LOCUS       NM_022341               2859 bp    mRNA    linear   PRI 20-SEP-2024
DEFINITION  Homo sapiens peptide deformylase, mitochondrial (PDF), mRNA;
            nuclear gene for mitochondrial product.
ACCESSION   NM_022341
VERSION     NM_022341.2
KEYWORDS    RefSeq; MANE Select.
SOURCE      Homo sapiens (human)
  ORGANISM  Homo sapiens
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
            Catarrhini; Hominidae; Homo.
REFERENCE   1  (bases 1 to 2859)
  AUTHORS   Morgenstern,M., Peikert,C.D., Lubbert,P., Suppanz,I., Klemm,C.,
            Alka,O., Steiert,C., Naumenko,N., Schendzielorz,A., Melchionda,L.,
            Muhlhauser,W.W.D., Knapp,B., Busch,J.D., Stiller,S.B.,
            Dannenmaier,S., Lindau,C., Licheva,M., Eickhorst,C., Galbusera,R.,
            Zerbes,R.M., Ryan,M.T., Kraft,C., Kozjak-Pavlovic,V., Drepper,F.,
            Dennerlein,S., Oeljeklaus,S., Pfanner,N., Wiedemann,N. and
            Warscheid,B.
  TITLE     Quantitative high-confidence human mitochondrial proteome and its
            dynamics in cellular context
  JOURNAL   Cell Metab 33 (12), 2464-2483 (2021)
   PUBMED   34800366
REFERENCE   2  (bases 1 to 2859)
  AUTHORS   Gao,J., Wang,T., Qiu,S., Zhu,Y., Liang,L. and Zheng,Y.
  TITLE     Structure-Based Drug Design of Small Molecule Peptide Deformylase
            Inhibitors to Treat Cancer
  JOURNAL   Molecules 21 (4), 396 (2016)
   PUBMED   27023495
  REMARK    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.
            Publication Status: Online-Only
REFERENCE   3  (bases 1 to 2859)
  AUTHORS   Sheth,A., Escobar-Alvarez,S., Gardner,J., Ran,L., Heaney,M.L. and
            Scheinberg,D.A.
  TITLE     Inhibition of human mitochondrial peptide deformylase causes
            apoptosis in c-myc-overexpressing hematopoietic cancers
  JOURNAL   Cell Death Dis 5 (3), e1152 (2014)
   PUBMED   24675470
  REMARK    GeneRIF: c-myc regulated the expression of human PDF.
            Publication Status: Online-Only
REFERENCE   4  (bases 1 to 2859)
  AUTHORS   Randhawa,H., Chikara,S., Gehring,D., Yildirim,T., Menon,J. and
            Reindl,K.M.
  TITLE     Overexpression of peptide deformylase in breast, colon, and lung
            cancers
  JOURNAL   BMC Cancer 13, 321 (2013)
   PUBMED   23815882
  REMARK    GeneRIF: This is the first report showing that PDF is
            over-expressed in breast, colon, and lung cancers
            Publication Status: Online-Only
REFERENCE   5  (bases 1 to 2859)
  AUTHORS   Pereira-Castro,I., Costa,L.T., Amorim,A. and Azevedo,L.
  TITLE     Transcriptional regulation of the human mitochondrial peptide
            deformylase (PDF)
  JOURNAL   Biochem Biophys Res Commun 421 (4), 825-831 (2012)
   PUBMED   22554513
  REMARK    GeneRIF: these data reveals that PDF has several transcription
            start sites, the most important of which only 18 bp from the
            initiation codon.
REFERENCE   6  (bases 1 to 2859)
  AUTHORS   Serero,A., Giglione,C., Sardini,A., Martinez-Sanz,J. and Meinnel,T.
  TITLE     An unusual peptide deformylase features in the human mitochondrial
            N-terminal methionine excision pathway
  JOURNAL   J Biol Chem 278 (52), 52953-52963 (2003)
   PUBMED   14532271
REFERENCE   7  (bases 1 to 2859)
  AUTHORS   Lee,M.D., Antczak,C., Li,Y., Sirotnak,F.M., Bornmann,W.G. and
            Scheinberg,D.A.
  TITLE     A new human peptide deformylase inhibitable by actinonin
  JOURNAL   Biochem Biophys Res Commun 312 (2), 309-315 (2003)
   PUBMED   14637138
  REMARK    GeneRIF: The inhibition of HsPDF may provide an explanation for the
            mechanism by which actinonin is cytotoxic against various human
            tumor cell lines.
REFERENCE   8  (bases 1 to 2859)
  AUTHORS   Nguyen,K.T., Hu,X., Colton,C., Chakrabarti,R., Zhu,M.X. and Pei,D.
  TITLE     Characterization of a human peptide deformylase: implications for
            antibacterial drug design
  JOURNAL   Biochemistry 42 (33), 9952-9958 (2003)
   PUBMED   12924944
REFERENCE   9  (bases 1 to 2859)
  AUTHORS   Chagnon,P., Michaud,J., Mitchell,G., Mercier,J., Marion,J.F.,
            Drouin,E., Rasquin-Weber,A., Hudson,T.J. and Richter,A.
  TITLE     A missense mutation (R565W) in cirhin (FLJ14728) in North American
            Indian childhood cirrhosis
  JOURNAL   Am J Hum Genet 71 (6), 1443-1449 (2002)
   PUBMED   12417987
REFERENCE   10 (bases 1 to 2859)
  AUTHORS   Giglione,C., Serero,A., Pierre,M., Boisson,B. and Meinnel,T.
  TITLE     Identification of eukaryotic peptide deformylases reveals
            universality of N-terminal protein processing mechanisms
  JOURNAL   EMBO J 19 (21), 5916-5929 (2000)
   PUBMED   11060042
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from AF239156.1 and AC026464.7.
            This sequence is a reference standard in the RefSeqGene project.
            
            On Nov 22, 2018 this sequence version replaced NM_022341.1.
            
            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].
            
            Publication Note:  This RefSeq record includes a subset of the
            publications that are available for this gene. Please see the Gene
            record to access additional publications.
            
            ##Evidence-Data-START##
            Transcript exon combination :: SRR1163657.381020.1, AF239156.1
                                           [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA1965299, SAMEA1966682
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            gene product(s) localized to mito. :: inferred from homology
            MANE Ensembl match                 :: ENST00000288022.2/
                                                  ENSP00000288022.1
            RefSeq Select criteria             :: based on single
                                                  protein-coding transcript
            ##RefSeq-Attributes-END##
            COMPLETENESS: full length.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-1151              AF239156.1         8-1158
            1152-2859           AC026464.7         52033-53740         c
FEATURES             Location/Qualifiers
     source          1..2859
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="16"
                     /map="16q22.1"
     gene            1..2859
                     /gene="PDF"
                     /note="peptide deformylase, mitochondrial"
                     /db_xref="GeneID:64146"
                     /db_xref="HGNC:HGNC:30012"
                     /db_xref="MIM:618720"
     exon            1..592
                     /gene="PDF"
                     /inference="alignment:Splign:2.1.0"
     CDS             19..750
                     /gene="PDF"
                     /EC_number="3.5.1.88"
                     /note="peptide deformylase-like protein; polypeptide
                     deformylase"
                     /codon_start=1
                     /product="peptide deformylase, mitochondrial precursor"
                     /protein_id="NP_071736.1"
                     /db_xref="CCDS:CCDS10875.1"
                     /db_xref="GeneID:64146"
                     /db_xref="HGNC:HGNC:30012"
                     /db_xref="MIM:618720"
                     /translation="MARLWGALSLWPLWAAVPWGGAAAVGVRACSSTAAPDGVEGPAL
                     RRSYWRHLRRLVLGPPEPPFSHVCQVGDPVLRGVAAPVERAQLGGPELQRLTQRLVQV
                     MRRRRCVGLSAPQLGVPRQVLALELPEALCRECPPRQRALRQMEPFPLRVFVNPSLRV
                     LDSRLVTFPEGCESVAGFLACVPRFQAVQISGLDPNGEQVVWQASGWAARIIQHEMDH
                     LQGCLFIDKMDSRTFTNVYWMKVND"
     exon            593..2859
                     /gene="PDF"
                     /inference="alignment:Splign:2.1.0"
     polyA_site      1151
                     /gene="PDF"
                     /note="major polyA site"
     regulatory      1216..1221
                     /regulatory_class="polyA_signal_sequence"
                     /gene="PDF"
                     /note="hexamer: AATGAA"
     polyA_site      1241
                     /gene="PDF"
     regulatory      2181..2186
                     /regulatory_class="polyA_signal_sequence"
                     /gene="PDF"
                     /note="hexamer: TATAAA"
     polyA_site      2201
                     /gene="PDF"
     regulatory      2837..2842
                     /regulatory_class="polyA_signal_sequence"
                     /gene="PDF"
                     /note="hexamer: AATAAA"
     polyA_site      2859
                     /gene="PDF"
ORIGIN      
        1 actgttaagg gggccgccat ggcccggctg tggggcgcgc tgagtctttg gccactgtgg
       61 gcggccgtgc cgtggggcgg ggcggcagcc gtcggtgtcc gggcttgcag ctccacggcc
      121 gccccggacg gcgtcgaggg cccggcgctg cggcgctcct attggcgcca cctgaggcgt
      181 ctggtgctgg gtcctcccga accgccgttc tcgcacgtgt gccaagtcgg ggacccggtg
      241 ctgcgcggcg tggcggcccc ggtggagcgg gcgcagctag gcgggcccga gctgcagcgg
      301 ctgacgcaac ggctggtcca ggtgatgcgg cggcggcgct gcgtgggcct aagcgcgccg
      361 cagctggggg tgccgcggca ggtgctggcg ctggagctcc ccgaggcgct gtgtcgggag
      421 tgcccgcccc gccagcgcgc gctccgccaa atggagccct tccccctgcg cgtgttcgtg
      481 aaccccagcc tgcgagtgct tgacagccgc ctggtcacct ttcccgaggg ctgcgagagc
      541 gtcgccggct tcctggcctg cgtgccccgc ttccaggcgg tgcagatctc agggctggac
      601 cccaatggag aacaggtggt gtggcaggcg agcgggtggg cagcccgcat catccagcac
      661 gagatggacc acctgcaggg ctgcctgttt attgacaaaa tggacagcag gacgttcaca
      721 aacgtctatt ggatgaaggt gaatgactaa agctttgcta ctggggctga ggattccgga
      781 taccaagacg caaacacttt cactttgagc tgggcaaatc ttacttggca tcaacttgga
      841 tggctcgcat atgacaggaa actggattgc caaggcatgg cagactgagc tggaggaaga
      901 tgtcagaaat gtttgccctg aaatcagtta cggacaaaat gttggctaca acttgaggag
      961 aaaaatcacc cccaaaggag tggacatttc ctaacaattc tgtatggagg aaggtggggt
     1021 aattgcattc gtctgcagta gacacgagtt cctcggacct gtataatctc ccaaagccaa
     1081 ggtttggtaa taatgtagtc cccaaatacc tgaaagctgt ctttaaaaat gcaggtaagc
     1141 atgtgactgg ccatttgtgc cgagttctta tttttacgga gggcttgtgg ccttagacgc
     1201 cagtttgctt atggaaatga aagagaatag tccctgttca aggatgtgtt tcatgacagc
     1261 acgagtgtaa atgagtgccc acacatttta acagccttgg gcaggatttt gctgctgaga
     1321 tccctagagc agctggttct tggctcattc ttggggtaga ggccgtggat cagggctggg
     1381 ggcaggggtg acaattgaga agtgcactga gccctttcct gttaacaatt gggcatagaa
     1441 agcaggatta gtacttcctg gttatacact tattttgtaa aaatagaatt aatatcacag
     1501 caaccaatgt gtaggtttaa gaaagtggcc aggtgcagtg gttcacgcct gtaatcccag
     1561 cactttggga gggcggggcg ggtggatcac gaggtcagga gctcaagacc agcctggcca
     1621 agatggtgaa accctgtctc tactaaagat acaaaaatta gccgggcgtg gtggcgagca
     1681 cctgtaatcc cagctactcg tgaagccaag gcagagaatt acttgaaccc aggaggcgga
     1741 ggttacagtg agctgagatc acgccactgc actccatcca gcctgggcga cagagcgaga
     1801 ctcaaaagta tgattctggc tgtagagttt tctttttttc tctgtctcaa aaaaaaaaag
     1861 tgtcagcttt gtcttgtcaa gaggtgaagg aacttgtttt attcttttat ttttttttta
     1921 agatagagac gggggtctta ctatgttgcc caggctggcc tcaaattcct ggtctcaggc
     1981 aatcctcctg cctcggcctc ccaaagtgct gggatcagtt gtgagccaca ctacccagcc
     2041 aaactccagt tttagttaaa ctgtttcacc tcatttttat gctgagtttt gtaaagtagg
     2101 tattcttgct gaacagagtc ctgaaaatca aactatacaa gtagtaggaa gtccattaag
     2161 ctgtttagag gaaaaagtgt tataaatggc agttaaatga acccaggaaa gacccatcct
     2221 cctttgtggc tttctctgag gccccatgag gccaagcaga agcaaactgg ctctaggtgc
     2281 agccagactt tgaaaaggaa tcccggccag gcttggtggc tcatgcctgt aatcccagca
     2341 ctttgggagg tcaaggcagg cagatcacct gaggtcagga gttcaagacc agcctggcca
     2401 acatggcgaa acactgtttc tactaaaaat atgaaaatta gctgggtgtg ctggtaggcg
     2461 cctgtaatca cagctacttg ggaggctgag gcgggagaat cgctcaaacc tgggaggcag
     2521 aggttgcagt gggctgagat ctcgccactg tactccagcc tgggcgacag accaaggctc
     2581 tgtctcaaaa aaaaaaaaaa aaaaaaaaaa agggaatccc aaccagatac tggtgcaagg
     2641 tcagagatgc agccaatggg gagatttgta gaaagctcat agatgctaaa aacatgggtc
     2701 tttaggaaaa ttagaattca gctgagcctc ctttcatttg gacaatgttc agaagctctt
     2761 acagggggct atggcaatct tttgatgctt cttatagctt tctgaggtta acgcttttgt
     2821 ggtgggcatc ggtagcaata aaatgcaaac tttattgca
//
