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

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: mouse all
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Genomic context

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)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	16	NC_000016.9 (69360816..69364491, complement)

Chromosome 16 - NC_000016.10 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 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?

compound M7594_0037 exhibited potent anticancer activities against HeLa, A549 and MCF-7 cell lines with IC50s of 35.26, 29.63 and 24.63 muM, respectively. Molecular docking studies suggested that M7594_0037 and its three derivatives could interact with Human peptide deformylase by several conserved hydrogen bonds.
Title: Structure-Based Drug Design of Small Molecule Peptide Deformylase Inhibitors to Treat Cancer.
c-myc regulated the expression of human PDF.
Title: Inhibition of human mitochondrial peptide deformylase causes apoptosis in c-myc-overexpressing hematopoietic cancers.
This is the first report showing that PDF is over-expressed in breast, colon, and lung cancers
Title: Overexpression of peptide deformylase in breast, colon, and lung cancers.
these data reveals that PDF has several transcription start sites, the most important of which only 18 bp from the initiation codon.
Title: Transcriptional regulation of the human mitochondrial peptide deformylase (PDF).
the origin, evolution and preservation of the COG8/PDF same-strand overlap follow similar mechanistic steps as those documented for antisense overlaps where gain and/or loss of splice sites and polyadenylation signals seems to drive the process.
Title: Successful COG8 and PDF overlap is mediated by alterations in splicing and polyadenylation signals.
Observational study of gene-disease association. (HuGE Navigator)
Title: Polymorphisms in mitochondrial genes and prostate cancer risk.
Despite the lack of true S2' and S3' binding pockets, confirmed through peptide binding modeling, enzyme kinetics suggest a combined contribution from P2'and P3' positions of a formylated peptide substrate to turnover.
Title: Structure and activity of human mitochondrial peptide deformylase, a novel cancer target.
The inhibition of HsPDF may provide an explanation for the mechanism by which actinonin is cytotoxic against various human tumor cell lines.
Title: A new human peptide deformylase inhibitable by actinonin.

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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

RH48796 (e-PCR)
- UniSTS:92195

SHGC-34961 (e-PCR)
- UniSTS:75180

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
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: peptide deformylase, mitochondrial

Names: peptide deformylase-like protein; polypeptide deformylase

NP_071736.1

EC 3.5.1.88

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_033043.1 RefSeqGene

Range

5008..8683

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_022341.2 → NP_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:67 → 224

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) ...