DEF_HELPY
ID DEF_HELPY Reviewed; 174 AA.
AC P56419;
DT 15-JUL-1998, integrated into UniProtKB/Swiss-Prot.
DT 15-JUL-1998, sequence version 1.
DT 03-AUG-2022, entry version 123.
DE RecName: Full=Peptide deformylase;
DE Short=PDF;
DE EC=3.5.1.88;
DE AltName: Full=Polypeptide deformylase;
GN Name=def; OrderedLocusNames=HP_0793;
OS Helicobacter pylori (strain ATCC 700392 / 26695) (Campylobacter pylori).
OC Bacteria; Proteobacteria; Epsilonproteobacteria; Campylobacterales;
OC Helicobacteraceae; Helicobacter.
OX NCBI_TaxID=85962;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 700392 / 26695;
RX PubMed=9252185; DOI=10.1038/41483;
RA Tomb J.-F., White O., Kerlavage A.R., Clayton R.A., Sutton G.G.,
RA Fleischmann R.D., Ketchum K.A., Klenk H.-P., Gill S.R., Dougherty B.A.,
RA Nelson K.E., Quackenbush J., Zhou L., Kirkness E.F., Peterson S.N.,
RA Loftus B.J., Richardson D.L., Dodson R.J., Khalak H.G., Glodek A.,
RA McKenney K., FitzGerald L.M., Lee N., Adams M.D., Hickey E.K., Berg D.E.,
RA Gocayne J.D., Utterback T.R., Peterson J.D., Kelley J.M., Cotton M.D.,
RA Weidman J.F., Fujii C., Bowman C., Watthey L., Wallin E., Hayes W.S.,
RA Borodovsky M., Karp P.D., Smith H.O., Fraser C.M., Venter J.C.;
RT "The complete genome sequence of the gastric pathogen Helicobacter
RT pylori.";
RL Nature 388:539-547(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 (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 -!- SIMILARITY: Belongs to the polypeptide deformylase family.
CC {ECO:0000305}.
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DR EMBL; AE000511; AAD07841.1; -; Genomic_DNA.
DR PIR; A64619; A64619.
DR RefSeq; NP_207586.1; NC_000915.1.
DR RefSeq; WP_001185845.1; NC_018939.1.
DR AlphaFoldDB; P56419; -.
DR SMR; P56419; -.
DR DIP; DIP-3266N; -.
DR IntAct; P56419; 5.
DR MINT; P56419; -.
DR STRING; 85962.C694_04065; -.
DR PaxDb; P56419; -.
DR PRIDE; P56419; -.
DR EnsemblBacteria; AAD07841; AAD07841; HP_0793.
DR KEGG; hpy:HP_0793; -.
DR PATRIC; fig|85962.47.peg.845; -.
DR eggNOG; COG0242; Bacteria.
DR OMA; VCIQHEI; -.
DR PhylomeDB; P56419; -.
DR BRENDA; 3.5.1.88; 2604.
DR Proteomes; UP000000429; Chromosome.
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:0031365; P:N-terminal protein amino acid modification; IBA:GO_Central.
DR GO; GO:0018206; P:peptidyl-methionine 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; -; 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 3: Inferred from homology;
KW Hydrolase; Iron; Metal-binding; Protein biosynthesis; Reference proteome.
FT CHAIN 1..174
FT /note="Peptide deformylase"
FT /id="PRO_0000082790"
FT ACT_SITE 139
FT /evidence="ECO:0000250"
FT BINDING 96
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /evidence="ECO:0000250"
FT BINDING 138
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /evidence="ECO:0000250"
FT BINDING 142
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /evidence="ECO:0000250"
SQ SEQUENCE 174 AA; 20057 MW; 375525F45E5CC774 CRC64;
MALLEIIHYP SKILRTISKE VVSFDSKLHQ QLDDMHETMI ASEGIGLAAI QVGLPLRMLI
INLPQEDGVQ HKEDCLEIIN PKFIETGGSM MYREGCLSVP GFYEEVERFE KVKIEYQNRF
AEVKVLEASE LLAVAIQHEI DHLNGVLFVD KLSILKRKKF EKELKELQKK QKHE
