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Aliases for PDF Gene

Aliases for PDF Gene

  • Peptide Deformylase, Mitochondrial 2 3 5
  • Peptide Deformylase (Mitochondrial) 2
  • 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. Gene Ontology (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

Additional gene information for PDF Gene

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

Genomics for PDF Gene

GeneHancer (GH) Regulatory Elements for PDF Gene

Promoters and enhancers for PDF Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH16I069328 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 550.8 +0.6 635 3.3 HDGF PKNOX1 MLX ZFP64 ARID4B SIN3A FEZF1 DMAP1 ZNF2 YY1 PIR46379 PDF UTP4 SNTB2 NIP7 TMED6 PIR53878 COG8
GH16I069097 Enhancer 0.4 dbSUPER 8.2 +232.9 232879 0.8 ZFHX2 EGR1 RNU6-898P UTP4 CHTF8 SNTB2 ENSG00000200164 PDF CDH1 HAS3 RPS2P45
GH16I069356 Enhancer 0.2 ENCODE 12.4 -26.6 -26602 0.8 ENSG00000260371 PDF WWP2 ENSG00000252443 PIR63038 TERF2
GH16I069756 Enhancer 0.7 FANTOM5 2 -426.5 -426541 0.9 CTBP1 CEBPA CEBPB CEBPG ZBTB33 ZNF24 NONOP1 ENSG00000252443 NPIPB14P LOC100506083 NOB1 PDF NIP7
GH16I069717 Enhancer 0.3 FANTOM5 1.2 -386.8 -386830 0.4 GC16M069712 NQO1 TERF2 PDF ENSG00000261602
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around PDF on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the PDF gene promoter:

Genomic Locations for PDF Gene

Genomic Locations for PDF Gene
chr16:69,328,621-69,330,595
(GRCh38/hg38)
Size:
1,975 bases
Orientation:
Minus strand
chr16:69,362,524-69,364,498
(GRCh37/hg19)

Genomic View for PDF Gene

Genes around PDF on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PDF Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
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;
    Quaternary structure:
    • Homodimer.

    Three dimensional structures from OCA and Proteopedia for PDF Gene

neXtProt entry for PDF Gene

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

Gene Families for PDF Gene

Human Protein Atlas (HPA):
  • Enzymes
  • Predicted secreted proteins

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

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:0016787 hydrolase activity IEA --
GO:0042586 peptide deformylase activity IDA 15489958
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with PDF: view
genes like me logo Genes that share phenotypes with PDF: view

Animal Model Products

CRISPR Products

miRNA for PDF Gene

miRTarBase miRNAs that target PDF

Inhibitory RNA Products

No data available for Phenotypes From GWAS Catalog , Human Phenotype Ontology , 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
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for PDF gene
Compartment Confidence
mitochondrion 5

Subcellular locations from the

Human Protein Atlas (HPA)
  • Mitochondria (2)
  • Nucleoplasm (2)
See all subcellular structures

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

No Data Available

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

(11) Drugs for PDF Gene - From: DrugBank, HMDB, and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Formic acid Approved, Experimental, Investigational Pharma 0
Water Approved Pharma 0
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

(12) Additional Compounds for PDF Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
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 :

CRISPR Products

Inhibitory RNA 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 from GTEx, Illumina, BioGPS, and CGAP SAGE 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, MaxQB, and MOPED for PDF Gene



NURSA nuclear receptor signaling pathways regulating expression of PDF Gene:

PDF

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

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , Protein tissue co-expression partners , Evidence on tissue expression from TISSUES and Phenotype-based relationships between genes and organs from Gene ORGANizer 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
dog
(Canis familiaris)
Mammalia PDF 33 34
  • 85.55 (n)
cow
(Bos Taurus)
Mammalia PDF 33 34
  • 84.43 (n)
mouse
(Mus musculus)
Mammalia Pdf 33 16 34
  • 80.09 (n)
rat
(Rattus norvegicus)
Mammalia Pdf 33
  • 76.49 (n)
oppossum
(Monodelphis domestica)
Mammalia PDF 34
  • 63 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia PDF 34
  • 64 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia pdf 33
  • 57.79 (n)
Str.15126 33
African clawed frog
(Xenopus laevis)
Amphibia Xl.23230 33
zebrafish
(Danio rerio)
Actinopterygii pdf 33 34
  • 53.18 (n)
Dr.12887 33
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.7415 33
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP003861 33
  • 54.58 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG31278 33 34
  • 52.3 (n)
CG31373 34
  • 36 (a)
OneToMany
thale cress
(Arabidopsis thaliana)
eudicotyledons PDF1A 33
  • 43.86 (n)
rice
(Oryza sativa)
Liliopsida Os01g0555800 33
  • 47.96 (n)
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.1450 33
Species where no ortholog for PDF was found in the sources mined by GeneCards:
  • 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 Variation AA Info Type
rs1055399 likely-benign, Congenital disorder of glycosylation 69,328,876(-) C/A 3_prime_UTR_variant
rs1055401 likely-benign, Congenital disorder of glycosylation 69,328,874(-) T/A 3_prime_UTR_variant
rs114861924 benign, not provided, not specified, Congenital disorder of glycosylation type 2H 69,331,089(-) G/A upstream_transcript_variant
rs121434387 pathogenic, Congenital disorder of glycosylation type 2H 69,331,067(-) G/A/C upstream_transcript_variant
rs189199610 uncertain-significance, likely-benign, Congenital disorder of glycosylation, not specified 69,331,058(-) T/G upstream_transcript_variant

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

Variant ID Type Subtype PubMed ID
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)

Additional Variant Information for PDF Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
PDF

SNP Genotyping and Copy Number Assay Products

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

Disorders for PDF Gene

Additional Disease Information for PDF

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology

No disorders were found for PDF Gene.

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

Publications for PDF Gene

  1. Identification of eukaryotic peptide deformylases reveals universality of N-terminal protein processing mechanisms. (PMID: 11060042) Giglione C … Meinnel T (The EMBO journal 2000) 2 3 4 22 58
  2. Human mitochondrial peptide deformylase, a new anticancer target of actinonin-based antibiotics. (PMID: 15489958) Lee MD … Scheinberg DA (The Journal of clinical investigation 2004) 2 3 22 58
  3. An unusual peptide deformylase features in the human mitochondrial N-terminal methionine excision pathway. (PMID: 14532271) Serero A … Meinnel T (The Journal of biological chemistry 2003) 3 4 22 58
  4. Structure and activity of human mitochondrial peptide deformylase, a novel cancer target. (PMID: 19236878) Escobar-Alvarez S … Scheinberg DA (Journal of molecular biology 2009) 3 4 58
  5. Polymorphisms in mitochondrial genes and prostate cancer risk. (PMID: 19064571) Wang L … Thibodeau SN (Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology 2008) 3 44 58

Products for PDF Gene

Sources for PDF Gene

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