DEF_STRMU
ID DEF_STRMU Reviewed; 204 AA.
AC Q8DWC2;
DT 15-DEC-2003, integrated into UniProtKB/Swiss-Prot.
DT 01-MAR-2003, sequence version 1.
DT 03-AUG-2022, entry version 109.
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=SMU_143c;
OS Streptococcus mutans serotype c (strain ATCC 700610 / UA159).
OC Bacteria; Firmicutes; Bacilli; Lactobacillales; Streptococcaceae;
OC Streptococcus.
OX NCBI_TaxID=210007;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 700610 / UA159;
RX PubMed=12397186; DOI=10.1073/pnas.172501299;
RA Ajdic D.J., McShan W.M., McLaughlin R.E., Savic G., Chang J., Carson M.B.,
RA Primeaux C., Tian R., Kenton S., Jia H.G., Lin S.P., Qian Y., Li S.,
RA Zhu H., Najar F.Z., Lai H., White J., Roe B.A., Ferretti J.J.;
RT "Genome sequence of Streptococcus mutans UA159, a cariogenic dental
RT pathogen.";
RL Proc. Natl. Acad. Sci. U.S.A. 99:14434-14439(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; AE014133; AAN57921.1; -; Genomic_DNA.
DR RefSeq; NP_720615.1; NC_004350.2.
DR RefSeq; WP_002263599.1; NC_004350.2.
DR PDB; 3L87; X-ray; 2.00 A; A=1-204.
DR PDBsum; 3L87; -.
DR AlphaFoldDB; Q8DWC2; -.
DR SMR; Q8DWC2; -.
DR STRING; 210007.SMU_143c; -.
DR PRIDE; Q8DWC2; -.
DR EnsemblBacteria; AAN57921; AAN57921; SMU_143c.
DR GeneID; 66818368; -.
DR KEGG; smu:SMU_143c; -.
DR PATRIC; fig|210007.7.peg.122; -.
DR eggNOG; COG0242; Bacteria.
DR HOGENOM; CLU_061901_4_0_9; -.
DR OMA; DMMEYLV; -.
DR PhylomeDB; Q8DWC2; -.
DR Proteomes; UP000002512; 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_0000082856"
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:3L87"
FT HELIX 25..27
FT /evidence="ECO:0007829|PDB:3L87"
FT HELIX 40..57
FT /evidence="ECO:0007829|PDB:3L87"
FT HELIX 59..65
FT /evidence="ECO:0007829|PDB:3L87"
FT STRAND 71..74
FT /evidence="ECO:0007829|PDB:3L87"
FT HELIX 75..78
FT /evidence="ECO:0007829|PDB:3L87"
FT STRAND 82..90
FT /evidence="ECO:0007829|PDB:3L87"
FT STRAND 101..118
FT /evidence="ECO:0007829|PDB:3L87"
FT STRAND 120..125
FT /evidence="ECO:0007829|PDB:3L87"
FT STRAND 144..146
FT /evidence="ECO:0007829|PDB:3L87"
FT STRAND 148..153
FT /evidence="ECO:0007829|PDB:3L87"
FT STRAND 159..164
FT /evidence="ECO:0007829|PDB:3L87"
FT HELIX 166..179
FT /evidence="ECO:0007829|PDB:3L87"
FT HELIX 184..187
FT /evidence="ECO:0007829|PDB:3L87"
FT STRAND 201..203
FT /evidence="ECO:0007829|PDB:3L87"
SQ SEQUENCE 204 AA; 22919 MW; CC8FB580FDFCB8A3 CRC64;
MSAIKTITKA SHLIDMNDII REGHPTLRAV AQDVTFPLNE DDIILGEKML QFLKNSQDPV
TAEKMELRGG VGLAAPQLDI SKRIIAVLIP NPEDKDGNPP KEAYALKEVM YNPRIIAHSV
QDAALADGEG CLSVDRVVEG YVIRHSRVTI EYYDKNSDKK KLKLKGYQSI VVQHEIDHTN
GIMFFDRINE KNPFEIKEGL LLIE
