ID DEF1_VIBCH Reviewed; 169 AA. AC Q9KVU3; DT 05-DEC-2001, integrated into UniProtKB/Swiss-Prot. DT 01-OCT-2000, sequence version 1. DT 27-MAR-2024, entry version 128. DE RecName: Full=Peptide deformylase 1 {ECO:0000255|HAMAP-Rule:MF_00163}; DE Short=PDF 1 {ECO:0000255|HAMAP-Rule:MF_00163}; DE EC=3.5.1.88 {ECO:0000255|HAMAP-Rule:MF_00163}; DE AltName: Full=Polypeptide deformylase 1 {ECO:0000255|HAMAP-Rule:MF_00163}; GN Name=def1 {ECO:0000255|HAMAP-Rule:MF_00163}; GN OrderedLocusNames=VC_0046; OS Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961). OC Bacteria; Pseudomonadota; Gammaproteobacteria; Vibrionales; Vibrionaceae; OC Vibrio. OX NCBI_TaxID=243277; RN [1] RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. RC STRAIN=ATCC 39315 / El Tor Inaba N16961; RX PubMed=10952301; DOI=10.1038/35020000; RA Heidelberg J.F., Eisen J.A., Nelson W.C., Clayton R.A., Gwinn M.L., RA Dodson R.J., Haft D.H., Hickey E.K., Peterson J.D., Umayam L.A., Gill S.R., RA Nelson K.E., Read T.D., Tettelin H., Richardson D.L., Ermolaeva M.D., RA Vamathevan J.J., Bass S., Qin H., Dragoi I., Sellers P., McDonald L.A., RA Utterback T.R., Fleischmann R.D., Nierman W.C., White O., Salzberg S.L., RA Smith H.O., Colwell R.R., Mekalanos J.J., Venter J.C., Fraser C.M.; RT "DNA sequence of both chromosomes of the cholera pathogen Vibrio RT cholerae."; RL Nature 406:477-483(2000). 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; AE003852; AAF93224.1; -; Genomic_DNA. DR PIR; A82373; A82373. DR RefSeq; NP_229705.1; NC_002505.1. DR RefSeq; WP_000115010.1; NZ_LT906614.1. DR PDB; 3FWX; X-ray; 2.00 A; A/B=1-169. DR PDBsum; 3FWX; -. DR AlphaFoldDB; Q9KVU3; -. DR SMR; Q9KVU3; -. DR STRING; 243277.VC_0046; -. DR DNASU; 2614445; -. DR EnsemblBacteria; AAF93224; AAF93224; VC_0046. DR GeneID; 69721201; -. DR KEGG; vch:VC_0046; -. DR PATRIC; fig|243277.26.peg.45; -. DR eggNOG; COG0242; Bacteria. DR HOGENOM; CLU_061901_2_1_6; -. DR EvolutionaryTrace; Q9KVU3; -. DR Proteomes; UP000000584; Chromosome 1. 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:SF21; 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; KW Reference proteome. FT CHAIN 1..169 FT /note="Peptide deformylase 1" FT /id="PRO_0000082873" FT ACT_SITE 134 FT /evidence="ECO:0000255|HAMAP-Rule:MF_00163" FT BINDING 91 FT /ligand="Fe cation" FT /ligand_id="ChEBI:CHEBI:24875" FT /evidence="ECO:0000255|HAMAP-Rule:MF_00163" FT BINDING 133 FT /ligand="Fe cation" FT /ligand_id="ChEBI:CHEBI:24875" FT /evidence="ECO:0000255|HAMAP-Rule:MF_00163" FT BINDING 137 FT /ligand="Fe cation" FT /ligand_id="ChEBI:CHEBI:24875" FT /evidence="ECO:0000255|HAMAP-Rule:MF_00163" FT HELIX 12..15 FT /evidence="ECO:0007829|PDB:3FWX" FT HELIX 26..41 FT /evidence="ECO:0007829|PDB:3FWX" FT STRAND 45..48 FT /evidence="ECO:0007829|PDB:3FWX" FT HELIX 49..52 FT /evidence="ECO:0007829|PDB:3FWX" FT STRAND 56..61 FT /evidence="ECO:0007829|PDB:3FWX" FT STRAND 71..83 FT /evidence="ECO:0007829|PDB:3FWX" FT STRAND 85..89 FT /evidence="ECO:0007829|PDB:3FWX" FT STRAND 99..103 FT /evidence="ECO:0007829|PDB:3FWX" FT STRAND 105..112 FT /evidence="ECO:0007829|PDB:3FWX" FT STRAND 118..123 FT /evidence="ECO:0007829|PDB:3FWX" FT HELIX 125..138 FT /evidence="ECO:0007829|PDB:3FWX" FT HELIX 143..146 FT /evidence="ECO:0007829|PDB:3FWX" FT HELIX 149..163 FT /evidence="ECO:0007829|PDB:3FWX" SQ SEQUENCE 169 AA; 19147 MW; 16DB00B08CA40FC7 CRC64; MSVLQVLTFP DDRLRTVAKP VEQVTPEIQQ IVDDMLETMY AEEGIGLAAT QVDIHQRIVV IDISETRDQP MVLINPEIIE KRGEDGIEEG CLSVPGARAL VPRAAEVTVK ALDRNGQEYQ FDADDLLAIC VQHELDHLAG KLFVDYLSPL KRNRIKEKLE KIKRFNEKK //