DEF_STRPN
ID DEF_STRPN Reviewed; 203 AA.
AC Q9F2F0;
DT 05-DEC-2001, integrated into UniProtKB/Swiss-Prot.
DT 01-MAR-2001, sequence version 1.
DT 03-AUG-2022, entry version 129.
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=SP_1456;
OS Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4).
OC Bacteria; Firmicutes; Bacilli; Lactobacillales; Streptococcaceae;
OC Streptococcus.
OX NCBI_TaxID=170187;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=11257016; DOI=10.1128/aac.45.4.1058-1064.2001;
RA Apfel C.M., Locher H., Evers S., Takacs B., Hubschwerlen C., Pirson W.,
RA Page M.G., Keck W.;
RT "Peptide deformylase as an antibacterial drug target: target validation and
RT resistance development.";
RL Antimicrob. Agents Chemother. 45:1058-1064(2001).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC BAA-334 / TIGR4;
RX PubMed=11463916; DOI=10.1126/science.1061217;
RA Tettelin H., Nelson K.E., Paulsen I.T., Eisen J.A., Read T.D.,
RA Peterson S.N., Heidelberg J.F., DeBoy R.T., Haft D.H., Dodson R.J.,
RA Durkin A.S., Gwinn M.L., Kolonay J.F., Nelson W.C., Peterson J.D.,
RA Umayam L.A., White O., Salzberg S.L., Lewis M.R., Radune D.,
RA Holtzapple E.K., Khouri H.M., Wolf A.M., Utterback T.R., Hansen C.L.,
RA McDonald L.A., Feldblyum T.V., Angiuoli S.V., Dickinson T., Hickey E.K.,
RA Holt I.E., Loftus B.J., Yang F., Smith H.O., Venter J.C., Dougherty B.A.,
RA Morrison D.A., Hollingshead S.K., Fraser C.M.;
RT "Complete genome sequence of a virulent isolate of Streptococcus
RT pneumoniae.";
RL Science 293:498-506(2001).
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;
CC Evidence={ECO:0000255|HAMAP-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}.
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DR EMBL; AJ278785; CAC15392.1; -; Genomic_DNA.
DR EMBL; AE005672; AAK75550.1; -; Genomic_DNA.
DR PIR; E95169; E95169.
DR RefSeq; WP_001272941.1; NZ_AKVY01000001.1.
DR PDB; 1LM6; X-ray; 1.75 A; A=1-203.
DR PDBsum; 1LM6; -.
DR AlphaFoldDB; Q9F2F0; -.
DR SMR; Q9F2F0; -.
DR STRING; 170187.SP_1456; -.
DR BindingDB; Q9F2F0; -.
DR ChEMBL; CHEMBL2029196; -.
DR EnsemblBacteria; AAK75550; AAK75550; SP_1456.
DR KEGG; spn:SP_1456; -.
DR eggNOG; COG0242; Bacteria.
DR OMA; DMMEYLV; -.
DR PhylomeDB; Q9F2F0; -.
DR BioCyc; SPNE170187:G1FZB-1472-MON; -.
DR BRENDA; 3.5.1.88; 1960.
DR EvolutionaryTrace; Q9F2F0; -.
DR Proteomes; UP000000585; 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; -; 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..203
FT /note="Peptide deformylase"
FT /id="PRO_0000082857"
FT ACT_SITE 174
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00163"
FT BINDING 130
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00163"
FT BINDING 173
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00163"
FT BINDING 177
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00163"
FT HELIX 3..7
FT /evidence="ECO:0007829|PDB:1LM6"
FT HELIX 16..18
FT /evidence="ECO:0007829|PDB:1LM6"
FT HELIX 25..28
FT /evidence="ECO:0007829|PDB:1LM6"
FT HELIX 40..56
FT /evidence="ECO:0007829|PDB:1LM6"
FT HELIX 59..65
FT /evidence="ECO:0007829|PDB:1LM6"
FT STRAND 71..74
FT /evidence="ECO:0007829|PDB:1LM6"
FT HELIX 75..78
FT /evidence="ECO:0007829|PDB:1LM6"
FT STRAND 82..89
FT /evidence="ECO:0007829|PDB:1LM6"
FT STRAND 105..117
FT /evidence="ECO:0007829|PDB:1LM6"
FT STRAND 119..124
FT /evidence="ECO:0007829|PDB:1LM6"
FT STRAND 143..145
FT /evidence="ECO:0007829|PDB:1LM6"
FT STRAND 147..152
FT /evidence="ECO:0007829|PDB:1LM6"
FT STRAND 158..163
FT /evidence="ECO:0007829|PDB:1LM6"
FT HELIX 165..178
FT /evidence="ECO:0007829|PDB:1LM6"
FT HELIX 183..186
FT /evidence="ECO:0007829|PDB:1LM6"
FT STRAND 199..202
FT /evidence="ECO:0007829|PDB:1LM6"
SQ SEQUENCE 203 AA; 22676 MW; 192F91B42375F8CD CRC64;
MSAIERITKA AHLIDMNDII REGNPTLRAI AEEVTFPLSD QEIILGEKMM QFLKHSQDPV
MAEKMGLRGG VGLAAPQLDI SKRIIAVLVP NIVEEGETPQ EAYDLEAIMY NPKIVSHSVQ
DAALGEGEGC LSVDRNVPGY VVRHARVTVD YFDKDGEKHR IKLKGYNSIV VQHEIDHING
IMFYDRINEK DPFAVKDGLL ILE
