ID   DEF_LEPIN               Reviewed;         178 AA.
AC   Q93LE9;
DT   19-SEP-2002, integrated into UniProtKB/Swiss-Prot.
DT   01-DEC-2001, sequence version 1.
DT   27-MAR-2024, entry version 134.
DE   RecName: Full=Peptide deformylase;
DE            Short=PDF;
DE            EC=3.5.1.88;
DE   AltName: Full=Polypeptide deformylase;
GN   Name=def; Synonyms=pdf; OrderedLocusNames=LA_2438;
OS   Leptospira interrogans serogroup Icterohaemorrhagiae serovar Lai (strain
OS   56601).
OC   Bacteria; Spirochaetota; Spirochaetia; Leptospirales; Leptospiraceae;
OC   Leptospira.
OX   NCBI_TaxID=189518;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND CRYSTALLIZATION.
RC   STRAIN=Lai / Serogroup Icterohaemorrhagiae / Serovar lai;
RX   PubMed=11976499; DOI=10.1107/s0907444902003736;
RA   Li Y., Ren S., Gong W.;
RT   "Cloning, high-level expression, purification and crystallization of
RT   peptide deformylase from Leptospira interrogans.";
RL   Acta Crystallogr. D 58:846-848(2002).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=56601;
RX   PubMed=12712204; DOI=10.1038/nature01597;
RA   Ren S.-X., Fu G., Jiang X.-G., Zeng R., Miao Y.-G., Xu H., Zhang Y.-X.,
RA   Xiong H., Lu G., Lu L.-F., Jiang H.-Q., Jia J., Tu Y.-F., Jiang J.-X.,
RA   Gu W.-Y., Zhang Y.-Q., Cai Z., Sheng H.-H., Yin H.-F., Zhang Y., Zhu G.-F.,
RA   Wan M., Huang H.-L., Qian Z., Wang S.-Y., Ma W., Yao Z.-J., Shen Y.,
RA   Qiang B.-Q., Xia Q.-C., Guo X.-K., Danchin A., Saint Girons I.,
RA   Somerville R.L., Wen Y.-M., Shi M.-H., Chen Z., Xu J.-G., Zhao G.-P.;
RT   "Unique physiological and pathogenic features of Leptospira interrogans
RT   revealed by whole-genome sequencing.";
RL   Nature 422:888-893(2003).
RN   [3]
RP   X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS), AND SUBUNIT.
RC   STRAIN=Lai / Serogroup Icterohaemorrhagiae / Serovar lai;
RX   PubMed=15123432; DOI=10.1016/j.jmb.2004.03.045;
RA   Zhou Z., Song X., Li Y., Gong W.;
RT   "Unique structural characteristics of peptide deformylase from pathogenic
RT   bacterium Leptospira interrogans.";
RL   J. Mol. Biol. 339:207-215(2004).
CC   -!- FUNCTION: Removes the formyl group from the N-terminal Met of newly
CC       synthesized proteins. Requires at least a dipeptide for an efficient
CC       rate of reaction. N-terminal L-methionine is a prerequisite for
CC       activity but the enzyme has broad specificity at other positions (By
CC       similarity). {ECO:0000250}.
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   -!- COFACTOR:
CC       Name=Fe(2+); Xref=ChEBI:CHEBI:29033; Evidence={ECO:0000250};
CC       Note=Binds 1 Fe(2+) ion. {ECO:0000250};
CC   -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:15123432}.
CC   -!- SIMILARITY: Belongs to the polypeptide deformylase family.
CC       {ECO:0000305}.
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DR   EMBL; AY040678; AAK70806.1; -; Genomic_DNA.
DR   EMBL; AE010300; AAN49637.1; -; Genomic_DNA.
DR   RefSeq; NP_712619.1; NC_004342.2.
DR   RefSeq; WP_000116243.1; NC_004342.2.
DR   PDB; 1SV2; X-ray; 3.00 A; A/B=2-178.
DR   PDB; 1SZZ; X-ray; 3.30 A; A/B/C/D/E/F/G/H=2-178.
DR   PDB; 1VEV; X-ray; 2.51 A; A/B=2-178.
DR   PDB; 1VEY; X-ray; 3.30 A; A/B=2-178.
DR   PDB; 1VEZ; X-ray; 2.30 A; A/B=2-178.
DR   PDB; 1Y6H; X-ray; 2.20 A; A/B=2-178.
DR   PDBsum; 1SV2; -.
DR   PDBsum; 1SZZ; -.
DR   PDBsum; 1VEV; -.
DR   PDBsum; 1VEY; -.
DR   PDBsum; 1VEZ; -.
DR   PDBsum; 1Y6H; -.
DR   AlphaFoldDB; Q93LE9; -.
DR   SMR; Q93LE9; -.
DR   STRING; 189518.LA_2438; -.
DR   DrugBank; DB04310; 2-[(Formyl-Hydroxy-Amino)-Methyl]-Heptanoic Acid [1-(2-Hydroxymethyl-Pyrrolidine-1-Carbonyl)-2-Methyl-Propyl]-Amide.
DR   PaxDb; 189518-LA_2438; -.
DR   EnsemblBacteria; AAN49637; AAN49637; LA_2438.
DR   GeneID; 61144810; -.
DR   KEGG; lil:LA_2438; -.
DR   PATRIC; fig|189518.3.peg.2418; -.
DR   HOGENOM; CLU_061901_5_2_12; -.
DR   InParanoid; Q93LE9; -.
DR   OrthoDB; 9784988at2; -.
DR   BRENDA; 3.5.1.88; 2986.
DR   EvolutionaryTrace; Q93LE9; -.
DR   Proteomes; UP000001408; Chromosome I.
DR   GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR   GO; GO:0042586; F:peptide deformylase activity; IBA:GO_Central.
DR   GO; GO:0043686; P:co-translational protein modification; IBA:GO_Central.
DR   GO; GO:0006412; P:translation; IEA:UniProtKB-UniRule.
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   NCBIfam; TIGR00079; pept_deformyl; 1.
DR   PANTHER; PTHR10458; PEPTIDE DEFORMYLASE; 1.
DR   PANTHER; PTHR10458:SF20; PEPTIDE DEFORMYLASE 1; 1.
DR   Pfam; PF01327; Pep_deformylase; 1.
DR   PIRSF; PIRSF004749; Pep_def; 1.
DR   PRINTS; PR01576; PDEFORMYLASE.
DR   SUPFAM; SSF56420; Peptide deformylase; 1.
PE   1: Evidence at protein level;
KW   3D-structure; Hydrolase; Iron; Metal-binding; Protein biosynthesis;
KW   Reference proteome.
FT   CHAIN           1..178
FT                   /note="Peptide deformylase"
FT                   /id="PRO_0000082795"
FT   ACT_SITE        145
FT                   /evidence="ECO:0000250"
FT   BINDING         102
FT                   /ligand="Fe cation"
FT                   /ligand_id="ChEBI:CHEBI:24875"
FT                   /evidence="ECO:0000250"
FT   BINDING         144
FT                   /ligand="Fe cation"
FT                   /ligand_id="ChEBI:CHEBI:24875"
FT                   /evidence="ECO:0000250"
FT   BINDING         148
FT                   /ligand="Fe cation"
FT                   /ligand_id="ChEBI:CHEBI:24875"
FT                   /evidence="ECO:0000250"
FT   HELIX           12..15
FT                   /evidence="ECO:0007829|PDB:1Y6H"
FT   HELIX           23..25
FT                   /evidence="ECO:0007829|PDB:1Y6H"
FT   HELIX           29..44
FT                   /evidence="ECO:0007829|PDB:1Y6H"
FT   STRAND          48..51
FT                   /evidence="ECO:0007829|PDB:1Y6H"
FT   HELIX           52..55
FT                   /evidence="ECO:0007829|PDB:1Y6H"
FT   STRAND          59..64
FT                   /evidence="ECO:0007829|PDB:1Y6H"
FT   STRAND          70..72
FT                   /evidence="ECO:0007829|PDB:1VEZ"
FT   STRAND          81..90
FT                   /evidence="ECO:0007829|PDB:1Y6H"
FT   STRAND          95..102
FT                   /evidence="ECO:0007829|PDB:1Y6H"
FT   STRAND          105..123
FT                   /evidence="ECO:0007829|PDB:1Y6H"
FT   STRAND          129..135
FT                   /evidence="ECO:0007829|PDB:1Y6H"
FT   HELIX           136..149
FT                   /evidence="ECO:0007829|PDB:1Y6H"
FT   HELIX           154..157
FT                   /evidence="ECO:0007829|PDB:1Y6H"
FT   STRAND          163..166
FT                   /evidence="ECO:0007829|PDB:1Y6H"
FT   HELIX           167..173
FT                   /evidence="ECO:0007829|PDB:1Y6H"
SQ   SEQUENCE   178 AA;  20379 MW;  8F6F3D2449A48B10 CRC64;
     MSVRKILRMG DPILRKISEP VTEDEIQTKE FKKLIRDMFD TMRHAEGVGL AAPQIGILKQ
     IVVVGSEDNE RYPGTPDVPE RIILNPVITP LTKDTSGFWE GCLSVPGMRG YVERPNQIRM
     QWMDEKGNQF DETIDGYKAI VYQHECDHLQ GILYVDRLKD TKLFGFNETL DSSHNVLD
//