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

Gene ID: 5110, updated on 2-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
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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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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

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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