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

Gene ID: 5110, updated on 4-Nov-2018

Summary

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; Vega:OTTHUMG00000015794
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

Genomic context

See PCMT1 in Genome Data Viewer
Location:
6q25.1
Exon count:
9
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 6 NC_000006.12 (149749695..149811421)
105 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 uncharacterized LOC645967 Neighboring gene nucleoporin 43 Neighboring gene uncharacterized LOC107986660 Neighboring gene BTB domain containing 10 pseudogene 2 Neighboring gene LDL receptor related protein 11 Neighboring gene RAET1E antisense RNA 1 Neighboring gene retinoic acid early transcript 1E Neighboring gene chaperonin containing TCP1 subunit 7 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?

Pathways from BioSystems

  • Metabolism of proteins, organism-specific biosystem (from REACTOME)
    Metabolism of proteins, organism-specific biosystemProtein metabolism comprises the pathways of translation, post-translational modification and protein folding.
  • Protein repair, organism-specific biosystem (from REACTOME)
    Protein repair, organism-specific biosystemReactive oxygen species (ROS) such as H2O2, superoxide anions and hydroxyl radicals interact with molecules in the cell causing damage that impairs cellular functions. Although cells have mechanisms ...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Process Evidence Code Pubs
protein methylation TAS
Traceable Author Statement
more info
PubMed 
protein repair TAS
Traceable Author Statement
more info
PubMed 
Component Evidence Code Pubs
cytoplasm 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
 
extracellular exosome HDA PubMed 
extracellular vesicle HDA PubMed 

General protein information

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_024302219.1

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_033960.1 RefSeqGene

    Range
    5001..66727
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001252049.1NP_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
    Consensus CDS
    CCDS59041.1
    UniProtKB/Swiss-Prot
    P22061
    UniProtKB/TrEMBL
    H7BY58
    Related
    ENSP00000497225.1, OTTHUMP00000017397, ENST00000649032.1, OTTHUMT00000042650
    Conserved Domains (2) summary
    pfam01135
    Location:66274
    PCMT; Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
    cl17173
    Location:71278
    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_001252050.1NP_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:66239
    PCMT; Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
    cl17173
    Location:71243
    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_001252051.1NP_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
    B7Z972
    Related
    ENSP00000356350.6, ENST00000367380.9
    Conserved Domains (1) summary
    cl17173
    Location:81243
    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_001252052.1NP_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:66239
    PCMT; Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
    cl17173
    Location:71243
    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_001252053.1NP_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
    Consensus CDS
    CCDS5219.2
    UniProtKB/Swiss-Prot
    P22061
    UniProtKB/TrEMBL
    A0A0A0MRJ6
    Related
    OTTHUMP00000017400, OTTHUMT00000042653
    Conserved Domains (2) summary
    pfam01135
    Location:66274
    PCMT; Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
    cl17173
    Location:71278
    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_001360452.1NP_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)
    BC018569, D25545, DB478200, H07872
    Related
    ENSP00000420813.2, ENST00000464889.6
    Conserved Domains (1) summary
    pfam01135
    Location:8216
    PCMT; Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
  7. NM_001360456.1NP_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
    Related
    ENSP00000356354.3, ENST00000367384.7
    Conserved Domains (1) summary
    pfam01135
    Location:8216
    PCMT; Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
  8. NM_005389.2NP_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
    Consensus CDS
    CCDS5219.2
    UniProtKB/Swiss-Prot
    P22061
    UniProtKB/TrEMBL
    A0A0A0MRJ6
    Related
    ENSP00000497235.1, OTTHUMP00000017398, ENST00000649295.1, OTTHUMT00000042651
    Conserved Domains (2) summary
    pfam01135
    Location:66274
    PCMT; Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
    cl17173
    Location:71278
    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: 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_000006.12 Reference GRCh38.p12 Primary Assembly

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

mRNA and Protein(s)

  1. XM_024446451.1XP_024302219.1  protein-L-isoaspartate(D-aspartate) O-methyltransferase isoform X2

    Conserved Domains (1) summary
    pfam01135
    Location:15211
    PCMT; Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
  2. XM_011535868.2XP_011534170.1  protein-L-isoaspartate(D-aspartate) O-methyltransferase isoform X1

    Conserved Domains (2) summary
    pfam01135
    Location:15211
    PCMT; Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
    cl17173
    Location:17215
    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). ...
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