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PDF peptide deformylase, mitochondrial [ Homo sapiens (human) ]

Gene ID: 64146, updated on 19-Sep-2024

Summary

Official Symbol
PDFprovided by HGNC
Official Full Name
peptide deformylase, mitochondrialprovided by HGNC
Primary source
HGNC:HGNC:30012
See related
Ensembl:ENSG00000258429 MIM:618720; AllianceGenome:HGNC:30012
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
Summary
Protein synthesis proceeds after formylation of methionine by methionyl-tRNA formyl transferase (FMT) and transfer of the charged initiator f-met tRNA to the ribosome. In eubacteria and eukaryotic organelles the product of this gene, peptide deformylase (PDF), removes the formyl group from the initiating methionine of nascent peptides. In eubacteria, deformylation of nascent peptides is required for subsequent cleavage of initiating methionines by methionine aminopeptidase. The discovery that a natural inhibitor of PDF, actinonin, acts as an antimicrobial agent in some bacteria has spurred intensive research into the design of bacterial-specific PDF inhibitors. In human cells, only mitochondrial proteins have N-formylation of initiating methionines. Protein inhibitors of PDF or siRNAs of PDF block the growth of cancer cell lines but have no effect on normal cell growth. In humans, PDF function may therefore be restricted to rapidly growing cells. [provided by RefSeq, Nov 2008]
Expression
Ubiquitous expression in kidney (RPKM 13.2), testis (RPKM 10.1) and 25 other tissues See more
Orthologs
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Genomic context

See PDF in Genome Data Viewer
Location:
16q22.1
Exon count:
2
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (69326913..69330588, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (75128608..75132285, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (69360816..69364491, complement)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene RNA, U6 small nuclear 22, pseudogene Neighboring gene syntrophin beta 2 Neighboring gene zinc finger CCHC-type and RNA binding motif containing 1 pseudogene Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:69344125-69345075 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:69345076-69346025 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr16:69349279-69350478 Neighboring gene vacuolar protein sorting 4 homolog A Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:69363857-69364504 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7657 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:69365153-69365800 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7658 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7659 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11036 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11037 Neighboring gene component of oligomeric golgi complex 8 Neighboring gene nucleolar pre-rRNA processing protein NIP7 Neighboring gene transmembrane p24 trafficking protein 6

Genomic regions, transcripts, and products

Expression

  • 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

Related articles in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
 
enables peptide deformylase activity IBA
Inferred from Biological aspect of Ancestor
more info
 
enables peptide deformylase activity IDA
Inferred from Direct Assay
more info
PubMed 
Process Evidence Code Pubs
involved_in N-terminal protein amino acid modification IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in N-terminal protein amino acid modification IDA
Inferred from Direct Assay
more info
PubMed 
involved_in co-translational protein modification IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in peptidyl-methionine modification IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in peptidyl-methionine modification IDA
Inferred from Direct Assay
more info
PubMed 
involved_in positive regulation of cell population proliferation IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in translation 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

Preferred Names
peptide deformylase, mitochondrial
Names
peptide deformylase-like protein
polypeptide deformylase
NP_071736.1

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.

Genomic

  1. NG_033043.1 RefSeqGene

    Range
    5008..8683
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_022341.2NP_071736.1  peptide deformylase, mitochondrial precursor

    See identical proteins and their annotated locations for NP_071736.1

    Status: REVIEWED

    Source sequence(s)
    AC026464, AF239156
    Consensus CDS
    CCDS10875.1
    UniProtKB/Swiss-Prot
    Q8WUN6, Q9HBH1
    Related
    ENSP00000288022.1, ENST00000288022.2
    Conserved Domains (1) summary
    cd00487
    Location:67224
    Pep_deformylase; Polypeptide or peptide deformylase; a family of metalloenzymes that catalyzes the removal of the N-terminal formyl group in a growing polypeptide chain following translation initiation during protein synthesis in prokaryotes. These enzymes utilize Fe(II) ...

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_000016.10 Reference GRCh38.p14 Primary Assembly

    Range
    69326913..69330588 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060940.1 Alternate T2T-CHM13v2.0

    Range
    75128608..75132285 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)