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    PCMT1 protein-L-isoaspartate (D-aspartate) O-methyltransferase [ Homo sapiens (human) ]

    Gene ID: 5110, updated on 3-Nov-2024

    Summary

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    Official Symbol
    PCMT1provided by HGNC
    Official Full Name
    protein-L-isoaspartate (D-aspartate) O-methyltransferaseprovided by HGNC
    Primary source
    HGNC:HGNC:8728
    See related
    Ensembl:ENSG00000120265 MIM:176851; AllianceGenome:HGNC:8728
    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
    PIMT
    Summary
    This gene encodes a member of the type II class of protein carboxyl methyltransferase enzymes. The encoded enzyme plays a role in protein repair by recognizing and converting D-aspartyl and L-isoaspartyl residues resulting from spontaneous deamidation back to the normal L-aspartyl form. The encoded protein may play a protective role in the pathogenesis of Alzheimer's disease, and single nucleotide polymorphisms in this gene have been associated with spina bifida and premature ovarian failure. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Oct 2011]
    Expression
    Ubiquitous expression in brain (RPKM 58.1), heart (RPKM 34.4) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See PCMT1 in Genome Data Viewer
    Location:
    6q25.1
    Exon count:
    9
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (149749695..149811421)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (150949463..151010794)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (150070831..150132557)

    Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene large tumor suppressor kinase 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17665 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:150045663-150045865 Neighboring gene uncharacterized LOC645967 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25267 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:150069877-150070842 Neighboring gene nucleoporin 43 Neighboring gene Sharpr-MPRA regulatory region 3985 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:150071808-150072310 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:150072311-150072813 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr6:150106480-150106982 Neighboring gene uncharacterized LOC107986660 Neighboring gene BTB domain containing 10 pseudogene 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25268 Neighboring gene RAET1E-LRP11 readthrough Neighboring gene LDL receptor related protein 11 Neighboring gene uncharacterized LOC124901427 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17667 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17668 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17669 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:150185306-150185806 Neighboring gene RAET1E antisense RNA 1 Neighboring gene chaperonin containing TCP1 subunit 7 pseudogene 1

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues 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 Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. Genome-wide CRISPR/Cas9 library screen identifies PCMT1 as a critical driver of ovarian cancer metastasis. Zhang J, et al. J Exp Clin Cancer Res, 2022 Jan 15. PMID 35033172, Free PMC Article
    2. Assignment of the protein L-isoaspartate (D-aspartate) O-methyltransferase gene (PCMT1) to human chromosome bands 6q24-->q25 with radiation hybrid mapping. DeVry CG, et al. Cytogenet Cell Genet, 1999. PMID 10343128
    3. Polymorphic forms of the protein L-isoaspartate (D-aspartate) O-methyltransferase involved in the repair of age-damaged proteins. DeVry CG, et al. J Hum Genet, 1999. PMID 10496068
    4. Crystal structure of human L-isoaspartyl methyltransferase. Ryttersgaard C, et al. J Biol Chem, 2002 Mar 22. PMID 11792715
    5. Crystal structure of human L-isoaspartyl-O-methyl-transferase with S-adenosyl homocysteine at 1.6-A resolution and modeling of an isoaspartyl-containing peptide at the active site. Smith CD, et al. Protein Sci, 2002 Mar. PMID 11847284, Free PMC Article

    See all (205) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. [Prognostic Value of PCMT1 Expression in Gastric Cancer and Its Regulatory Effect on Spindle Assembly Checkpoints].
      Title: [Prognostic Value of PCMT1 Expression in Gastric Cancer and Its Regulatory Effect on Spindle Assembly Checkpoints].
    2. The role of PIMT in Alzheimer's disease pathogenesis: A novel hypothesis.
      Title: The role of PIMT in Alzheimer's disease pathogenesis: A novel hypothesis.
    3. PCMT1 regulates the migration, invasion, and apoptosis of prostate cancer through modulating the PI3K/AKT/GSK-3beta pathway.
      Title: PCMT1 regulates the migration, invasion, and apoptosis of prostate cancer through modulating the PI3K/AKT/GSK-3β pathway.
    4. PCMT1 knockdown attenuates malignant properties by globally regulating transcriptome profiles in triple-negative breast cancer cells.
      Title: PCMT1 knockdown attenuates malignant properties by globally regulating transcriptome profiles in triple-negative breast cancer cells.
    5. PCMT1 is a potential target related to tumor progression and immune infiltration in liver cancer.
      Title: PCMT1 is a potential target related to tumor progression and immune infiltration in liver cancer.
    6. The Role of Protein-L-isoaspartyl Methyltransferase (PIMT) in the Suppression of Toxicity of the Oligomeric Form of Abeta42, in Addition to the Inhibition of Its Fibrillization.
      Title: The Role of Protein-L-isoaspartyl Methyltransferase (PIMT) in the Suppression of Toxicity of the Oligomeric Form of Aβ42, in Addition to the Inhibition of Its Fibrillization.
    7. In vitro Anti-malignant Property of PCMT1 Silencing and Identification of the SNHG16/miR-195/PCMT1 Regulatory Axis in Breast Cancer Cells.
      Title: In vitro Anti-malignant Property of PCMT1 Silencing and Identification of the SNHG16/miR-195/PCMT1 Regulatory Axis in Breast Cancer Cells.
    8. PIMT/TGS1: An evolving metabolic molecular switch with conserved methyl transferase activity.
      Title: PIMT/TGS1: An evolving metabolic molecular switch with conserved methyl transferase activity.
    9. The Protein L-Isoaspartyl (D-Aspartyl) Methyltransferase Regulates Glial-to-Mesenchymal Transition and Migration Induced by TGF-beta1 in Human U-87 MG Glioma Cells.
      Title: The Protein L-Isoaspartyl (D-Aspartyl) Methyltransferase Regulates Glial-to-Mesenchymal Transition and Migration Induced by TGF-β1 in Human U-87 MG Glioma Cells.
    10. PCMT1 Is a Potential Prognostic Biomarker and Is Correlated with Immune Infiltrates in Breast Cancer.
      Title: PCMT1 Is a Potential Prognostic Biomarker and Is Correlated with Immune Infiltrates in Breast Cancer.
    Submit: New GeneRIF Correction See all GeneRIFs (38)

    Phenotypes

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    Review eQTL and phenotype association data in this region using PheGenI

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables cadherin binding HDA PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables protein-L-isoaspartate (D-aspartate) O-methyltransferase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables protein-L-isoaspartate (D-aspartate) O-methyltransferase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein-L-isoaspartate (D-aspartate) O-methyltransferase activity TAS
    Traceable Author Statement
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in protein methylation IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in protein repair TAS
    Traceable Author Statement
    more info
    		 PubMed 
    Component Evidence Code Pubs
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		  
    located_in cytosol TAS
    Traceable Author Statement
    more info
    		  
    located_in extracellular exosome HDA PubMed 
    located_in extracellular vesicle HDA PubMed 

    General protein information

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    Preferred Names
    protein-L-isoaspartate(D-aspartate) O-methyltransferase
    Names
    L-isoaspartyl protein carboxyl methyltransferase
    epididymis secretory sperm binding protein
    protein L-isoaspartyl/D-aspartyl methyltransferase
    protein-beta-aspartate methyltransferase
    NP_001238978.1
    NP_001238979.1
    NP_001238980.1
    NP_001238981.1
    NP_001238982.1
    NP_001347381.1
    NP_001347385.1
    NP_005380.2
    XP_011534170.1
    XP_054211531.1

    NCBI Reference Sequences (RefSeq)

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    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_033960.1 RefSeqGene

      Range
      5047..66725
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001252049.1 → NP_001238978.1  protein-L-isoaspartate(D-aspartate) O-methyltransferase isoform 2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) uses an alternate splice site in the 3' coding region, which results in a frameshift compared to variant 1. The encoded isoform (2) has a longer and distinct C-terminus, compared to isoform 1.
      Source sequence(s)
      BX438393, CA441980, D13892, DC339361
      UniProtKB/Swiss-Prot
      P22061
      UniProtKB/TrEMBL
      H7BY58
      Conserved Domains (2) summary
      pfam01135
      Location:66 → 274
      PCMT; Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
      cl17173
      Location:71 → 278
      AdoMet_MTases; S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). ...

    2. NM_001252050.1 → NP_001238979.1  protein-L-isoaspartate(D-aspartate) O-methyltransferase isoform 3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) lacks an exon in the coding region but maintains the reading frame, compared to variant 1. The encoded isoform (3) is shorter than isoform 1.
      Source sequence(s)
      AK098739, BC018569, BX438393, CA441980
      Consensus CDS
      CCDS75533.1
      UniProtKB/TrEMBL
      F6S8N6
      Related
      ENSP00000438247.2, ENST00000544496.5
      Conserved Domains (2) summary
      pfam01135
      Location:66 → 239
      PCMT; Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
      cl17173
      Location:71 → 243
      AdoMet_MTases; S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). ...

    3. NM_001252051.1 → NP_001238980.1  protein-L-isoaspartate(D-aspartate) O-methyltransferase isoform 4

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) lacks an exon in the coding region but maintains the reading frame, compared to variant 1. The encoded isoform (4) is shorter than isoform 1.
      Source sequence(s)
      AA442100, AK304532, BC018569, BX438393, CA441980, DC339361
      Consensus CDS
      CCDS75534.1
      UniProtKB/TrEMBL
      A0A3F2YNX8
      Related
      ENSP00000356350.6, ENST00000367380.9
      Conserved Domains (1) summary
      cl17173
      Location:81 → 243
      AdoMet_MTases; S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). ...

    4. NM_001252052.1 → NP_001238981.1  protein-L-isoaspartate(D-aspartate) O-methyltransferase isoform 5

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) lacks an in-frame coding exon and uses an alternate splice site in the 3' coding region, which results in a frameshift, compared to variant 1. The encoded isoform (5) is shorter and has a distinct C-terminus, compared to isoform 1.
      Source sequence(s)
      AL539512, AW025538, BE262147, BX438393, CA441980, DB478200
      Conserved Domains (2) summary
      pfam01135
      Location:66 → 239
      PCMT; Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
      cl17173
      Location:71 → 243
      AdoMet_MTases; S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). ...

    5. NM_001252053.1 → NP_001238982.1  protein-L-isoaspartate(D-aspartate) O-methyltransferase isoform 1

      See identical proteins and their annotated locations for NP_001238982.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (6) differs in the 3' UTR compared to variant 1. Variants 1 and 6 encode the same isoform (1).
      Source sequence(s)
      AI220702, BX438393, D25547, DC421281
      UniProtKB/Swiss-Prot
      P22061
      UniProtKB/TrEMBL
      A0A0A0MRJ6
      Conserved Domains (2) summary
      pfam01135
      Location:66 → 274
      PCMT; Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
      cl17173
      Location:71 → 278
      AdoMet_MTases; S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). ...

    6. NM_001360452.2 → NP_001347381.1  protein-L-isoaspartate(D-aspartate) O-methyltransferase isoform 6

      Status: REVIEWED

      Description
      Transcript Variant: This variant (7) has the same exon structure, but a different 5' UTR and uses an alternate start codon, compared to variant 1. It encodes isoform 6, which has a shorter N-terminus, compared to isoform 1.
      Source sequence(s)
      AK129778, AL355312
      Consensus CDS
      CCDS94017.1
      UniProtKB/Swiss-Prot
      A8K109, J3KP72, P22061, Q14661, Q16556, Q5VYC1, Q5VYC2, Q93061, Q96II9, Q99625, Q9BQV7, Q9BQV8, Q9NP03
      UniProtKB/TrEMBL
      A0A384MDK7, B7Z972
      Related
      ENSP00000420813.2, ENST00000464889.7
      Conserved Domains (1) summary
      pfam01135
      Location:8 → 216
      PCMT; Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)

    7. NM_001360456.1 → NP_001347385.1  protein-L-isoaspartate(D-aspartate) O-methyltransferase isoform 7

      Status: REVIEWED

      Description
      Transcript Variant: This variant (8) differs in the 5' UTR, uses an alternate start codon and uses an alternate splice site in the 3' CDS, resulting in a frameshift, compared to variant 1. It encodes isoform 7, which is shorter and has a distinct C-terminus, compared to isoform 1.
      Source sequence(s)
      BC007501, DB478200, H07872
      Consensus CDS
      CCDS59041.2
      UniProtKB/TrEMBL
      B7Z972
      Related
      ENSP00000356354.3, ENST00000367384.8
      Conserved Domains (1) summary
      pfam01135
      Location:8 → 216
      PCMT; Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)

    8. NM_005389.2 → NP_005380.2  protein-L-isoaspartate(D-aspartate) O-methyltransferase isoform 1

      See identical proteins and their annotated locations for NP_005380.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript. Variants 1 and 6 encode the same isoform (1).
      Source sequence(s)
      BC018569, BX438393, CA441980, CX786396, DC356391
      UniProtKB/Swiss-Prot
      P22061
      UniProtKB/TrEMBL
      A0A0A0MRJ6
      Conserved Domains (2) summary
      pfam01135
      Location:66 → 274
      PCMT; Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
      cl17173
      Location:71 → 278
      AdoMet_MTases; S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). ...

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000006.12 Reference GRCh38.p14 Primary Assembly

      Range
      149749695..149811421
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011535868.3 → XP_011534170.1  protein-L-isoaspartate(D-aspartate) O-methyltransferase isoform X1

      Conserved Domains (1) summary
      TIGR00080
      Location:15 → 218
      pimt; protein-L-isoaspartate(D-aspartate) O-methyltransferase

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060930.1 Alternate T2T-CHM13v2.0

      Range
      150949463..151010794
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054355556.1 → XP_054211531.1  protein-L-isoaspartate(D-aspartate) O-methyltransferase isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P22061.4 GenPept UniProtKB/Swiss-Prot:P22061

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