ID   DEFM_HUMAN              Reviewed;         243 AA.
AC   Q9HBH1; Q8WUN6;
DT   05-DEC-2001, integrated into UniProtKB/Swiss-Prot.
DT   01-MAR-2001, sequence version 1.
DT   27-MAR-2024, entry version 173.
DE   RecName: Full=Peptide deformylase, mitochondrial {ECO:0000303|PubMed:19236878};
DE            EC=3.5.1.88 {ECO:0000269|PubMed:19236878};
DE   AltName: Full=Polypeptide deformylase;
DE   Flags: Precursor;
GN   Name=PDF {ECO:0000303|PubMed:19236878};
GN   Synonyms=PDF1A {ECO:0000303|PubMed:11060042};
OS   Homo sapiens (Human).
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC   Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae;
OC   Homo.
OX   NCBI_TaxID=9606;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [MRNA].
RX   PubMed=11060042; DOI=10.1093/emboj/19.21.5916;
RA   Giglione C., Serero A., Pierre M., Boisson B., Meinnel T.;
RT   "Identification of eukaryotic peptide deformylases reveals universality of
RT   N-terminal protein processing mechanisms.";
RL   EMBO J. 19:5916-5929(2000).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [MRNA].
RA   Lonetto M.A., Zhu Y., Li X., Southan C.;
RT   "A human homolog of bacterial peptide deformylases.";
RL   Submitted (NOV-2000) to the EMBL/GenBank/DDBJ databases.
RN   [3]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA], AND VARIANT ARG-11.
RC   TISSUE=Placenta;
RX   PubMed=15489334; DOI=10.1101/gr.2596504;
RG   The MGC Project Team;
RT   "The status, quality, and expansion of the NIH full-length cDNA project:
RT   the Mammalian Gene Collection (MGC).";
RL   Genome Res. 14:2121-2127(2004).
RN   [4]
RP   FUNCTION, CATALYTIC ACTIVITY, SUBCELLULAR LOCATION, TISSUE SPECIFICITY, AND
RP   TRANSIT PEPTIDE CLEAVAGE SITE.
RX   PubMed=14532271; DOI=10.1074/jbc.m309770200;
RA   Serero A., Giglione C., Sardini A., Martinez-Sanz J., Meinnel T.;
RT   "An unusual peptide deformylase features in the human mitochondrial N-
RT   terminal methionine excision pathway.";
RL   J. Biol. Chem. 278:52953-52963(2003).
RN   [5]
RP   FUNCTION, CATALYTIC ACTIVITY, AND SUBCELLULAR LOCATION.
RX   PubMed=15489958; DOI=10.1172/jci22269;
RA   Lee M.D., She Y., Soskis M.J., Borella C.P., Gardner J.R., Hayes P.A.,
RA   Dy B.M., Heaney M.L., Philips M.R., Bornmann W.G., Sirotnak F.M.,
RA   Scheinberg D.A.;
RT   "Human mitochondrial peptide deformylase, a new anticancer target of
RT   actinonin-based antibiotics.";
RL   J. Clin. Invest. 114:1107-1116(2004).
RN   [6]
RP   IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX   PubMed=25944712; DOI=10.1002/pmic.201400617;
RA   Vaca Jacome A.S., Rabilloud T., Schaeffer-Reiss C., Rompais M., Ayoub D.,
RA   Lane L., Bairoch A., Van Dorsselaer A., Carapito C.;
RT   "N-terminome analysis of the human mitochondrial proteome.";
RL   Proteomics 15:2519-2524(2015).
RN   [7]
RP   X-RAY CRYSTALLOGRAPHY (1.7 ANGSTROMS) OF 64-243 IN COMPLEX WITH SUBSTRATE
RP   ANALOG AND COBALT ION, FUNCTION, CATALYTIC ACTIVITY, COFACTOR,
RP   METAL-BINDING SITES, SUBSTRATE-BINDING SITES, AND SUBUNIT.
RX   PubMed=19236878; DOI=10.1016/j.jmb.2009.02.032;
RA   Escobar-Alvarez S., Goldgur Y., Yang G., Ouerfelli O., Li Y.,
RA   Scheinberg D.A.;
RT   "Structure and activity of human mitochondrial peptide deformylase, a novel
RT   cancer target.";
RL   J. Mol. Biol. 387:1211-1228(2009).
CC   -!- FUNCTION: Removes the formyl group from the N-terminal Met of newly
CC       synthesized proteins. {ECO:0000269|PubMed:14532271,
CC       ECO:0000269|PubMed:15489958, ECO:0000269|PubMed:19236878}.
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=H2O + N-terminal N-formyl-L-methionyl-[peptide] = formate + N-
CC         terminal L-methionyl-[peptide]; Xref=Rhea:RHEA:24420, Rhea:RHEA-
CC         COMP:10639, Rhea:RHEA-COMP:10640, ChEBI:CHEBI:15377,
CC         ChEBI:CHEBI:15740, ChEBI:CHEBI:49298, ChEBI:CHEBI:64731; EC=3.5.1.88;
CC         Evidence={ECO:0000269|PubMed:14532271, ECO:0000269|PubMed:15489958,
CC         ECO:0000269|PubMed:19236878};
CC   -!- COFACTOR:
CC       Name=Co(2+); Xref=ChEBI:CHEBI:48828;
CC         Evidence={ECO:0000305|PubMed:19236878};
CC       Note=Binds 1 Co(2+) ion. {ECO:0000305|PubMed:19236878};
CC   -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:19236878}.
CC   -!- SUBCELLULAR LOCATION: Mitochondrion {ECO:0000269|PubMed:14532271,
CC       ECO:0000269|PubMed:15489958}.
CC   -!- TISSUE SPECIFICITY: Ubiquitous. {ECO:0000269|PubMed:14532271}.
CC   -!- SIMILARITY: Belongs to the polypeptide deformylase family.
CC       {ECO:0000305}.
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DR   EMBL; AF239156; AAG33968.1; -; mRNA.
DR   EMBL; AF322879; AAK15624.1; -; mRNA.
DR   EMBL; BC019912; AAH19912.1; -; mRNA.
DR   CCDS; CCDS10875.1; -.
DR   RefSeq; NP_071736.1; NM_022341.1.
DR   PDB; 3G5K; X-ray; 1.70 A; A/B/C/D=64-243.
DR   PDB; 3G5P; X-ray; 1.70 A; A/B/C/D=64-243.
DR   PDBsum; 3G5K; -.
DR   PDBsum; 3G5P; -.
DR   AlphaFoldDB; Q9HBH1; -.
DR   SMR; Q9HBH1; -.
DR   BioGRID; 122085; 112.
DR   IntAct; Q9HBH1; 47.
DR   STRING; 9606.ENSP00000288022; -.
DR   BindingDB; Q9HBH1; -.
DR   ChEMBL; CHEMBL4647; -.
DR   DrugBank; DB04310; 2-[(Formyl-Hydroxy-Amino)-Methyl]-Heptanoic Acid [1-(2-Hydroxymethyl-Pyrrolidine-1-Carbonyl)-2-Methyl-Propyl]-Amide.
DR   DrugBank; DB04368; Bb-3497.
DR   SwissPalm; Q9HBH1; -.
DR   BioMuta; PDF; -.
DR   DMDM; 17433054; -.
DR   EPD; Q9HBH1; -.
DR   jPOST; Q9HBH1; -.
DR   MassIVE; Q9HBH1; -.
DR   MaxQB; Q9HBH1; -.
DR   PaxDb; 9606-ENSP00000288022; -.
DR   PeptideAtlas; Q9HBH1; -.
DR   ProteomicsDB; 81550; -.
DR   Pumba; Q9HBH1; -.
DR   Antibodypedia; 56384; 197 antibodies from 22 providers.
DR   DNASU; 64146; -.
DR   Ensembl; ENST00000288022.2; ENSP00000288022.1; ENSG00000258429.2.
DR   GeneID; 64146; -.
DR   KEGG; hsa:64146; -.
DR   MANE-Select; ENST00000288022.2; ENSP00000288022.1; NM_022341.2; NP_071736.1.
DR   UCSC; uc002ewx.1; human.
DR   AGR; HGNC:30012; -.
DR   CTD; 64146; -.
DR   DisGeNET; 64146; -.
DR   GeneCards; PDF; -.
DR   HGNC; HGNC:30012; PDF.
DR   HPA; ENSG00000258429; Tissue enhanced (liver).
DR   MIM; 618720; gene.
DR   neXtProt; NX_Q9HBH1; -.
DR   OpenTargets; ENSG00000258429; -.
DR   PharmGKB; PA144596394; -.
DR   VEuPathDB; HostDB:ENSG00000258429; -.
DR   eggNOG; KOG3137; Eukaryota.
DR   GeneTree; ENSGT00390000018698; -.
DR   HOGENOM; CLU_061901_5_1_1; -.
DR   InParanoid; Q9HBH1; -.
DR   OMA; ILYPMRI; -.
DR   OrthoDB; 1442148at2759; -.
DR   PhylomeDB; Q9HBH1; -.
DR   TreeFam; TF323637; -.
DR   BRENDA; 3.5.1.88; 2681.
DR   PathwayCommons; Q9HBH1; -.
DR   SABIO-RK; Q9HBH1; -.
DR   SignaLink; Q9HBH1; -.
DR   BioGRID-ORCS; 64146; 12 hits in 1153 CRISPR screens.
DR   EvolutionaryTrace; Q9HBH1; -.
DR   GeneWiki; PDF_(gene); -.
DR   GenomeRNAi; 64146; -.
DR   Pharos; Q9HBH1; Tchem.
DR   PRO; PR:Q9HBH1; -.
DR   Proteomes; UP000005640; Chromosome 16.
DR   RNAct; Q9HBH1; Protein.
DR   Bgee; ENSG00000258429; Expressed in male germ line stem cell (sensu Vertebrata) in testis and 97 other cell types or tissues.
DR   ExpressionAtlas; Q9HBH1; baseline and differential.
DR   GO; GO:0005739; C:mitochondrion; IDA:HGNC-UCL.
DR   GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR   GO; GO:0042586; F:peptide deformylase activity; IDA:UniProtKB.
DR   GO; GO:0043686; P:co-translational protein modification; IBA:GO_Central.
DR   GO; GO:0031365; P:N-terminal protein amino acid modification; IDA:HGNC-UCL.
DR   GO; GO:0018206; P:peptidyl-methionine modification; IDA:UniProtKB.
DR   GO; GO:0008284; P:positive regulation of cell population proliferation; IMP:HGNC-UCL.
DR   GO; GO:0006412; P:translation; IEA:UniProtKB-KW.
DR   CDD; cd00487; Pep_deformylase; 1.
DR   Gene3D; 3.90.45.10; Peptide deformylase; 1.
DR   HAMAP; MF_00163; Pep_deformylase; 1.
DR   InterPro; IPR023635; Peptide_deformylase.
DR   InterPro; IPR036821; Peptide_deformylase_sf.
DR   PANTHER; PTHR10458; PEPTIDE DEFORMYLASE; 1.
DR   PANTHER; PTHR10458:SF2; PEPTIDE DEFORMYLASE, MITOCHONDRIAL; 1.
DR   Pfam; PF01327; Pep_deformylase; 1.
DR   PRINTS; PR01576; PDEFORMYLASE.
DR   SUPFAM; SSF56420; Peptide deformylase; 1.
DR   Genevisible; Q9HBH1; HS.
PE   1: Evidence at protein level;
KW   3D-structure; Cobalt; Hydrolase; Metal-binding; Mitochondrion;
KW   Protein biosynthesis; Reference proteome; Transit peptide.
FT   TRANSIT         1..39
FT                   /note="Mitochondrion"
FT                   /evidence="ECO:0000305|PubMed:14532271"
FT   CHAIN           40..243
FT                   /note="Peptide deformylase, mitochondrial"
FT                   /id="PRO_0000006729"
FT   REGION          165..175
FT                   /note="Hydrophobic dimerization interface"
FT                   /evidence="ECO:0000269|PubMed:19236878"
FT   ACT_SITE        215
FT                   /evidence="ECO:0000250|UniProtKB:P0A6K3"
FT   BINDING         71
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000269|PubMed:19236878"
FT   BINDING         169
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000269|PubMed:19236878"
FT   BINDING         171
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000269|PubMed:19236878"
FT   BINDING         172
FT                   /ligand="Co(2+)"
FT                   /ligand_id="ChEBI:CHEBI:48828"
FT                   /ligand_note="catalytic"
FT                   /evidence="ECO:0000269|PubMed:19236878"
FT   BINDING         214
FT                   /ligand="Co(2+)"
FT                   /ligand_id="ChEBI:CHEBI:48828"
FT                   /ligand_note="catalytic"
FT                   /evidence="ECO:0000269|PubMed:19236878"
FT   BINDING         218
FT                   /ligand="Co(2+)"
FT                   /ligand_id="ChEBI:CHEBI:48828"
FT                   /ligand_note="catalytic"
FT                   /evidence="ECO:0000269|PubMed:19236878"
FT   VARIANT         11
FT                   /note="W -> R (in dbSNP:rs8057004)"
FT                   /evidence="ECO:0000269|PubMed:15489334"
FT                   /id="VAR_060122"
FT   HELIX           73..75
FT                   /evidence="ECO:0007829|PDB:3G5K"
FT   HELIX           84..86
FT                   /evidence="ECO:0007829|PDB:3G5K"
FT   HELIX           90..105
FT                   /evidence="ECO:0007829|PDB:3G5K"
FT   STRAND          109..112
FT                   /evidence="ECO:0007829|PDB:3G5K"
FT   HELIX           113..116
FT                   /evidence="ECO:0007829|PDB:3G5K"
FT   STRAND          120..127
FT                   /evidence="ECO:0007829|PDB:3G5K"
FT   HELIX           129..133
FT                   /evidence="ECO:0007829|PDB:3G5K"
FT   HELIX           137..143
FT                   /evidence="ECO:0007829|PDB:3G5K"
FT   STRAND          148..170
FT                   /evidence="ECO:0007829|PDB:3G5K"
FT   STRAND          178..193
FT                   /evidence="ECO:0007829|PDB:3G5K"
FT   STRAND          199..205
FT                   /evidence="ECO:0007829|PDB:3G5K"
FT   HELIX           206..219
FT                   /evidence="ECO:0007829|PDB:3G5K"
FT   HELIX           224..226
FT                   /evidence="ECO:0007829|PDB:3G5K"
FT   HELIX           230..232
FT                   /evidence="ECO:0007829|PDB:3G5K"
SQ   SEQUENCE   243 AA;  27013 MW;  B15A3456F0F8D689 CRC64;
     MARLWGALSL WPLWAAVPWG GAAAVGVRAC SSTAAPDGVE GPALRRSYWR HLRRLVLGPP
     EPPFSHVCQV GDPVLRGVAA PVERAQLGGP ELQRLTQRLV QVMRRRRCVG LSAPQLGVPR
     QVLALELPEA LCRECPPRQR ALRQMEPFPL RVFVNPSLRV LDSRLVTFPE GCESVAGFLA
     CVPRFQAVQI SGLDPNGEQV VWQASGWAAR IIQHEMDHLQ GCLFIDKMDS RTFTNVYWMK
     VND
//