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Aliases for PCMT1 Gene

Aliases for PCMT1 Gene

  • Protein-L-Isoaspartate (D-Aspartate) O-Methyltransferase 2 3 5
  • Protein L-Isoaspartyl/D-Aspartyl Methyltransferase 3 4
  • L-Isoaspartyl Protein Carboxyl Methyltransferase 3 4
  • Protein-Beta-Aspartate Methyltransferase 3 4
  • EC 2.1.1.77 4 56
  • PIMT 3 4
  • Protein-L-Isoaspartate(D-Aspartate) O-Methyltransferase 3
  • EC 2.1.1 56

External Ids for PCMT1 Gene

Previous GeneCards Identifiers for PCMT1 Gene

  • GC06P149632
  • GC06P149966
  • GC06P150101
  • GC06P150163
  • GC06P150112
  • GC06P150070
  • GC06P147636

Summaries for PCMT1 Gene

Entrez Gene Summary for PCMT1 Gene

  • 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]

GeneCards Summary for PCMT1 Gene

PCMT1 (Protein-L-Isoaspartate (D-Aspartate) O-Methyltransferase) is a Protein Coding gene. Diseases associated with PCMT1 include Type 1 Diabetes Mellitus 5 and Neural Tube Defects. Among its related pathways are Metabolism of proteins and Protein repair. Gene Ontology (GO) annotations related to this gene include S-adenosylmethionine-dependent methyltransferase activity and protein-L-isoaspartate (D-aspartate) O-methyltransferase activity.

UniProtKB/Swiss-Prot for PCMT1 Gene

  • Catalyzes the methyl esterification of L-isoaspartyl and D-aspartyl residues in peptides and proteins that result from spontaneous decomposition of normal L-aspartyl and L-asparaginyl residues. It plays a role in the repair and/or degradation of damaged proteins. Acts on EIF4EBP2, microtubule-associated protein 2, calreticulin, clathrin light chains a and b, Ubiquitin carboxyl-terminal hydrolase isozyme L1, phosphatidylethanolamine-binding protein 1, stathmin, beta-synuclein and alpha-synuclein.

Gene Wiki entry for PCMT1 Gene

Additional gene information for PCMT1 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PCMT1 Gene

Genomics for PCMT1 Gene

GeneHancer (GH) Regulatory Elements for PCMT1 Gene

Promoters and enhancers for PCMT1 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH06I149748 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 550.8 +0.4 443 3.3 HDGF PKNOX1 ZFP64 ARID4B SIN3A DMAP1 ZNF2 POLR2B ZNF766 E2F8 NUP43 PCMT1 ENSG00000231760 LATS1 GINM1 PPIL4 RPS18P9 BTBD10P2 GC06P149237
GH06I149565 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 4.9 -182.9 -182900 3.1 PKNOX1 CLOCK FOXA2 SMAD1 ARNT ARID4B SIN3A DMAP1 ZNF2 IRF4 GINM1 ENSG00000231760 RAET1E PCMT1 GC06M149575 GC06P149237
GH06I149745 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 0.8 -3.0 -3033 2 HDGF ARID4B SIN3A DMAP1 YY1 POLR2B ZNF766 CBX5 ZNF207 ZNF143 NUP43 ENSG00000231760 PCMT1 LATS1 GC06P149237
GH06I149755 Enhancer 1.2 FANTOM5 Ensembl ENCODE 0.4 +6.4 6356 1.2 ZBTB6 MZF1 PAX8 ZNF2 FOXK2 VEZF1 ZNF548 PRDM10 IKZF2 RUNX3 ENSG00000231760 LATS1 NUP43 PPIL4 KATNA1 RAET1E PCMT1 BTBD10P2 GC06P149237
GH06I149761 Enhancer 0.9 Ensembl ENCODE 0.4 +12.2 12234 0.6 HDAC1 MEIS2 PKNOX1 FOSL1 CTBP1 ATF7 IKZF2 RUNX3 SMARCE1 ZNF687 ENSG00000231760 RPS18P9 LATS1 ENSG00000202343 ENSG00000233330 PCMT1 NUP43 BTBD10P2 GC06P149237
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around PCMT1 on UCSC Golden Path with GeneCards custom track

Genomic Locations for PCMT1 Gene

Genomic Locations for PCMT1 Gene
chr6:149,749,443-149,811,421
(GRCh38/hg38)
Size:
61,979 bases
Orientation:
Plus strand
chr6:150,070,579-150,132,557
(GRCh37/hg19)

Genomic View for PCMT1 Gene

Genes around PCMT1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PCMT1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PCMT1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PCMT1 Gene

Proteins for PCMT1 Gene

  • Protein details for PCMT1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P22061-PIMT_HUMAN
    Recommended name:
    Protein-L-isoaspartate(D-aspartate) O-methyltransferase
    Protein Accession:
    P22061
    Secondary Accessions:
    • A8K109
    • J3KP72
    • Q14661
    • Q16556
    • Q5VYC1
    • Q5VYC2
    • Q93061
    • Q96II9
    • Q99625
    • Q9BQV7
    • Q9BQV8
    • Q9NP03

    Protein attributes for PCMT1 Gene

    Size:
    227 amino acids
    Molecular mass:
    24636 Da
    Quaternary structure:
    • Monomer.
    SequenceCaution:
    • Sequence=EAW47786.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for PCMT1 Gene

    Alternative splice isoforms for PCMT1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for PCMT1 Gene

Selected DME Specific Peptides for PCMT1 Gene

P22061:
  • GAKALDV
  • LKPGGRL
  • GSGSGIL
  • TISAPHM
  • GKVIGIDHIKELV
  • NLRKNGIIK
  • PYMDSPQSIG
  • PQALIDQL
  • KDDPTLLSSGRV
  • KMKPLMGVIYVPLTDK
  • DQLKPGGRLILPVGPAGGNQMLEQYDKL

Post-translational modifications for PCMT1 Gene

  • Ubiquitination at isoforms=24, isoforms=2105, and Lys206

Domains & Families for PCMT1 Gene

Gene Families for PCMT1 Gene

HGNC:
Human Protein Atlas (HPA):
  • Enzymes
  • Plasma proteins
  • Predicted intracellular proteins
  • Predicted membrane proteins

Protein Domains for PCMT1 Gene

Suggested Antigen Peptide Sequences for PCMT1 Gene

Graphical View of Domain Structure for InterPro Entry

P22061

UniProtKB/Swiss-Prot:

PIMT_HUMAN :
  • Belongs to the methyltransferase superfamily. L-isoaspartyl/D-aspartyl protein methyltransferase family.
Family:
  • Belongs to the methyltransferase superfamily. L-isoaspartyl/D-aspartyl protein methyltransferase family.
genes like me logo Genes that share domains with PCMT1: view

Function for PCMT1 Gene

Molecular function for PCMT1 Gene

GENATLAS Biochemistry:
L-isoaspartyl/D-aspartyl methyltransferase,widely expressed
UniProtKB/Swiss-Prot CatalyticActivity:
S-adenosyl-L-methionine + protein L-isoaspartate = S-adenosyl-L-homocysteine + protein L-isoaspartate alpha-methyl ester.
UniProtKB/Swiss-Prot Function:
Catalyzes the methyl esterification of L-isoaspartyl and D-aspartyl residues in peptides and proteins that result from spontaneous decomposition of normal L-aspartyl and L-asparaginyl residues. It plays a role in the repair and/or degradation of damaged proteins. Acts on EIF4EBP2, microtubule-associated protein 2, calreticulin, clathrin light chains a and b, Ubiquitin carboxyl-terminal hydrolase isozyme L1, phosphatidylethanolamine-binding protein 1, stathmin, beta-synuclein and alpha-synuclein.

Enzyme Numbers (IUBMB) for PCMT1 Gene

Gene Ontology (GO) - Molecular Function for PCMT1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004719 protein-L-isoaspartate (D-aspartate) O-methyltransferase activity TAS 8074695
GO:0005515 protein binding IPI 25416956
GO:0008168 methyltransferase activity IEA --
GO:0016740 transferase activity IEA --
GO:0045296 cadherin binding IDA 25468996
genes like me logo Genes that share ontologies with PCMT1: view
genes like me logo Genes that share phenotypes with PCMT1: view

Animal Model Products

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Addgene plasmids for PCMT1

No data available for Phenotypes From GWAS Catalog , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for PCMT1 Gene

Localization for PCMT1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PCMT1 Gene

Cytoplasm.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for PCMT1 gene
Compartment Confidence
extracellular 5
cytosol 5
cytoskeleton 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for PCMT1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IBA --
GO:0005829 cytosol IDA,TAS --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
GO:0070062 extracellular exosome IDA,HDA 23376485
genes like me logo Genes that share ontologies with PCMT1: view

Pathways & Interactions for PCMT1 Gene

SuperPathways for PCMT1 Gene

SuperPathway Contained pathways
1 Metabolism of proteins
2 Protein repair
genes like me logo Genes that share pathways with PCMT1: view

Pathways by source for PCMT1 Gene

2 Reactome pathways for PCMT1 Gene

Gene Ontology (GO) - Biological Process for PCMT1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006464 cellular protein modification process IEA --
GO:0006479 protein methylation TAS,IEA 3355545
GO:0030091 protein repair TAS 8074695
GO:0032259 methylation IEA --
genes like me logo Genes that share ontologies with PCMT1: view

No data available for SIGNOR curated interactions for PCMT1 Gene

Drugs & Compounds for PCMT1 Gene

(1) Drugs for PCMT1 Gene - From: DrugBank, HMDB, and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
s-adenosylhomocysteine Experimental Pharma Target 0

(2) Additional Compounds for PCMT1 Gene - From: Novoseek and HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
s-adenosylmethionine
  • (3S)-5'-[(3-amino-3-carboxypropyl)methylsulfonio]-5'-deoxyadenosine
  • 2-S-Adenosyl-L-methionine
  • 5'-Deoxyadenosine-5'-L-methionine disulfate ditosylate
  • 5'-Deoxyadenosine-5'-L-methionine disulphate ditosylate
  • Active methionine
29908-03-0
genes like me logo Genes that share compounds with PCMT1: view

Transcripts for PCMT1 Gene

Unigene Clusters for PCMT1 Gene

Protein-L-isoaspartate (D-aspartate) O-methyltransferase:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Addgene plasmids for PCMT1

Alternative Splicing Database (ASD) splice patterns (SP) for PCMT1 Gene

ExUns: 1a · 1b · 1c · 1d · 1e · 1f ^ 2 ^ 3 ^ 4 ^ 5 ^ 6a · 6b ^ 7a · 7b ^ 8 ^ 9 ^ 10 ^ 11a · 11b · 11c ^ 12 ^ 13a · 13b · 13c ^ 14
SP1: - - - - - - - - -
SP2: - - - - - - - -
SP3: - - - - - - - - -
SP4: - - - - - - -
SP5: - - - - - -
SP6: - - - -
SP7: - - - - - -
SP8: - - - - - -
SP9: - - - - - -
SP10: - - - -
SP11: -
SP12: - - - - - - - - - -

Relevant External Links for PCMT1 Gene

GeneLoc Exon Structure for
PCMT1
ECgene alternative splicing isoforms for
PCMT1

Expression for PCMT1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for PCMT1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for PCMT1 Gene



Protein tissue co-expression partners for PCMT1 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of PCMT1 Gene:

PCMT1

SOURCE GeneReport for Unigene cluster for PCMT1 Gene:

Hs.279257

Evidence on tissue expression from TISSUES for PCMT1 Gene

  • Nervous system(5)
  • Skin(4.5)
  • Blood(4.4)
  • Liver(4.4)
  • Muscle(4.4)
  • Lung(2.3)
  • Heart(2.1)
  • Intestine(2.1)
genes like me logo Genes that share expression patterns with PCMT1: view

No data available for mRNA differential expression in normal tissues , Protein differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for PCMT1 Gene

Orthologs for PCMT1 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for PCMT1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia PCMT1 33 34
  • 99.88 (n)
dog
(Canis familiaris)
Mammalia PCMT1 33 34
  • 93.52 (n)
cow
(Bos Taurus)
Mammalia PCMT1 33 34
  • 93.25 (n)
mouse
(Mus musculus)
Mammalia Pcmt1 34
  • 93 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia PCMT1 34
  • 81 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia PCMT1 34
  • 80 (a)
OneToOne
chicken
(Gallus gallus)
Aves PCMT1 33 34
  • 86.37 (n)
lizard
(Anolis carolinensis)
Reptilia PCMT1 34
  • 92 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia pcmt1 33
  • 81.93 (n)
Str.12222 33
African clawed frog
(Xenopus laevis)
Amphibia Xl.6342 33
zebrafish
(Danio rerio)
Actinopterygii pcmt 33 34
  • 75.85 (n)
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.1437 33
fruit fly
(Drosophila melanogaster)
Insecta Pcmt 35 33 34
  • 56.12 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP000457 33
  • 54.45 (n)
worm
(Caenorhabditis elegans)
Secernentea pcm-1 35 33 34
  • 57.14 (n)
thale cress
(Arabidopsis thaliana)
eudicotyledons PIMT1 33
  • 54.81 (n)
Alicante grape
(Vitis vinifera)
eudicotyledons Vvi.817 33
rice
(Oryza sativa)
Liliopsida Os08g0557000 33
  • 53.67 (n)
Os.6061 33
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes pcm2 33
  • 51.04 (n)
bread mold
(Neurospora crassa)
Ascomycetes NCU05078 33
  • 50.23 (n)
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.1090 33
Species where no ortholog for PCMT1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rat (Rattus norvegicus)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for PCMT1 Gene

ENSEMBL:
Gene Tree for PCMT1 (if available)
TreeFam:
Gene Tree for PCMT1 (if available)

Paralogs for PCMT1 Gene

No data available for Paralogs for PCMT1 Gene

Variants for PCMT1 Gene

Polymorphic Variants from UniProtKB/Swiss-Prot for PCMT1 Gene

PIMT_HUMAN-P22061
The allele frequencies for the polymorphism at codon 120 differ between ethnic groups; in the Caucasian population Ile-120 is present at a frequency of 0.45, while it is found at a frequency of 0.88 and 0.81 in the Asian and the African populations respectively. Val-120 is found at a frequency of 0.55 in the Caucasians, 0.12 and 0.19 in the Asian and African populations respectively. The Ile-120 variant has higher specific activity and thermostability than the Val-120 variant. The Val-120 variant has a higher affinity for protein substrates.

Sequence variations from dbSNP and Humsavar for PCMT1 Gene

SNP ID Clin Chr 06 pos Variation AA Info Type
rs1000015020 -- 149,758,096(+) A/C genic_upstream_transcript_variant, intron_variant
rs1000080890 -- 149,804,680(+) T/A genic_downstream_transcript_variant, intron_variant
rs1000097864 -- 149,756,742(+) T/G genic_upstream_transcript_variant, intron_variant
rs1000118515 -- 149,751,423(+) C/T genic_upstream_transcript_variant, intron_variant
rs1000191618 -- 149,751,682(+) A/G genic_upstream_transcript_variant, intron_variant

Structural Variations from Database of Genomic Variants (DGV) for PCMT1 Gene

Variant ID Type Subtype PubMed ID
nsv349268 CNV deletion 16902084
nsv1148946 CNV deletion 26484159
nsv1141827 CNV insertion 24896259
esv2732864 CNV deletion 23290073
esv2732861 CNV deletion 23290073
esv2678537 CNV deletion 23128226
esv2600122 CNV deletion 19546169
esv2259693 CNV deletion 18987734
dgv1023e201 CNV deletion 23290073

Variation tolerance for PCMT1 Gene

Residual Variation Intolerance Score: 72.3% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.10; 22.39% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for PCMT1 Gene

Human Gene Mutation Database (HGMD)
PCMT1
SNPedia medical, phenotypic, and genealogical associations of SNPs for
PCMT1

Disorders for PCMT1 Gene

MalaCards: The human disease database

(2) MalaCards diseases for PCMT1 Gene - From: HGMD, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
type 1 diabetes mellitus 5
  • diabetes mellitus, insulin-dependent, 5
neural tube defects
  • neural tube defects, susceptibility to
- elite association - COSMIC cancer census association via MalaCards
Search PCMT1 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for PCMT1

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with PCMT1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for PCMT1 Gene

Publications for PCMT1 Gene

  1. Association between polymorphisms in the protein L-isoaspartate (D-aspartate) O-methyltransferase gene and premature ovarian failure. (PMID: 18582870) Pyun JA … Kwack K (Fertility and sterility 2009) 3 22 44 58
  2. A known functional polymorphism (Ile120Val) of the human PCMT1 gene and risk of spina bifida. (PMID: 16256389) Zhu H … Finnell RH (Molecular genetics and metabolism 2006) 3 22 44 58
  3. 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. (PMID: 11847284) Smith CD … Chattopadhyay D (Protein science : a publication of the Protein Society 2002) 3 4 22 58
  4. Polymorphic forms of the protein L-isoaspartate (D-aspartate) O-methyltransferase involved in the repair of age-damaged proteins. (PMID: 10496068) DeVry CG … Clarke S (Journal of human genetics 1999) 3 4 22 58
  5. Assignment of the protein L-isoaspartate (D-aspartate) O-methyltransferase gene (PCMT1) to human chromosome bands 6q24-->q25 with radiation hybrid mapping. (PMID: 10343128) DeVry CG … Clarke S (Cytogenetics and cell genetics 1999) 2 3 22 58

Products for PCMT1 Gene

  • Addgene plasmids for PCMT1

Sources for PCMT1 Gene

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