ID DEF_STRA3 Reviewed; 204 AA. AC Q8E378; DT 15-DEC-2003, integrated into UniProtKB/Swiss-Prot. DT 01-MAR-2003, sequence version 1. DT 27-MAR-2024, entry version 110. DE RecName: Full=Peptide deformylase {ECO:0000255|HAMAP-Rule:MF_00163}; DE Short=PDF {ECO:0000255|HAMAP-Rule:MF_00163}; DE EC=3.5.1.88 {ECO:0000255|HAMAP-Rule:MF_00163}; DE AltName: Full=Polypeptide deformylase {ECO:0000255|HAMAP-Rule:MF_00163}; GN Name=def {ECO:0000255|HAMAP-Rule:MF_00163}; OrderedLocusNames=gbs1883; OS Streptococcus agalactiae serotype III (strain NEM316). OC Bacteria; Bacillota; Bacilli; Lactobacillales; Streptococcaceae; OC Streptococcus. OX NCBI_TaxID=211110; RN [1] RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. RC STRAIN=NEM316; RX PubMed=12354221; DOI=10.1046/j.1365-2958.2002.03126.x; RA Glaser P., Rusniok C., Buchrieser C., Chevalier F., Frangeul L., Msadek T., RA Zouine M., Couve E., Lalioui L., Poyart C., Trieu-Cuot P., Kunst F.; RT "Genome sequence of Streptococcus agalactiae, a pathogen causing invasive RT neonatal disease."; RL Mol. Microbiol. 45:1499-1513(2002). 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 {ECO:0000255|HAMAP-Rule:MF_00163}. 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:0000255|HAMAP-Rule:MF_00163}; CC -!- COFACTOR: CC Name=Fe(2+); Xref=ChEBI:CHEBI:29033; Evidence={ECO:0000255|HAMAP- CC Rule:MF_00163}; CC Note=Binds 1 Fe(2+) ion. {ECO:0000255|HAMAP-Rule:MF_00163}; CC -!- SIMILARITY: Belongs to the polypeptide deformylase family. CC {ECO:0000255|HAMAP-Rule:MF_00163}. CC --------------------------------------------------------------------------- CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms CC Distributed under the Creative Commons Attribution (CC BY 4.0) License CC --------------------------------------------------------------------------- DR EMBL; AL766854; CAD47542.1; -; Genomic_DNA. DR RefSeq; WP_001272875.1; NC_004368.1. DR PDB; 5JEX; X-ray; 2.00 A; A=1-204. DR PDB; 5JEY; X-ray; 2.80 A; A=1-204. DR PDB; 5JEZ; X-ray; 1.70 A; A=1-204. DR PDB; 5JF0; X-ray; 1.60 A; A=1-204. DR PDB; 5JF1; X-ray; 2.00 A; A=1-204. DR PDB; 5JF2; X-ray; 2.00 A; A=1-204. DR PDB; 5JF3; X-ray; 1.60 A; A=1-204. DR PDB; 5JF4; X-ray; 2.40 A; A=1-204. DR PDB; 5JF5; X-ray; 1.80 A; A=1-204. DR PDB; 5JF6; X-ray; 1.70 A; A=1-204. DR PDB; 5JF7; X-ray; 2.10 A; A=1-204. DR PDB; 5JF8; X-ray; 1.80 A; A=1-204. DR PDBsum; 5JEX; -. DR PDBsum; 5JEY; -. DR PDBsum; 5JEZ; -. DR PDBsum; 5JF0; -. DR PDBsum; 5JF1; -. DR PDBsum; 5JF2; -. DR PDBsum; 5JF3; -. DR PDBsum; 5JF4; -. DR PDBsum; 5JF5; -. DR PDBsum; 5JF6; -. DR PDBsum; 5JF7; -. DR PDBsum; 5JF8; -. DR AlphaFoldDB; Q8E378; -. DR SMR; Q8E378; -. DR GeneID; 66886680; -. DR KEGG; san:gbs1883; -. DR eggNOG; COG0242; Bacteria. DR HOGENOM; CLU_061901_4_0_9; -. DR BRENDA; 3.5.1.88; 5917. DR Proteomes; UP000000823; Chromosome. 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; 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:SF8; PEPTIDE DEFORMYLASE; 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. FT CHAIN 1..204 FT /note="Peptide deformylase" FT /id="PRO_0000082847" FT ACT_SITE 175 FT /evidence="ECO:0000255|HAMAP-Rule:MF_00163" FT BINDING 131 FT /ligand="Fe cation" FT /ligand_id="ChEBI:CHEBI:24875" FT /evidence="ECO:0000255|HAMAP-Rule:MF_00163" FT BINDING 174 FT /ligand="Fe cation" FT /ligand_id="ChEBI:CHEBI:24875" FT /evidence="ECO:0000255|HAMAP-Rule:MF_00163" FT BINDING 178 FT /ligand="Fe cation" FT /ligand_id="ChEBI:CHEBI:24875" FT /evidence="ECO:0000255|HAMAP-Rule:MF_00163" FT HELIX 3..8 FT /evidence="ECO:0007829|PDB:5JF0" FT HELIX 16..18 FT /evidence="ECO:0007829|PDB:5JF0" FT HELIX 25..28 FT /evidence="ECO:0007829|PDB:5JF0" FT HELIX 40..57 FT /evidence="ECO:0007829|PDB:5JF0" FT HELIX 59..65 FT /evidence="ECO:0007829|PDB:5JF0" FT STRAND 70..74 FT /evidence="ECO:0007829|PDB:5JF0" FT HELIX 75..78 FT /evidence="ECO:0007829|PDB:5JF0" FT STRAND 82..90 FT /evidence="ECO:0007829|PDB:5JF0" FT STRAND 101..118 FT /evidence="ECO:0007829|PDB:5JF0" FT STRAND 120..125 FT /evidence="ECO:0007829|PDB:5JF0" FT STRAND 144..153 FT /evidence="ECO:0007829|PDB:5JF0" FT STRAND 159..164 FT /evidence="ECO:0007829|PDB:5JF0" FT HELIX 166..179 FT /evidence="ECO:0007829|PDB:5JF0" FT HELIX 184..187 FT /evidence="ECO:0007829|PDB:5JF0" FT STRAND 201..203 FT /evidence="ECO:0007829|PDB:5JF0" SQ SEQUENCE 204 AA; 22830 MW; 50097F6CCF8524EF CRC64; MSAIDKLVKA SHLIDMNDII REGNPTLRKV AEEVTFPLSE KEEILGEKMM QFLKHSQDPI MAEKLGLRGG VGLAAPQLDI SKRIIAVLVP NVEDAQGNPP KEAYSLQEVM YNPKVVSHSV QDAALSDGEG CLSVDREVPG YVVRHARVTI EYFDKTGEKH RLKLKGYNSI VVQHEIDHID GIMFYDRINE KNPFAVKEGL LILE //