DEF_STRP1
ID DEF_STRP1 Reviewed; 204 AA.
AC P68771; P82590; Q48WI8; Q99XY7;
DT 21-DEC-2004, integrated into UniProtKB/Swiss-Prot.
DT 21-DEC-2004, sequence version 1.
DT 03-AUG-2022, entry version 118.
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};
GN OrderedLocusNames=SPy_1958, M5005_Spy1669;
OS Streptococcus pyogenes serotype M1.
OC Bacteria; Firmicutes; Bacilli; Lactobacillales; Streptococcaceae;
OC Streptococcus.
OX NCBI_TaxID=301447;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 700294 / SF370 / Serotype M1;
RX PubMed=11296296; DOI=10.1073/pnas.071559398;
RA Ferretti J.J., McShan W.M., Ajdic D.J., Savic D.J., Savic G., Lyon K.,
RA Primeaux C., Sezate S., Suvorov A.N., Kenton S., Lai H.S., Lin S.P.,
RA Qian Y., Jia H.G., Najar F.Z., Ren Q., Zhu H., Song L., White J., Yuan X.,
RA Clifton S.W., Roe B.A., McLaughlin R.E.;
RT "Complete genome sequence of an M1 strain of Streptococcus pyogenes.";
RL Proc. Natl. Acad. Sci. U.S.A. 98:4658-4663(2001).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC BAA-947 / MGAS5005 / Serotype M1;
RX PubMed=16088826; DOI=10.1086/432514;
RA Sumby P., Porcella S.F., Madrigal A.G., Barbian K.D., Virtaneva K.,
RA Ricklefs S.M., Sturdevant D.E., Graham M.R., Vuopio-Varkila J., Hoe N.P.,
RA Musser J.M.;
RT "Evolutionary origin and emergence of a highly successful clone of serotype
RT M1 group A Streptococcus involved multiple horizontal gene transfer
RT events.";
RL J. Infect. Dis. 192:771-782(2005).
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; AE004092; AAK34651.1; -; Genomic_DNA.
DR EMBL; CP000017; AAZ52287.1; -; Genomic_DNA.
DR RefSeq; NP_269930.1; NC_002737.2.
DR PDB; 2OS3; X-ray; 2.26 A; A=2-204.
DR PDBsum; 2OS3; -.
DR AlphaFoldDB; P68771; -.
DR SMR; P68771; -.
DR STRING; 1314.HKU360_01786; -.
DR DrugBank; DB04310; 2-[(Formyl-Hydroxy-Amino)-Methyl]-Heptanoic Acid [1-(2-Hydroxymethyl-Pyrrolidine-1-Carbonyl)-2-Methyl-Propyl]-Amide.
DR PaxDb; P68771; -.
DR EnsemblBacteria; AAK34651; AAK34651; SPy_1958.
DR KEGG; spy:SPy_1958; -.
DR KEGG; spz:M5005_Spy1669; -.
DR PATRIC; fig|160490.10.peg.1705; -.
DR HOGENOM; CLU_061901_4_0_9; -.
DR OMA; DMMEYLV; -.
DR EvolutionaryTrace; P68771; -.
DR Proteomes; UP000000750; 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;
KW Reference proteome.
FT CHAIN 1..204
FT /note="Peptide deformylase"
FT /id="PRO_0000082859"
FT ACT_SITE 175
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00163"
FT BINDING 131
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00163"
FT BINDING 174
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00163"
FT BINDING 178
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:2OS3"
FT HELIX 16..18
FT /evidence="ECO:0007829|PDB:2OS3"
FT HELIX 25..28
FT /evidence="ECO:0007829|PDB:2OS3"
FT HELIX 40..56
FT /evidence="ECO:0007829|PDB:2OS3"
FT HELIX 59..65
FT /evidence="ECO:0007829|PDB:2OS3"
FT STRAND 71..74
FT /evidence="ECO:0007829|PDB:2OS3"
FT HELIX 75..78
FT /evidence="ECO:0007829|PDB:2OS3"
FT STRAND 82..90
FT /evidence="ECO:0007829|PDB:2OS3"
FT STRAND 101..118
FT /evidence="ECO:0007829|PDB:2OS3"
FT STRAND 120..125
FT /evidence="ECO:0007829|PDB:2OS3"
FT STRAND 144..153
FT /evidence="ECO:0007829|PDB:2OS3"
FT STRAND 159..164
FT /evidence="ECO:0007829|PDB:2OS3"
FT HELIX 166..178
FT /evidence="ECO:0007829|PDB:2OS3"
FT TURN 179..181
FT /evidence="ECO:0007829|PDB:2OS3"
FT HELIX 184..187
FT /evidence="ECO:0007829|PDB:2OS3"
FT STRAND 200..203
FT /evidence="ECO:0007829|PDB:2OS3"
SQ SEQUENCE 204 AA; 22862 MW; 89F8EDE94D94DC05 CRC64;
MSAQDKLIKP SHLITMDDII REGNPTLRAV AKEVSLPLCD EDILLGEKMM QFLKHSQDPV
MAEKLGLRAG VGLAAPQIDV SKRIIAVLVP NLPDKEGNPP KEAYSWQEVL YNPKIVSHSV
QDAALSDGEG CLSVDRVVEG YVVRHARVTV DYYDKEGQQH RIKLKGYNAI VVQHEIDHIN
GVLFYDRINA KNPFETKEEL LILD
