Free for academic non-profit institutions. Other users need a Commercial license

Aliases for PDF Gene

Aliases for PDF Gene

  • Peptide Deformylase (Mitochondrial) 2 3
  • Polypeptide Deformylase 4
  • EC 3.5.1.88 4
  • PDF1A 4

External Ids for PDF Gene

Previous GeneCards Identifiers for PDF Gene

  • GC16M069740
  • GC16M069097
  • GC16M069138
  • GC16M067920
  • GC16M069360
  • GC16M069362

Summaries for PDF Gene

Entrez Gene Summary for PDF Gene

  • 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]

GeneCards Summary for PDF Gene

PDF (Peptide Deformylase (Mitochondrial)) is a Protein Coding gene. GO annotations related to this gene include iron ion binding and peptide deformylase activity.

UniProtKB/Swiss-Prot for PDF Gene

  • Removes the formyl group from the N-terminal Met of newly synthesized proteins.

Gene Wiki entry for PDF Gene

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

Genomics for PDF Gene

Regulatory Elements for PDF Gene

Genomic Location for PDF Gene

Chromosome:
16
Start:
69,328,621 bp from pter
End:
69,330,595 bp from pter
Size:
1,975 bases
Orientation:
Minus strand

Genomic View for PDF Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for PDF Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PDF Gene

Proteins for PDF Gene

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

    Protein Symbol:
    Q9HBH1-DEFM_HUMAN
    Recommended name:
    Peptide deformylase, mitochondrial
    Protein Accession:
    Q9HBH1
    Secondary Accessions:
    • Q8WUN6

    Protein attributes for PDF Gene

    Size:
    243 amino acids
    Molecular mass:
    27013 Da
    Cofactor:
    Name=Co(2+); Xref=ChEBI:CHEBI:48828; Note=Binds 1 Co(2+) ion.;
    Quaternary structure:
    • Homodimer.

    Three dimensional structures from OCA and Proteopedia for PDF Gene

neXtProt entry for PDF Gene

Proteomics data for PDF Gene at MOPED

Post-translational modifications for PDF Gene

No Post-translational modifications

Other Protein References for PDF Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for PDF Gene

Domains & Families for PDF Gene

Protein Domains for PDF Gene

Suggested Antigen Peptide Sequences for PDF Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q9HBH1

UniProtKB/Swiss-Prot:

DEFM_HUMAN :
  • Belongs to the polypeptide deformylase family.
Family:
  • Belongs to the polypeptide deformylase family.
genes like me logo Genes that share domains with PDF: view

No data available for Gene Families for PDF Gene

Function for PDF Gene

Molecular function for PDF Gene

UniProtKB/Swiss-Prot CatalyticActivity:
Formyl-L-methionyl peptide + H(2)O = formate + methionyl peptide
UniProtKB/Swiss-Prot Function:
Removes the formyl group from the N-terminal Met of newly synthesized proteins.

Enzyme Numbers (IUBMB) for PDF Gene

Gene Ontology (GO) - Molecular Function for PDF Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005506 iron ion binding IEA --
GO:0042586 peptide deformylase activity IDA 15489958
genes like me logo Genes that share ontologies with PDF: view

Phenotypes for PDF Gene

genes like me logo Genes that share phenotypes with PDF: view

Animal Model Products

miRNA Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for PDF

In Situ Assay Products

Flow Cytometry Products

No data available for Animal Models , Transcription Factor Targets and HOMER Transcription for PDF Gene

Localization for PDF Gene

Subcellular locations from UniProtKB/Swiss-Prot for PDF Gene

Mitochondrion.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for PDF Gene COMPARTMENTS Subcellular localization image for PDF gene
Compartment Confidence
mitochondrion 4
chloroplast 1

Gene Ontology (GO) - Cellular Components for PDF Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005739 mitochondrion IDA 15489958
genes like me logo Genes that share ontologies with PDF: view

Pathways & Interactions for PDF Gene

SuperPathways for PDF Gene

No Data Available

Interacting Proteins for PDF Gene

Gene Ontology (GO) - Biological Process for PDF Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006412 translation IEA --
GO:0008284 positive regulation of cell proliferation IMP 15489958
GO:0018206 peptidyl-methionine modification IDA 15489958
GO:0031365 N-terminal protein amino acid modification IDA 15489958
GO:0043686 co-translational protein modification IBA --
genes like me logo Genes that share ontologies with PDF: view

No data available for Pathways by source and SIGNOR curated interactions for PDF Gene

Drugs & Compounds for PDF Gene

(8) Drugs for PDF Gene - From: NovoSeek, DrugBank, and HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Iron Approved Pharma 957
Zinc Approved Pharma 1404
2-[(Formyl-Hydroxy-Amino)-Methyl]-Heptanoic Acid [1-(2-Hydroxymethyl-Pyrrolidine-1-Carbonyl)-2-Methyl-Propyl]-Amide Experimental Pharma Target 0
Bb-3497 Experimental Pharma Target, inhibitor 0
Formic acid Experimental Pharma 0

(15) Additional Compounds for PDF Gene - From: NovoSeek and HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
Water
  • Dihydrogen oxide
  • Steam
7732-18-5
ACTINONIN
amide
carboxylate
Fatty acid
genes like me logo Genes that share compounds with PDF: view

Transcripts for PDF Gene

mRNA/cDNA for PDF Gene

(1) REFSEQ mRNAs :
(266) Selected AceView cDNA sequences:
(1) Ensembl transcripts including schematic representations, and UCSC links where relevant :

miRNA Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for PDF

Flow Cytometry Products

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

No ASD Table

Relevant External Links for PDF Gene

GeneLoc Exon Structure for
PDF
ECgene alternative splicing isoforms for
PDF

Expression for PDF Gene

mRNA expression in normal human tissues for PDF Gene

mRNA differential expression in normal tissues according to GTEx for PDF Gene

This gene is overexpressed in Kidney - Cortex (x4.6) and Liver (x4.3).

Protein differential expression in normal tissues from HIPED for PDF Gene

This gene is overexpressed in Tlymphocyte (16.7), Plasma (8.6), and Monocytes (7.3).

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



mRNA Expression by UniProt/SwissProt for PDF Gene

Q9HBH1-DEFM_HUMAN
Tissue specificity: Ubiquitous
genes like me logo Genes that share expression patterns with PDF: view

Primer Products

  • QuantiTect SYBR Green Assays in human,mouse,rat
  • Pre-validated RT² qPCR Primer Assay in human,mouse,rat
  • QuantiFast Probe-based Assays in human,mouse,rat

In Situ Assay Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery and Protein tissue co-expression partners for PDF Gene

Orthologs for PDF Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for PDF Gene

Organism Taxonomy Gene Similarity Type Details
cow
(Bos Taurus)
Mammalia PDF 35
  • 84.43 (n)
  • 82.1 (a)
PDF 36
  • 81 (a)
OneToOne
dog
(Canis familiaris)
Mammalia PDF 35
  • 85.55 (n)
  • 82.74 (a)
PDF 36
  • 78 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Pdf 35
  • 80.09 (n)
  • 82.46 (a)
Pdf 16
Pdf 36
  • 74 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Pdf 35
  • 76.49 (n)
  • 77.23 (a)
oppossum
(Monodelphis domestica)
Mammalia PDF 36
  • 63 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia PDF 36
  • 64 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia pdf 35
  • 57.79 (n)
  • 55.61 (a)
Str.15126 35
African clawed frog
(Xenopus laevis)
Amphibia Xl.23230 35
zebrafish
(Danio rerio)
Actinopterygii Dr.12887 35
pdf 35
  • 53.18 (n)
  • 51.63 (a)
pdf 36
  • 47 (a)
OneToOne
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.7415 35
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP003861 35
  • 54.58 (n)
  • 42.86 (a)
fruit fly
(Drosophila melanogaster)
Insecta CG31278 35
  • 52.3 (n)
  • 44.75 (a)
CG31278 36
  • 35 (a)
OneToMany
CG31373 36
  • 36 (a)
OneToMany
thale cress
(Arabidopsis thaliana)
eudicotyledons PDF1A 35
  • 43.86 (n)
  • 39.77 (a)
rice
(Oryza sativa)
Liliopsida Os01g0555800 35
  • 47.96 (n)
  • 46.94 (a)
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.1450 35
Species with no ortholog for PDF:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • chicken (Gallus gallus)
  • chimpanzee (Pan troglodytes)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • 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)
  • platypus (Ornithorhynchus anatinus)
  • 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)
  • worm (Caenorhabditis elegans)

Evolution for PDF Gene

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

Paralogs for PDF Gene

No data available for Paralogs for PDF Gene

Variants for PDF Gene

Sequence variations from dbSNP and Humsavar for PDF Gene

SNP ID Clin Chr 16 pos Sequence Context AA Info Type MAF
rs758001382 -- 69,331,904(+) CCTGC(-/A)AGCAG upstream-variant-2KB
VAR_060122 -

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

Variant ID Type Subtype PubMed ID
nsv906820 CNV Loss 21882294
nsv827715 CNV Loss 20364138

Variation tolerance for PDF Gene

Gene Damage Index Score: 4.90; 67.67% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for PDF Gene

HapMap Linkage Disequilibrium report
PDF

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PDF Gene

Disorders for PDF Gene

Relevant External Links for PDF

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

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for PDF Gene

Publications for PDF Gene

  1. Human mitochondrial peptide deformylase, a new anticancer target of actinonin-based antibiotics. (PMID: 15489958) Lee M.D. … Scheinberg D.A. (J. Clin. Invest. 2004) 2 23 67
  2. Identification of eukaryotic peptide deformylases reveals universality of N-terminal protein processing mechanisms. (PMID: 11060042) Giglione C. … Meinnel T. (EMBO J. 2000) 2 23 67
  3. Codon optimization enhances protein expression of human peptide deformylase in E. coli. (PMID: 19825416) Han J.H. … Ryu K.S. (Protein Expr. Purif. 2010) 23 67
  4. Solvent-assisted slow conversion of a dithiazole derivative produces a competitive inhibitor of peptide deformylase. (PMID: 19922819) Berg A.K. … Srivastava D.K. (Biochim. Biophys. Acta 2010) 23 67
  5. Formyl peptide receptor-mediated proinflammatory consequences of peptide deformylase inhibition in Staphylococcus aureus. (PMID: 20156579) Mader D. … Peschel A. (Microbes Infect. 2010) 23 67

Products for PDF Gene

Sources for PDF Gene

Back to Top

Content