DEF_STRR6
ID DEF_STRR6 Reviewed; 203 AA.
AC Q8DP79;
DT 15-DEC-2003, integrated into UniProtKB/Swiss-Prot.
DT 01-MAR-2003, sequence version 1.
DT 03-AUG-2022, entry version 125.
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=spr1310;
OS Streptococcus pneumoniae (strain ATCC BAA-255 / R6).
OC Bacteria; Firmicutes; Bacilli; Lactobacillales; Streptococcaceae;
OC Streptococcus.
OX NCBI_TaxID=171101;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC BAA-255 / R6;
RX PubMed=11544234; DOI=10.1128/jb.183.19.5709-5717.2001;
RA Hoskins J., Alborn W.E. Jr., Arnold J., Blaszczak L.C., Burgett S.,
RA DeHoff B.S., Estrem S.T., Fritz L., Fu D.-J., Fuller W., Geringer C.,
RA Gilmour R., Glass J.S., Khoja H., Kraft A.R., Lagace R.E., LeBlanc D.J.,
RA Lee L.N., Lefkowitz E.J., Lu J., Matsushima P., McAhren S.M., McHenney M.,
RA McLeaster K., Mundy C.W., Nicas T.I., Norris F.H., O'Gara M., Peery R.B.,
RA Robertson G.T., Rockey P., Sun P.-M., Winkler M.E., Yang Y.,
RA Young-Bellido M., Zhao G., Zook C.A., Baltz R.H., Jaskunas S.R.,
RA Rosteck P.R. Jr., Skatrud P.L., Glass J.I.;
RT "Genome of the bacterium Streptococcus pneumoniae strain R6.";
RL J. Bacteriol. 183:5709-5717(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; AE007317; AAL00114.1; -; Genomic_DNA.
DR PIR; E98035; E98035.
DR RefSeq; NP_358903.1; NC_003098.1.
DR RefSeq; WP_001272961.1; NC_003098.1.
DR PDB; 2AI7; X-ray; 2.00 A; A=1-202.
DR PDB; 2AIA; X-ray; 1.70 A; A=1-202.
DR PDB; 2AIE; X-ray; 1.70 A; P=1-202.
DR PDB; 3SVJ; X-ray; 1.55 A; P=1-203.
DR PDB; 4EOX; X-ray; 1.78 A; P=1-203.
DR PDB; 6OW2; X-ray; 1.70 A; P=2-203.
DR PDB; 6OW7; X-ray; 1.45 A; P/Q=2-203.
DR PDBsum; 2AI7; -.
DR PDBsum; 2AIA; -.
DR PDBsum; 2AIE; -.
DR PDBsum; 3SVJ; -.
DR PDBsum; 4EOX; -.
DR PDBsum; 6OW2; -.
DR PDBsum; 6OW7; -.
DR AlphaFoldDB; Q8DP79; -.
DR SMR; Q8DP79; -.
DR STRING; 171101.spr1310; -.
DR BindingDB; Q8DP79; -.
DR DrugBank; DB08524; 2-(3-BENZOYLPHENOXY)ETHYL(HYDROXY)FORMAMIDE.
DR DrugBank; DB08523; [HYDROXY(3-PHENYLPROPYL)AMINO]METHANOL.
DR DrugBank; DB08525; HYDROXY[3-(6-METHYLPYRIDIN-2-YL)PROPYL]FORMAMIDE.
DR EnsemblBacteria; AAL00114; AAL00114; spr1310.
DR GeneID; 60233589; -.
DR GeneID; 66806556; -.
DR KEGG; spr:spr1310; -.
DR PATRIC; fig|171101.6.peg.1422; -.
DR eggNOG; COG0242; Bacteria.
DR HOGENOM; CLU_061901_4_0_9; -.
DR OMA; DMMEYLV; -.
DR EvolutionaryTrace; Q8DP79; -.
DR PRO; PR:Q8DP79; -.
DR Proteomes; UP000000586; 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 1: Evidence at protein level;
KW 3D-structure; Hydrolase; Iron; Metal-binding; Protein biosynthesis;
KW Reference proteome.
FT CHAIN 1..203
FT /note="Peptide deformylase"
FT /id="PRO_0000082858"
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:6OW7"
FT HELIX 16..18
FT /evidence="ECO:0007829|PDB:6OW7"
FT HELIX 25..28
FT /evidence="ECO:0007829|PDB:6OW7"
FT HELIX 40..57
FT /evidence="ECO:0007829|PDB:6OW7"
FT HELIX 59..65
FT /evidence="ECO:0007829|PDB:6OW7"
FT STRAND 71..74
FT /evidence="ECO:0007829|PDB:6OW7"
FT HELIX 75..78
FT /evidence="ECO:0007829|PDB:6OW7"
FT STRAND 82..90
FT /evidence="ECO:0007829|PDB:6OW7"
FT STRAND 100..117
FT /evidence="ECO:0007829|PDB:6OW7"
FT STRAND 119..124
FT /evidence="ECO:0007829|PDB:6OW7"
FT STRAND 143..152
FT /evidence="ECO:0007829|PDB:6OW7"
FT STRAND 158..163
FT /evidence="ECO:0007829|PDB:6OW7"
FT HELIX 165..178
FT /evidence="ECO:0007829|PDB:6OW7"
FT HELIX 183..186
FT /evidence="ECO:0007829|PDB:6OW7"
FT STRAND 189..191
FT /evidence="ECO:0007829|PDB:4EOX"
FT STRAND 199..202
FT /evidence="ECO:0007829|PDB:6OW7"
SQ SEQUENCE 203 AA; 22692 MW; E332956982A67161 CRC64;
MSAIERITKA AHLIDMNDII REGNPTLRTV AEEVTFPLSD QEIILGEKMM QFLKHSQDPV
MAEKMGLRGG VGLAAPQLDI SKRIIAVLVP NIVEEGETPQ EAYDLEAIMY NPKIVSHSVQ
DAALGEGEGC LSVDRNVPGY VVRHARVTVD YFDKDGEKHR IKLKGYNSIV VQHEIDHING
IMFYDRINEK DPFAVKDGLL ILE
