; B12 binding domain (B12-BD). Most of the members bind different cobalamid derivates, like B12 (adenosylcobamide) or methylcobalamin or methyl-Co(III) 5-hydroxybenzimidazolylcobamide. This domain is found in several enzymes, such as glutamate mutase, ...
    3. NM_001291940.1NP_001278869.1  methionine synthase isoform 3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) lacks an internal exon, which causes translation initiation at a downstream AUG, compared to variant 1. The resulting isoform (3) has a shorter N-terminus, compared to isoform 1.
      Source sequence(s)
      AL359259, BC136440, BC144098, CB241165, DC377743
      UniProtKB/Swiss-Prot
      Q99707
      Related
      ENSP00000355535.3, OTTHUMP00000037965, ENST00000366576.3, OTTHUMT00000096633
      Conserved Domains (4) summary
      COG1410
      Location:2823
      MetH2; Methionine synthase I, cobalamin-binding domain [Amino acid transport and metabolism]
      cd00740
      Location:1220
      MeTr; MeTr subgroup of pterin binding enzymes. This family includes cobalamin-dependent methyltransferases such as methyltetrahydrofolate, corrinoid iron-sulfur protein methyltransferase (MeTr) and methionine synthase (MetH). Cobalamin-dependent ...
      cd02069
      Location:264490
      methionine_synthase_B12_BD; B12 binding domain of methionine synthase. This domain binds methylcobalamin, which it uses as an intermediate methyl carrier from methyltetrahydrofolate (CH3H4folate) to homocysteine (Hcy).
      pfam02965
      Location:558839
      Met_synt_B12; Vitamin B12 dependent methionine synthase, activation domain

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p12 Primary Assembly

    Genomic

    1. NC_000001.11 Reference GRCh38.p12 Primary Assembly

      Range
      236794304..236903981
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011544194.3XP_011542496.1  methionine synthase isoform X1

      Conserved Domains (5) summary
      COG0646
      Location:140396
      MetH1; Methionine synthase I (cobalamin-dependent), methyltransferase domain [Amino acid transport and metabolism]
      PRK09490
      Location:1401317
      metH; B12-dependent methionine synthase; Provisional
      cd00740
      Location:427683
      MeTr; MeTr subgroup of pterin binding enzymes. This family includes cobalamin-dependent methyltransferases such as methyltetrahydrofolate, corrinoid iron-sulfur protein methyltransferase (MeTr) and methionine synthase (MetH). Cobalamin-dependent ...
      cd02069
      Location:727953
      methionine_synthase_B12_BD; B12 binding domain of methionine synthase. This domain binds methylcobalamin, which it uses as an intermediate methyl carrier from methyltetrahydrofolate (CH3H4folate) to homocysteine (Hcy).
      pfam02965
      Location:10211302
      Met_synt_B12; Vitamin B12 dependent methionine synthase, activation domain
    2. XM_017001330.2XP_016856819.1  methionine synthase isoform X4

    3. XM_017001329.2XP_016856818.1  methionine synthase isoform X2

    4. XM_005273141.5XP_005273198.1  methionine synthase isoform X3

      Conserved Domains (5) summary
      COG0646
      Location:20339
      MetH1; Methionine synthase I (cobalamin-dependent), methyltransferase domain [Amino acid transport and metabolism]
      PRK09490
      Location:181260
      metH; B12-dependent methionine synthase; Provisional
      cd00740
      Location:370626
      MeTr; MeTr subgroup of pterin binding enzymes. This family includes cobalamin-dependent methyltransferases such as methyltetrahydrofolate, corrinoid iron-sulfur protein methyltransferase (MeTr) and methionine synthase (MetH). Cobalamin-dependent ...
      cd02069
      Location:670896
      methionine_synthase_B12_BD; B12 binding domain of methionine synthase. This domain binds methylcobalamin, which it uses as an intermediate methyl carrier from methyltetrahydrofolate (CH3H4folate) to homocysteine (Hcy).
      pfam02965
      Location:9641245
      Met_synt_B12; Vitamin B12 dependent methionine synthase, activation domain
    5. XM_006711770.3XP_006711833.1  methionine synthase isoform X5

      Conserved Domains (5) summary
      COG1410
      Location:30918
      MetH2; Methionine synthase I, cobalamin-binding domain [Amino acid transport and metabolism]
      cd00740
      Location:59315
      MeTr; MeTr subgroup of pterin binding enzymes. This family includes cobalamin-dependent methyltransferases such as methyltetrahydrofolate, corrinoid iron-sulfur protein methyltransferase (MeTr) and methionine synthase (MetH). Cobalamin-dependent ...
      cd02069
      Location:359585
      methionine_synthase_B12_BD; B12 binding domain of methionine synthase. This domain binds methylcobalamin, which it uses as an intermediate methyl carrier from methyltetrahydrofolate (CH3H4folate) to homocysteine (Hcy).
      pfam02965
      Location:653934
      Met_synt_B12; Vitamin B12 dependent methionine synthase, activation domain
      cl22882
      Location:228
      S-methyl_trans; Homocysteine S-methyltransferase
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