FB2022_03, released June 9, 2022

Gene: Dmel\Pcmt

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General Information
Symbol
Dmel\Pcmt
Species
D. melanogaster
Name
Protein-L-isoaspartate (D-aspartate) O-methyltransferase
Annotation Symbol
CG2152
Feature Type
protein_coding_gene
FlyBase ID
FBgn0086768
Gene Model Status
Current
Stock Availability
11 publicly available
Enzyme Name (EC)
Protein-L-isoaspartate(D-aspartate) O-methyltransferase (2.1.1.77)
Gene Summary
Initiates the repair of damaged proteins by catalyzing methyl esterification of L-isoaspartyl and D-aspartyl residues produced by spontaneous isomerization and racemization of L-aspartyl and L-asparaginyl residues in aging peptides and proteins. (UniProt, Q27869)
Contribute a Gene Snapshot for this gene.
All Summaries
Also Known As

PIMT

Key Links
Genomic Location
Cytogenetic map
83B1-102A
Sequence location
Recombination map
3-47.5
RefSeq locus
NT_033777 REGION:5552823..5554316
Sequence
Get Decorated FASTA
Genomic Maps
Other Genome Views
The following external sites may use different assemblies or annotations than FlyBase.
NCBI
UCSC
Ensembl
PopFly
Function
GO Summary Ribbons
Gene Ontology (GO) Annotations (4 terms)
Molecular Function (1 term)
Terms Based on Experimental Evidence (1 term)
CV Term
Evidence
References
enables protein-L-isoaspartate (D-aspartate) O-methyltransferase activity
inferred from direct assay
(Bennett et al., 2003)
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
enables protein-L-isoaspartate (D-aspartate) O-methyltransferase activity
inferred from biological aspect of ancestor with PANTHER:PTN000171727
(assigned by GO_Central )
(Gaudet et al., 2011)
Biological Process (2 terms)
Terms Based on Experimental Evidence (1 term)
CV Term
Evidence
References
involved_in defense response to bacterium
inferred from mutant phenotype
(Ayres et al., 2008)
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
involved_in cellular protein modification process
inferred from electronic annotation with InterPro:IPR000682
(assigned by InterPro )
(FlyBase Curators et al., 2004-)
Cellular Component (1 term)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
is_active_in cytoplasm
inferred from biological aspect of ancestor with PANTHER:PTN000171727
(assigned by GO_Central )
(Gaudet et al., 2011)
Gene Group (FlyBase)
Protein Family (UniProt)
Belongs to the methyltransferase superfamily. L-isoaspartyl/D-aspartyl protein methyltransferase family. (Q27869)
Protein Signatures (InterPro)
Catalytic Activity (EC)
Experimental Evidence
S-adenosyl-L-methionine + protein L-isoaspartate = S-adenosyl-L- homocysteine + protein L-isoaspartate alpha-methyl ester (2.1.1.77)
Predictions / Assertions
S-adenosyl-L-methionine + protein L-isoaspartate = S-adenosyl-L- homocysteine + protein L-isoaspartate alpha-methyl ester (2.1.1.77)
Summaries
Gene Group (FlyBase)
PROTEIN CARBOXYL O-METHYLTRANSFERASES -
Protein carboxyl O-methyltransferases catalyze the transfer of a methyl group to a carboxyl group on a protein.
Protein Function (UniProtKB)
Initiates the repair of damaged proteins by catalyzing methyl esterification of L-isoaspartyl and D-aspartyl residues produced by spontaneous isomerization and racemization of L-aspartyl and L-asparaginyl residues in aging peptides and proteins.
(UniProt, Q27869)
Gene Model and Products
Number of Transcripts
2
Number of Unique Polypeptides
2

Please see the JBrowse view of Dmel\Pcmt for information on other features

To submit a correction to a gene model please use the Contact FlyBase form

Protein Domains (via Pfam)
Isoform displayed:
Pfam protein domains
InterPro name
classification
start
end
Protein Domains (via SMART)
Isoform displayed:
SMART protein domains
InterPro name
classification
start
end
Structure New Section
Protein 3D structure   (Predicted by AlphaFold)   (AlphaFold entry Q27869)

If you don't see the viewer to the right, refresh your browser.
Model Confidence:
  • Very high (pLDDT > 90)
  • Confident (90 > pLDDT > 70)
  • Low (70 > pLDDT > 50)
  • Very low (pLDDT < 50)

AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100. Some regions with low pLDDT may be unstructured in isolation.

Comments on Gene Model

Gene model reviewed during 5.48

Low-frequency RNA-Seq exon junction(s) not annotated.

Gene model reviewed during 5.43

Gene model reviewed during 5.49

Sequence Ontology: Class of Gene
gene
nuclear_gene
protein_coding_gene
Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
Pcmt-RA
FBtr0078758
NM_080508
953
226
Pcmt-RC
FBtr0339519
NM_001275358
998
203
Additional Transcript Data and Comments
Reported size (kB)
Comments
External Data
Crossreferences
Polypeptide Data
Annotated Polypeptides
Name
FlyBase ID
Predicted MW (kDa)
Length (aa)
Theoretical pI
UniProt
RefSeq ID
GenBank
Pcmt-PA
FBpp0078405
24.6
226
7.23
Q27869
NP_536756
AAF52012
Pcmt-PC
FBpp0308602
21.9
203
7.70
A0A0B4KGK0
NP_001262287
AGB95670
Polypeptides with Identical Sequences

None of the polypeptides share 100% sequence identity.

Additional Polypeptide Data and Comments
Reported size (kDa)
Comments
External Data
Subunit Structure (UniProtKB)

Monomer.

(UniProt, Q27869)
Crossreferences
InterPro - A database of protein families, domains and functional sites
Linkouts
Sequences Consistent with the Gene Model
Mapped Features

Click to get a list of regulatory features (enhancers, TFBS, etc.) and gene disruptions (point mutations, indels, etc.) within or overlapping Dmel\Pcmt using the Feature Mapper tool.

External Data
Crossreferences
Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.
Linkouts
Expression Data
Expression Summary Ribbons
Colored tiles in ribbon indicate that the Fly Cell Atlas project found the gene expressed in that cell type. Darker colors mean that more cells of that cell type express the gene:
 low
high 
Colorless tiles indicate that there is no scRNAseq data for the gene in that cell type.
Colored tiles in ribbon indicate that expression data (RNA and/or protein) has been curated by FlyBase for that anatomical location. Colorless tiles indicate that there is no curated data for that location.
Colored tiles in the ribbon indicate the average RNA expression level of the gene at the indicated stages:
 low
high 
as determined by RNA-seq (RPKM) using whole organism samples modENCODE, Brown et al., 2014. For complete stage-specific expression data, view the modENCODE Development RNA-Seq section under High-Throughput Expression below.
Transcript Expression
in situ
Stage
Tissue/Position (including subcellular localization)
Reference
embryonic stage 1 -- 3
organism

Comment: maternally deposited

(Fisher et al., 2012)
embryonic stage 4 -- 6
organism | ubiquitous
(Fisher et al., 2012)
embryonic stage 7 -- 8
organism | ubiquitous
(Fisher et al., 2012)
embryonic stage 9 -- 10
organism | ubiquitous
(Fisher et al., 2012)
embryonic stage 11 -- 12
organism | ubiquitous
(Fisher et al., 2012)
embryonic stage 13 -- 16
organism | ubiquitous
(Fisher et al., 2012)
Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Polypeptide Expression
mass spectroscopy
Stage
Tissue/Position (including subcellular localization)
Reference
adult stage
adult head
(Aradska et al., 2015)
Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Evidence
References
Expression Deduced from Reporters
High-Throughput Expression Data
Associated Tools

GBrowse - Visual display of RNA-Seq signals

View Dmel\Pcmt in GBrowse 2
RNA-Seq by Region - Search RNA-Seq expression levels by exon or genomic region
Bulk Downloads
RNA-Seq RPKM values for all genes
Reference
See Gelbart and Emmert, 2013 for analysis details and data files for all genes.
Developmental Proteome: Life Cycle
Developmental Proteome: Embryogenesis
External Data and Images
Linkouts
BDGP expression data - Patterns of gene expression in Drosophila embryogenesis
DRscDB - A single-cell RNA-seq resource for data mining and data comparison across species
EMBL-EBI Single Cell Expression Atlas - Single cell expression across species
FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data
Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns
Flygut - An atlas of the Drosophila adult midgut
Images
FlyBase Wiki
Image Based Resources
Alleles, Insertions, Transgenic Constructs, and Aberrations
Classical and Insertion Alleles ( 3 )
For All Classical and Insertion Alleles Show
 
Other relevant insertions
Transgenic Constructs ( 4 )
For All Alleles Carried on Transgenic Constructs Show
Transgenic constructs containing/affecting coding region of Pcmt
Transgenic constructs containing regulatory region of Pcmt
Aberrations (Deficiencies and Duplications) ( 2 )
Inferred from experimentation ( 2 )
Gene partially disrupted in
Df(3R)LT
(O'Connor and Tanini, 2009.6.24)
Gene disrupted in
Df(3R)Exel6144
(Ryder, 2004.4.26)
Inferred from location ( 0 )
Alleles Representing Disease-Implicated Variants
Phenotypes
Orthologs
Downloads
Download All DIOPT Orthologs
Human Orthologs (via DIOPT v8.0)
Homo sapiens (Human) (3)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Source
Compara
eggNOG
Hieranoid
Homologene
Inparanoid
Isobase
OMA
OrthoDB
OrthoFinder
OrthoInspector
orthoMCL
Panther
Phylome
RoundUp
TreeFam
ZFIN
Alignment
Complementation?
Transgene?
Hsap\PCMT1
15 of 15
Yes
Yes
Hsap\PCMTD1
1 of 15
No
Yes
Hsap\PCMTD2
1 of 15
No
Yes
Model Organism Orthologs (via DIOPT v8.0)
Mus musculus (laboratory mouse) (3)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Source
Compara
eggNOG
Hieranoid
Homologene
Inparanoid
Isobase
OMA
OrthoDB
OrthoFinder
OrthoInspector
orthoMCL
Panther
Phylome
RoundUp
TreeFam
ZFIN
Alignment
Complementation?
Transgene?
Mmus\Pcmt1
14 of 15
Yes
Yes
Mmus\Pcmtd1
1 of 15
No
Yes
Mmus\Pcmtd2
1 of 15
No
Yes
Rattus norvegicus (Norway rat) (2)
Rnor\Pcmt1
11 of 13
Yes
Yes
Rnor\Pcmtd2
1 of 13
No
Yes
Xenopus tropicalis (Western clawed frog) (3)
Xtro\pcmt1
9 of 12
Yes
Yes
Xtro\LOC100216173
8 of 12
No
Yes
Xtro\pcmtd2
1 of 12
No
Yes
Danio rerio (Zebrafish) (5)
Drer\pcmt
14 of 15
Yes
Yes
Drer\pcmtl
12 of 15
No
Yes
Drer\LOC100536777
1 of 15
No
Yes
Drer\pcmtd1
1 of 15
No
Yes
Drer\pcmtd2a
1 of 15
No
Yes
Caenorhabditis elegans (Nematode, roundworm) (2)
Cele\pcm-1
15 of 15
Yes
Yes
Cele\R119.5
1 of 15
No
Yes
Arabidopsis thaliana (thale-cress) (2)
Atha\PIMT1
9 of 9
Yes
Yes
Atha\PIMT2
8 of 9
No
Yes
Saccharomyces cerevisiae (Brewer's yeast) (0)
No records found.
Schizosaccharomyces pombe (Fission yeast) (1)
Spom\pcm2
11 of 12
Yes
Yes
Other Organism Orthologs (via OrthoDB)
Paralogs
Downloads
Download All DIOPT Paralogs
Paralogs (via DIOPT v8.0)
Drosophila melanogaster (Fruit fly) (0)
No records found.
Human Disease Associations
FlyBase Human Disease Model Reports
    Disease Model Summary Ribbon
    Disease Ontology (DO) Annotations
    Models Based on Experimental Evidence ( 0 )
    Allele
    Disease
    Evidence
    References
    Potential Models Based on Orthology ( 0 )
    Human Ortholog
    Disease
    Evidence
    References
    Modifiers Based on Experimental Evidence ( 0 )
    Allele
    Disease
    Interaction
    References
    Disease Associations of Human Orthologs (via DIOPT v8.0 and OMIM)
    Note that ortholog calls supported by only 1 or 2 algorithms (DIOPT score < 3) are not shown.
    Homo sapiens (Human)
    Gene name
    Score
    OMIM
    OMIM Phenotype
    DO term
    Complementation?
    Transgene?
    PCMT1; protein-L-isoaspartate (D-aspartate) O-methyltransferase
    15 of 15
    176851
        Functional Complementation Data
        Functional complementation data is computed by FlyBase using a combination of the orthology data obtained from DIOPT and OrthoDB and the allele-level genetic interaction data curated from the literature.
        Interactions
        Summary of Physical Interactions
        esyN Network Diagram
        Interactions Browser
        Summary of Genetic Interactions
        esyN Network Diagram
        Starting gene(s)
        Interaction type
        Interacting gene(s)
        Reference
        Starting gene(s)
        Interaction type
        Interacting gene(s)
        Reference
        External Data
        Subunit Structure (UniProtKB)
        Monomer.
        (UniProt, Q27869 )
        Linkouts
        DroID - A comprehensive database of gene and protein interactions.
        Pathways
        Signaling Pathways (FlyBase)
        Metabolic Pathways
        FlyMet - A comprehensive tissue-specific metabolomics resource for Drosophila.
        External Data
        Linkouts
        Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.
        Genomic Location and Detailed Mapping Data
        Chromosome (arm)
        3R
        Recombination map
        3-47.5
        Cytogenetic map
        83B1-102A
        Sequence location
        FlyBase Computed Cytological Location
        Cytogenetic map
        Evidence for location
        83B1-102A
        Limits computationally determined from genome sequence between P{PZ}Snr101319&P{PZ}Itp-r83A05616 and P{lacW}Atus1938; Left limit from in situ hybridisation (FBrf0085080) Right limit from in situ hybridisation (FBrf0085080)
        Experimentally Determined Cytological Location
        Cytogenetic map
        Notes
        References
        83A5-83A6
        (O'Connor, 2000.1.4)
        83A-83B
        (O'Connor, 1995.12.21)
        83A-83B
        (determined by in situ hybridisation)
        (O'Connor et al., 1997)
        101F-102A
        (determined by in situ hybridisation)
        (Galus et al., 1995)
        Experimentally Determined Recombination Data
        Location

        3-47.5

        (FlyBase, 2016)

        3-44.1

        (Comeron et al., 2012)

        3-

        (O'Connor, 1995.12.21)
        Left of (cM)
        Right of (cM)
        Notes
        Stocks and Reagents
        Stocks (11)
        Genomic Clones (19)
        cDNA Clones (42)
         

        Please Note This section lists cDNAs and ESTs that fall within the genomic extent of the gene model, which may include cDNAs and ESTs of genes within introns, or of overlapping genes. Please see GBrowse for alignment of the cDNAs and ESTs to the gene model.

        cDNA clones, fully sequenced
        BDGP DGC clones
        Other clones
        Drosophila Genomics Resource Center cDNA clones

        For each fully sequenced cDNA the DGRC maintains various forms of the cDNA (e.g tagged or untagged) in several different host vectors for subsequent cloning and expression in Drosophila and Drosophila cell lines.

        cDNA Clones, End Sequenced (ESTs)
        BDGP DGC clones
        Other clones
        RNAi and Array Information
        Linkouts
        DRSC - Results frm RNAi screens
        GenomeRNAi - A database for cell-based and in vivo RNAi phenotypes and reagents
        Antibody Information
        Laboratory Generated Antibodies
         
        Commercially Available Antibodies
         
        Other Information
        Relationship to Other Genes
        Source for database identify of

        Source for identity of: Pcmt CG2152

        (Gong, 1999.11)
        Source for database merge of

        Source for merge of: Pcmt Pimt

        (Bennett et al., 2003)
        Additional comments

        FlyBase curator comment: As pointed out by Terence Murphy of NCBI, the amino acid sequence given in Figure 1 for Pimt is identical to that of Pcmt. Therefore, this publication is the source of the merge for the two genes.

        (Bennett et al., 2003)
        Other Comments

        Nonsense-mediated mRNA decay (NMD) down-regulates a distinct splice isoform(s) of this gene.

        (Hansen et al., 2009)

        Pcmt has been cloned and sequenced.

        (O'Connor et al., 1997)
        Origin and Etymology
        Discoverer
        Etymology
        Identification
        External Crossreferences and Linkouts ( 44 )
        Sequence Crossreferences
        NCBI Gene - Gene integrates information from a wide range of species. A record may include nomenclature, Reference Sequences (RefSeqs), maps, pathways, variations, phenotypes, and links to genome-, phenotype-, and locus-specific resources worldwide.
        GenBank Nucleotide - A collection of sequences from several sources, including GenBank, RefSeq, TPA, and PDB.
        GenBank Protein - A collection of sequences from several sources, including translations from annotated coding regions in GenBank, RefSeq and TPA, as well as records from SwissProt, PIR, PRF, and PDB.
        RefSeq - A comprehensive, integrated, non-redundant, well-annotated set of reference sequences including genomic, transcript, and protein.
        UniProt/GCRP - The gene-centric reference proteome (GCRP) provides a 1:1 mapping between genes and UniProt accessions in which a single 'canonical' isoform represents the product(s) of each protein-coding gene.
        UniProt/Swiss-Prot - Manually annotated and reviewed records of protein sequence and functional information
        UniProt/TrEMBL - Automatically annotated and unreviewed records of protein sequence and functional information
        Other crossreferences
        AlphaFold DB - AlphaFold provides open access to protein structure predictions for the human proteome and other key proteins of interest, to accelerate scientific research.
        BDGP expression data - Patterns of gene expression in Drosophila embryogenesis
        Drosophila Genomics Resource Center - Drosophila Genomics Resource Center (DGRC) cDNA clones
        DRscDB - A single-cell RNA-seq resource for data mining and data comparison across species
        EMBL-EBI Single Cell Expression Atlas - Single cell expression across species
        Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.
        FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data
        Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns
        Flygut - An atlas of the Drosophila adult midgut
        FlyMet - A comprehensive tissue-specific metabolomics resource for Drosophila.
        GenomeRNAi - A database for cell-based and in vivo RNAi phenotypes and reagents
        iBeetle-Base - RNAi phenotypes in the red flour beetle (Tribolium castaneum)
        InterPro - A database of protein families, domains and functional sites
        KEGG Genes - Molecular building blocks of life in the genomic space.
        MARRVEL_MODEL - MARRVEL (model organism gene)
        modMine - A data warehouse for the modENCODE project
        Linkouts
        DroID - A comprehensive database of gene and protein interactions.
        DRSC - Results frm RNAi screens
        FlyCyc Genes - Genes from a BioCyc PGDB for Dmel
        FlyMine - An integrated database for Drosophila genomics
        Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.
        Synonyms and Secondary IDs (10)
        Reported As
        Symbol Synonym
        CG2152
        (Çiçek et al., 2016, Ni et al., 2010.12.1, Hansen et al., 2009, Ayres et al., 2008)
        PCMT
        (Jones and Grotewiel, 2011)
        PIMT
        (David et al., 1999, Galus et al., 1995)
        Pcmt
        (Cho et al., 2020, Al-Ramahi et al., 2018, Louie et al., 2016, Kwon et al., 2013, Hansen et al., 2009, O'Connor, 2009.5.11, O'Connor and Tanini, 2009.6.24)
        Pimt
        dPIMT
        (Bennett et al., 2003)
        pcmt
        (Ayres et al., 2008)
        Name Synonyms
        Protein isoaspartyl methyltransferase
        (Galus et al., 1995)
        Protein-L-isoaspartate (D-aspartate) O-methyltransferase
        protein D-aspartyl, L-isoaspartyl O-methyltransferase
        (O'Connor, 1995.10.2)
        Secondary FlyBase IDs
        • FBgn0015276
        • FBgn0015280
        • FBgn0022769
        Datasets (0)
        Study focus (0)
        Experimental Role
        Project
        Project Type
        Title
        Study result (0)
        Result
        Result Type
        Title
        References (47)