DEF_STRA3
ID DEF_STRA3 Reviewed; 204 AA.
AC Q8E378;
DT 15-DEC-2003, integrated into UniProtKB/Swiss-Prot.
DT 01-MAR-2003, sequence version 1.
DT 03-AUG-2022, entry version 104.
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=gbs1883;
OS Streptococcus agalactiae serotype III (strain NEM316).
OC Bacteria; Firmicutes; Bacilli; Lactobacillales; Streptococcaceae;
OC Streptococcus.
OX NCBI_TaxID=211110;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=NEM316;
RX PubMed=12354221; DOI=10.1046/j.1365-2958.2002.03126.x;
RA Glaser P., Rusniok C., Buchrieser C., Chevalier F., Frangeul L., Msadek T.,
RA Zouine M., Couve E., Lalioui L., Poyart C., Trieu-Cuot P., Kunst F.;
RT "Genome sequence of Streptococcus agalactiae, a pathogen causing invasive
RT neonatal disease.";
RL Mol. Microbiol. 45:1499-1513(2002).
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; AL766854; CAD47542.1; -; Genomic_DNA.
DR RefSeq; WP_001272875.1; NC_004368.1.
DR PDB; 5JEX; X-ray; 2.00 A; A=1-204.
DR PDB; 5JEY; X-ray; 2.80 A; A=1-204.
DR PDB; 5JEZ; X-ray; 1.70 A; A=1-204.
DR PDB; 5JF0; X-ray; 1.60 A; A=1-204.
DR PDB; 5JF1; X-ray; 2.00 A; A=1-204.
DR PDB; 5JF2; X-ray; 2.00 A; A=1-204.
DR PDB; 5JF3; X-ray; 1.60 A; A=1-204.
DR PDB; 5JF4; X-ray; 2.40 A; A=1-204.
DR PDB; 5JF5; X-ray; 1.80 A; A=1-204.
DR PDB; 5JF6; X-ray; 1.70 A; A=1-204.
DR PDB; 5JF7; X-ray; 2.10 A; A=1-204.
DR PDB; 5JF8; X-ray; 1.80 A; A=1-204.
DR PDBsum; 5JEX; -.
DR PDBsum; 5JEY; -.
DR PDBsum; 5JEZ; -.
DR PDBsum; 5JF0; -.
DR PDBsum; 5JF1; -.
DR PDBsum; 5JF2; -.
DR PDBsum; 5JF3; -.
DR PDBsum; 5JF4; -.
DR PDBsum; 5JF5; -.
DR PDBsum; 5JF6; -.
DR PDBsum; 5JF7; -.
DR PDBsum; 5JF8; -.
DR AlphaFoldDB; Q8E378; -.
DR SMR; Q8E378; -.
DR STRING; 211110.gbs1883; -.
DR EnsemblBacteria; CAD47542; CAD47542; CAD47542.
DR GeneID; 66886680; -.
DR KEGG; san:gbs1883; -.
DR eggNOG; COG0242; Bacteria.
DR HOGENOM; CLU_061901_4_0_9; -.
DR OMA; DMMEYLV; -.
DR BRENDA; 3.5.1.88; 5917.
DR Proteomes; UP000000823; 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..204
FT /note="Peptide deformylase"
FT /id="PRO_0000082847"
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..8
FT /evidence="ECO:0007829|PDB:5JF0"
FT HELIX 16..18
FT /evidence="ECO:0007829|PDB:5JF0"
FT HELIX 25..28
FT /evidence="ECO:0007829|PDB:5JF0"
FT HELIX 40..57
FT /evidence="ECO:0007829|PDB:5JF0"
FT HELIX 59..65
FT /evidence="ECO:0007829|PDB:5JF0"
FT STRAND 70..74
FT /evidence="ECO:0007829|PDB:5JF0"
FT HELIX 75..78
FT /evidence="ECO:0007829|PDB:5JF0"
FT STRAND 82..90
FT /evidence="ECO:0007829|PDB:5JF0"
FT STRAND 101..118
FT /evidence="ECO:0007829|PDB:5JF0"
FT STRAND 120..125
FT /evidence="ECO:0007829|PDB:5JF0"
FT STRAND 144..153
FT /evidence="ECO:0007829|PDB:5JF0"
FT STRAND 159..164
FT /evidence="ECO:0007829|PDB:5JF0"
FT HELIX 166..179
FT /evidence="ECO:0007829|PDB:5JF0"
FT HELIX 184..187
FT /evidence="ECO:0007829|PDB:5JF0"
FT STRAND 201..203
FT /evidence="ECO:0007829|PDB:5JF0"
SQ SEQUENCE 204 AA; 22830 MW; 50097F6CCF8524EF CRC64;
MSAIDKLVKA SHLIDMNDII REGNPTLRKV AEEVTFPLSE KEEILGEKMM QFLKHSQDPI
MAEKLGLRGG VGLAAPQLDI SKRIIAVLVP NVEDAQGNPP KEAYSLQEVM YNPKVVSHSV
QDAALSDGEG CLSVDREVPG YVVRHARVTI EYFDKTGEKH RLKLKGYNSI VVQHEIDHID
GIMFYDRINE KNPFAVKEGL LILE
