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

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; 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

Location:: 6q25.1

Exon count:: 9

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	6	NC_000006.12 (149749695..149811421)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	6	NC_060930.1 (150949463..151010794)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	6	NC_000006.11 (150070831..150132557)

Chromosome 6 - NC_000006.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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 Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

[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].
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.
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.
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.
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.
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.
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.
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.
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.
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)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

STS-D13892 (e-PCR)
- UniSTS:55836

HSC0WD062 (e-PCR)
- UniSTS:815

STS-T68453 (e-PCR)
- UniSTS:44633

G54073 (e-PCR)
- UniSTS:109455

RH37416 (e-PCR)
- UniSTS:24723

G20319 (e-PCR)
- UniSTS:5592

A005L39 (e-PCR)
- UniSTS:5593

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables cadherin binding	HDA more info	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 more info	PubMed
located_in extracellular vesicle	HDA more info	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

EC 2.1.1.77

NP_001238979.1

EC 2.1.1.77

NP_001238980.1

EC 2.1.1.77

NP_001238981.1

EC 2.1.1.77

NP_001238982.1

EC 2.1.1.77

NP_001347381.1

EC 2.1.1.77

NP_001347385.1

EC 2.1.1.77

NP_005380.2

EC 2.1.1.77

XP_011534170.1

EC 2.1.1.77

XP_054211531.1

EC 2.1.1.77

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

NG_033960.1 RefSeqGene

Range

5047..66725

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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). ...
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). ...
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). ...
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). ...
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). ...
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)
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)
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_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000006.12 Reference GRCh38.p14 Primary Assembly

Range

149749695..149811421

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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