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METAP1D methionyl aminopeptidase type 1D, mitochondrial [ Homo sapiens (human) ]

Gene ID: 254042, updated on 2-Nov-2024

Summary

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Official Symbol
METAP1Dprovided by HGNC
Official Full Name
methionyl aminopeptidase type 1D, mitochondrialprovided by HGNC
Primary source
HGNC:HGNC:32583
See related
Ensembl:ENSG00000172878 MIM:610267; AllianceGenome:HGNC:32583
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
MAP1D; MAP 1D; Metap1l; MetAP 1D
Summary
The N-terminal methionine excision pathway is an essential process in which the N-terminal methionine is removed from many proteins, thus facilitating subsequent protein modification. In mitochondria, enzymes that catalyze this reaction are celled methionine aminopeptidases (MetAps, or MAPs; EC 3.4.11.18) (Serero et al., 2003 [PubMed 14532271]).[supplied by OMIM, Mar 2008]
Expression
Ubiquitous expression in ovary (RPKM 4.2), endometrium (RPKM 2.3) and 25 other tissues See more
Orthologs
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Genomic context

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See METAP1D in Genome Data Viewer
Location:
2q31.1
Exon count:
13
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (171999953..172082430)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (172486172..172568673)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (172864860..172947158)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene histone acetyltransferase 1 Neighboring gene PDGFA associated protein 1 pseudogene Neighboring gene uncharacterized LOC124905590 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12106 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16761 Neighboring gene VISTA enhancer hs553 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:172945060-172945588 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:172945589-172946118 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:172948655-172949268 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:172949269-172949880 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:172949881-172950494 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:172950495-172951106 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:172951721-172952332 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:172952946-172953557 Neighboring gene VISTA enhancer hs422 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12108 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12109 Neighboring gene distal-less homeobox 1 Neighboring gene distal-less homeobox 2

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. Structural insights into N-terminal methionine cleavage by the human mitochondrial methionine aminopeptidase, MetAP1D. Lee Y, et al. Sci Rep, 2023 Dec 15. PMID 38102161, Free PMC Article
  2. MAP1D, a novel methionine aminopeptidase family member is overexpressed in colon cancer. Leszczyniecka M, et al. Oncogene, 2006 Jun 8. PMID 16568094
  3. An unusual peptide deformylase features in the human mitochondrial N-terminal methionine excision pathway. Serero A, et al. J Biol Chem, 2003 Dec 26. PMID 14532271
  4. Apocrine glands are bystanders in hidradenitis suppurativa and their involvement is gender specific. Zouboulis CC, et al. J Eur Acad Dermatol Venereol, 2020 Jul. PMID 32031713
  5. Large-scale genotyping identifies 41 new loci associated with breast cancer risk. Michailidou K, et al. Nat Genet, 2013 Apr. PMID 23535729, Free PMC Article

See all (21) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Structural insights into N-terminal methionine cleavage by the human mitochondrial methionine aminopeptidase, MetAP1D.
    Title: Structural insights into N-terminal methionine cleavage by the human mitochondrial methionine aminopeptidase, MetAP1D.
  2. Observational study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
    Title: Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study.
  3. Observational study of gene-disease association. (HuGE Navigator)
    Title: Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression.
  4. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
    Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
  5. MAP1D is a potentially oncogenic, novel member of the MAP gene family that may play an important role in colon tumorigenesis
    Title: MAP1D, a novel methionine aminopeptidase family member is overexpressed in colon cancer.
Submit: New GeneRIF Correction

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

EBI GWAS Catalog

Description
Large-scale genotyping identifies 41 new loci associated with breast cancer risk.
EBI GWAS Catalog

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

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 aminopeptidase activity TAS
Traceable Author Statement
more info
 PubMed 
enables initiator methionyl aminopeptidase activity IEA
Inferred from Electronic Annotation
more info
  
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
enables metalloaminopeptidase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables metalloexopeptidase activity TAS
Traceable Author Statement
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in N-terminal protein amino acid modification TAS
Traceable Author Statement
more info
 PubMed 
involved_in peptidyl-methionine modification TAS
Traceable Author Statement
more info
 PubMed 
involved_in proteolysis IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
located_in mitochondrion HTP PubMed 
is_active_in mitochondrion IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in mitochondrion IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
methionine aminopeptidase 1D, mitochondrial
Names
CDS of metAP-3 within PCR fragment
metAP 1D
peptidase M 1D
NP_001309207.1
NP_001309208.1
NP_954697.1
XP_047299826.1
XP_047299827.1
XP_047299828.1
XP_054188845.1
XP_054188846.1
XP_054188847.1
XP_054197245.1
XP_054197246.1
XP_054197247.1

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.

mRNA and Protein(s)

  1. NM_001322278.2 → NP_001309207.1  methionine aminopeptidase 1D, mitochondrial isoform 2

    Status: VALIDATED

    Source sequence(s)
    AC015976, BC143913, BM982111
    UniProtKB/Swiss-Prot
    Q6UB28
    Conserved Domains (1) summary
    cd01086
    Location:1 → 212
    MetAP1; Methionine Aminopeptidase 1. E.C. 3.4.11.18. Also known as methionyl aminopeptidase and Peptidase M. Catalyzes release of N-terminal amino acids, preferentially methionine, from peptides and arylamides.

  2. NM_001322279.2 → NP_001309208.1  methionine aminopeptidase 1D, mitochondrial isoform 2

    Status: VALIDATED

    Source sequence(s)
    AC015976, AC114745, AY374142, BM982111
    UniProtKB/Swiss-Prot
    Q6UB28
    Conserved Domains (1) summary
    cd01086
    Location:1 → 212
    MetAP1; Methionine Aminopeptidase 1. E.C. 3.4.11.18. Also known as methionyl aminopeptidase and Peptidase M. Catalyzes release of N-terminal amino acids, preferentially methionine, from peptides and arylamides.

  3. NM_199227.3 → NP_954697.1  methionine aminopeptidase 1D, mitochondrial isoform 1 precursor

    See identical proteins and their annotated locations for NP_954697.1

    Status: VALIDATED

    Source sequence(s)
    AC015976, AY374142, BM982111
    Consensus CDS
    CCDS2246.1
    UniProtKB/Swiss-Prot
    Q1WNX3, Q6UB28
    Related
    ENSP00000315152.4, ENST00000315796.5
    Conserved Domains (1) summary
    cd01086
    Location:94 → 330
    MetAP1; Methionine Aminopeptidase 1. E.C. 3.4.11.18. Also known as methionyl aminopeptidase and Peptidase M. Catalyzes release of N-terminal amino acids, preferentially methionine, from peptides and arylamides.

RNA

  1. NR_136273.2 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AC015976, AC114745, BM982111

  2. NR_136276.2 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AC015976, AY374142, BM982111

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_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    171999953..172082430
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047443870.1 → XP_047299826.1  methionine aminopeptidase 1D, mitochondrial isoform X1

  2. XM_047443871.1 → XP_047299827.1  methionine aminopeptidase 1D, mitochondrial isoform X2

  3. XM_047443872.1 → XP_047299828.1  methionine aminopeptidase 1D, mitochondrial isoform X3

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_025791761.1 Reference GRCh38.p14 PATCHES

    Range
    439003..521197
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054332870.1 → XP_054188845.1  methionine aminopeptidase 1D, mitochondrial isoform X1

  2. XM_054332871.1 → XP_054188846.1  methionine aminopeptidase 1D, mitochondrial isoform X2

  3. XM_054332872.1 → XP_054188847.1  methionine aminopeptidase 1D, mitochondrial isoform X3

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    172486172..172568673
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054341270.1 → XP_054197245.1  methionine aminopeptidase 1D, mitochondrial isoform X1

  2. XM_054341271.1 → XP_054197246.1  methionine aminopeptidase 1D, mitochondrial isoform X2

  3. XM_054341272.1 → XP_054197247.1  methionine aminopeptidase 1D, mitochondrial isoform X3

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q6UB28.1 GenPept UniProtKB/Swiss-Prot:Q6UB28

Gene LinkOut

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