Seroatlas · Human Serome Atlas

PDF

Peptide deformylase, mitochondrial

Also known as: DEFM_HUMAN

Cross-references: UniProt · Ensembl · Human Protein Atlas · GeneCards · NCBI Gene

Protein identityUniProt · HPA

UniProt accession: Q9HBH1
Gene: PDF
Ensembl: ENSG00000258429
Chromosome: 16
Canonical length: 243 aa
Protein class: Enzymes, Metabolic proteins, Predicted intracellular proteins
Subcellular location: Nucleoplasm,Mitochondria
Secretome location: Intracellular and membrane
Quaternary structure: Homodimer

OverviewNCBI 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]

Canonical amino-acid sequenceUniProt

243 residues, UniProt reviewed canonical sequence.

>Q9HBH1|PDF
     1  MARLWGALSL WPLWAAVPWG GAAAVGVRAC SSTAAPDGVE GPALRRSYWR HLRRLVLGPP
    61  EPPFSHVCQV GDPVLRGVAA PVERAQLGGP ELQRLTQRLV QVMRRRRCVG LSAPQLGVPR
   121  QVLALELPEA LCRECPPRQR ALRQMEPFPL RVFVNPSLRV LDSRLVTFPE GCESVAGFLA
   181  CVPRFQAVQI SGLDPNGEQV VWQASGWAAR IIQHEMDHLQ GCLFIDKMDS RTFTNVYWMK
   241  VND

LocalizationUniProt · AlphaFold · HPA

Whether an antibody against PDF can act on the native protein depends on physical access: surface and secreted proteins are reachable by circulating antibodies, intracellular proteins usually are not.

Antibody reachability: Intracellular
Secreted: No
Transmembrane segments: 0
Mean surface accessibility (rSASA): 0.36
Highest tissue expression: 6 nTPM

Expression across tissuesHPA

Tissue

liver: 6 nTPM
kidney: 4.8 nTPM
skeletal muscle: 4.2 nTPM
pancreas: 3.2 nTPM
esophagus: 2.9 nTPM
adrenal gland: 2.4 nTPM

Single-cell type

conjunctival goblet cells: 1 nCPM
megakaryocyte progenitors: 0.9 nCPM
plasma cells: 0.7 nCPM
megakaryocyte-erythroid progenitors: 0.6 nCPM
alveolar cells type 1: 0.4 nCPM
endometrial ciliated cells: 0.4 nCPM

Immune cell

naive B-cell: 4.1 nTPM
naive CD4 T-cell: 1.5 nTPM
basophil: 1.3 nTPM
plasmacytoid DC: 1.3 nTPM
memory B-cell: 1.2 nTPM
memory CD8 T-cell: 1.2 nTPM

Brain region

hippocampal formation: 9.8 nTPM
cerebellum: 9 nTPM
cerebral cortex: 8.9 nTPM
choroid plexus: 8.4 nTPM
white matter: 8.2 nTPM
medulla oblongata: 8 nTPM

Genetic constraint and essentialitygnomAD · DepMap

Does the body need this protein intact? Low LOEUF or a strong DepMap dependency means loss or blockade of the protein is likely to be felt.

gnomAD LOEUF (loss-of-function intolerance): 1.9
gnomAD pLI: 0
gnomAD missense Z: -1.19
DepMap mean gene effect: -0.08
DepMap dependency class: selective

Cancer expressionTCGA

Across TCGA tumor cohorts, this protein is over-expressed in roughly 4% of surveyed tumor types (aggregate summary; per-cohort expression, alteration, and survival load in the interactive view).

OntologyGO

Biological processes

Molecular functions

metal ion binding
peptide deformylase activity

Cellular components

mitochondrion

Protein domainsUniProt · Pfam · InterPro

Peptide deformylase
Peptide deformylase superfamily
Polypeptide deformylase

KeywordsUniProt

Antibody and autoantibody relevanceSeroatlas analysis

Seroatlas reads PDF as an antibody target. Whether an autoantibody or antibody against PDF could matter depends on whether native PDF is physically reachable, whether the body needs it intact, and whether it acts in a disease-relevant tissue.

PDF is annotated as predominantly intracellular. Intracellular proteins are common autoantibody markers, becoming visible to the immune system after cell injury or altered processing, but are usually markers of disease rather than direct drivers.

Annotation status

The present source text does not explicitly label PDF as an autoantigen. Seroatlas presents hypothesis context only and does not manufacture a known-serology claim.

Loading the interactive Seroatlas protein explorer...