ID Q672W7_HELPX Unreviewed; 174 AA. AC Q672W7; DT 11-OCT-2004, integrated into UniProtKB/TrEMBL. DT 11-OCT-2004, sequence version 1. DT 24-JAN-2024, entry version 98. DE RecName: Full=Peptide deformylase {ECO:0000256|HAMAP-Rule:MF_00163}; DE Short=PDF {ECO:0000256|HAMAP-Rule:MF_00163}; DE EC=3.5.1.88 {ECO:0000256|HAMAP-Rule:MF_00163}; DE AltName: Full=Polypeptide deformylase {ECO:0000256|HAMAP-Rule:MF_00163}; GN Name=def {ECO:0000256|HAMAP-Rule:MF_00163, GN ECO:0000313|EMBL:AAT51863.1}; GN ORFNames=HPPMSS1_c00889 {ECO:0000313|EMBL:BBI24432.1}; OS Helicobacter pylori (Campylobacter pylori). OC Bacteria; Campylobacterota; Epsilonproteobacteria; Campylobacterales; OC Helicobacteraceae; Helicobacter. OX NCBI_TaxID=210 {ECO:0000313|EMBL:AAT51863.1}; RN [1] {ECO:0000313|EMBL:AAT51863.1} RP NUCLEOTIDE SEQUENCE. RC STRAIN=SS1 {ECO:0000313|EMBL:AAT51863.1}; RX PubMed=15194508; DOI=10.1016/j.bbrc.2004.05.120; RA Han C., Wang Q., Dong L., Sun H., Peng S., Chen J., Yang Y., Yue J., RA Shen X., Jiang H.; RT "Molecular cloning and characterization of a new peptide deformylase from RT human pathogenic bacterium Helicobacter pylori."; RL Biochem. Biophys. Res. Commun. 319:1292-1298(2004). RN [2] {ECO:0007829|PDB:2EW5, ECO:0007829|PDB:2EW6} RP X-RAY CRYSTALLOGRAPHY (2.20 ANGSTROMS) OF 2-174. RX PubMed=16882991; DOI=10.1110/ps.062238406; RA Cai J., Han C., Hu T., Zhang J., Wu D., Wang F., Liu Y., Ding J., Chen K., RA Yue J., Shen X., Jiang H.; RT "Peptide deformylase is a potential target for anti-Helicobacter pylori RT drugs: reverse docking, enzymatic assay, and X-ray crystallography RT validation."; RL Protein Sci. 15:2071-2081(2006). RN [3] {ECO:0007829|PDB:4E9A, ECO:0007829|PDB:4E9B} RP X-RAY CRYSTALLOGRAPHY (1.66 ANGSTROMS) OF 2-174. RA Cui K., Zhu L., Lu W., Huang J.; RT "Identification of Novel Peptide Deformylase Inhibitors from Natural RT Products."; RL Submitted (MAR-2012) to the PDB data bank. RN [4] {ECO:0000313|EMBL:BBI24432.1, ECO:0000313|Proteomes:UP000289502} RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. RC STRAIN=PMSS1 {ECO:0000313|EMBL:BBI24432.1, RC ECO:0000313|Proteomes:UP000289502}; RA Mimuro H., Ogura Y., Katsura K., Hayashi T.; RT "Whole genome shotgun sequence of Helicobacter pylori strain PMSS1."; RL Submitted (AUG-2016) to the EMBL/GenBank/DDBJ databases. 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:0000256|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:0000256|HAMAP-Rule:MF_00163}; CC -!- COFACTOR: CC Name=Fe(2+); Xref=ChEBI:CHEBI:29033; Evidence={ECO:0000256|HAMAP- CC Rule:MF_00163}; CC Note=Binds 1 Fe(2+) ion. {ECO:0000256|HAMAP-Rule:MF_00163}; CC -!- SIMILARITY: Belongs to the polypeptide deformylase family. CC {ECO:0000256|ARBA:ARBA00010759, ECO:0000256|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; AY559449; AAT51863.1; -; Genomic_DNA. DR EMBL; AP017633; BBI24432.1; -; Genomic_DNA. DR RefSeq; WP_077231960.1; NZ_CP109885.1. DR PDB; 2EW5; X-ray; 2.20 A; A=2-174. DR PDB; 2EW6; X-ray; 2.20 A; A=2-174. DR PDB; 2EW7; X-ray; 2.20 A; A=2-174. DR PDB; 4E9A; X-ray; 1.66 A; A=2-174. DR PDB; 4E9B; X-ray; 1.70 A; A=2-174. DR PDBsum; 2EW5; -. DR PDBsum; 2EW6; -. DR PDBsum; 2EW7; -. DR PDBsum; 4E9A; -. DR PDBsum; 4E9B; -. DR AlphaFoldDB; Q672W7; -. DR SMR; Q672W7; -. DR DrugBank; DB08753; 4-{(1E)-3-OXO-3-[(2-PHENYLETHYL)AMINO]PROP-1-EN-1-YL}-1,2-PHENYLENE DIACETATE. DR DrugBank; DB08754; N-Caffeoyltyramine. DR BRENDA; 3.5.1.88; 2604. DR EvolutionaryTrace; Q672W7; -. DR Proteomes; UP000289502; 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:SF22; 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 {ECO:0007829|PDB:2EW5, ECO:0007829|PDB:2EW6}; KW Hydrolase {ECO:0000256|HAMAP-Rule:MF_00163}; KW Iron {ECO:0000256|HAMAP-Rule:MF_00163}; KW Metal-binding {ECO:0000256|HAMAP-Rule:MF_00163}; KW Protein biosynthesis {ECO:0000256|HAMAP-Rule:MF_00163}. FT ACT_SITE 139 FT /evidence="ECO:0000256|HAMAP-Rule:MF_00163" FT BINDING 96 FT /ligand="Fe cation" FT /ligand_id="ChEBI:CHEBI:24875" FT /evidence="ECO:0000256|HAMAP-Rule:MF_00163" FT BINDING 138 FT /ligand="Fe cation" FT /ligand_id="ChEBI:CHEBI:24875" FT /evidence="ECO:0000256|HAMAP-Rule:MF_00163" FT BINDING 142 FT /ligand="Fe cation" FT /ligand_id="ChEBI:CHEBI:24875" FT /evidence="ECO:0000256|HAMAP-Rule:MF_00163" SQ SEQUENCE 174 AA; 20038 MW; A10BEAEBE6CC4C85 CRC64; MALLEIIHYP SKILRTISKE VVSFDAKLHQ QLDDMYETMI ASEGIGLAAI QVGLPLRMLI INLPQEDGVQ HKEDCLEIIN PKFIETGGSM MYKEGCLSVP GFYEEVERFE KVKIEYQNRF AEVKVLEASE LLAVAIQHEI DHLNGVLFVD KLSILKRKKF EKELKELQKK QKHK //