ID   DEF2_GEOSE              Reviewed;         184 AA.
AC   O31410;
DT   30-MAY-2000, integrated into UniProtKB/Swiss-Prot.
DT   01-JAN-1998, sequence version 1.
DT   03-AUG-2022, entry version 105.
DE   RecName: Full=Peptide deformylase 2;
DE            Short=PDF 2;
DE            EC=3.5.1.88;
DE   AltName: Full=Polypeptide deformylase 2;
OS   Geobacillus stearothermophilus (Bacillus stearothermophilus).
OC   Bacteria; Firmicutes; Bacilli; Bacillales; Bacillaceae; Geobacillus.
OX   NCBI_TaxID=1422;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND CHARACTERIZATION.
RC   STRAIN=ATCC 1518;
RX   PubMed=9126850; DOI=10.1006/jmbi.1997.0904;
RA   Meinnel T., Lazennec C., Villoing S., Blanquet S.;
RT   "Structure-function relationships within the peptide deformylase family.
RT   Evidence for a conserved architecture of the active site involving three
RT   conserved motifs and a metal ion.";
RL   J. Mol. Biol. 267:749-761(1997).
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.
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   -!- SIMILARITY: Belongs to the polypeptide deformylase family.
CC       {ECO:0000305}.
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DR   EMBL; Y10549; CAA71581.1; -; Genomic_DNA.
DR   RefSeq; WP_033016217.1; NZ_RCTK01000001.1.
DR   PDB; 1LQY; X-ray; 1.90 A; A=1-184.
DR   PDBsum; 1LQY; -.
DR   AlphaFoldDB; O31410; -.
DR   SMR; O31410; -.
DR   DrugBank; DB04310; 2-[(Formyl-Hydroxy-Amino)-Methyl]-Heptanoic Acid [1-(2-Hydroxymethyl-Pyrrolidine-1-Carbonyl)-2-Methyl-Propyl]-Amide.
DR   GeneID; 58572152; -.
DR   BRENDA; 3.5.1.88; 623.
DR   EvolutionaryTrace; O31410; -.
DR   GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR   GO; GO:0042586; F:peptide deformylase activity; IEA:UniProtKB-UniRule.
DR   GO; GO:0006412; P:translation; IEA:UniProtKB-UniRule.
DR   CDD; cd00487; Pep_deformylase; 1.
DR   Gene3D; 3.90.45.10; -; 1.
DR   HAMAP; MF_00163; Pep_deformylase; 1.
DR   InterPro; IPR023635; Peptide_deformylase.
DR   InterPro; IPR036821; Peptide_deformylase_sf.
DR   PANTHER; PTHR10458; PTHR10458; 1.
DR   Pfam; PF01327; Pep_deformylase; 1.
DR   PIRSF; PIRSF004749; Pep_def; 1.
DR   PRINTS; PR01576; PDEFORMYLASE.
DR   SUPFAM; SSF56420; SSF56420; 1.
DR   TIGRFAMs; TIGR00079; pept_deformyl; 1.
PE   1: Evidence at protein level;
KW   3D-structure; Hydrolase; Iron; Metal-binding; Protein biosynthesis.
FT   CHAIN           1..184
FT                   /note="Peptide deformylase 2"
FT                   /id="PRO_0000082738"
FT   ACT_SITE        154
FT                   /evidence="ECO:0000250"
FT   BINDING         110
FT                   /ligand="Fe cation"
FT                   /ligand_id="ChEBI:CHEBI:24875"
FT                   /evidence="ECO:0000250"
FT   BINDING         153
FT                   /ligand="Fe cation"
FT                   /ligand_id="ChEBI:CHEBI:24875"
FT                   /evidence="ECO:0000250"
FT   BINDING         157
FT                   /ligand="Fe cation"
FT                   /ligand_id="ChEBI:CHEBI:24875"
FT                   /evidence="ECO:0000250"
FT   HELIX           4..6
FT                   /evidence="ECO:0007829|PDB:1LQY"
FT   HELIX           13..16
FT                   /evidence="ECO:0007829|PDB:1LQY"
FT   HELIX           28..44
FT                   /evidence="ECO:0007829|PDB:1LQY"
FT   HELIX           47..53
FT                   /evidence="ECO:0007829|PDB:1LQY"
FT   STRAND          59..62
FT                   /evidence="ECO:0007829|PDB:1LQY"
FT   HELIX           63..66
FT                   /evidence="ECO:0007829|PDB:1LQY"
FT   STRAND          70..78
FT                   /evidence="ECO:0007829|PDB:1LQY"
FT   STRAND          84..97
FT                   /evidence="ECO:0007829|PDB:1LQY"
FT   STRAND          99..104
FT                   /evidence="ECO:0007829|PDB:1LQY"
FT   STRAND          123..132
FT                   /evidence="ECO:0007829|PDB:1LQY"
FT   STRAND          138..144
FT                   /evidence="ECO:0007829|PDB:1LQY"
FT   HELIX           145..158
FT                   /evidence="ECO:0007829|PDB:1LQY"
FT   HELIX           163..166
FT                   /evidence="ECO:0007829|PDB:1LQY"
FT   STRAND          180..182
FT                   /evidence="ECO:0007829|PDB:1LQY"
SQ   SEQUENCE   184 AA;  20383 MW;  9CD85DEE53632FA0 CRC64;
     MITMKDIIKE GHPTLRKVAE PVPLPPSEED KRILQSLLDY VKMSQDPELA AKYGLRPGIG
     LAAPQINVSK RMIAVHVTDE NGTLYSYALF NPKIVSHSVQ QCYLTTGEGC LSVDRDVPGY
     VLRYARITVT GTTLDGEEVT LRLKGLPAIV FQHEIDHLNG IMFYDRINPA DPFQVPDGAI
     PIGR