DEF_LACP3
ID DEF_LACP3 Reviewed; 184 AA.
AC Q039N7;
DT 11-SEP-2007, integrated into UniProtKB/Swiss-Prot.
DT 14-NOV-2006, sequence version 1.
DT 03-AUG-2022, entry version 88.
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=LSEI_1303;
OS Lacticaseibacillus paracasei (strain ATCC 334 / BCRC 17002 / CCUG 31169 /
OS CIP 107868 / KCTC 3260 / NRRL B-441) (Lactobacillus paracasei).
OC Bacteria; Firmicutes; Bacilli; Lactobacillales; Lactobacillaceae;
OC Lacticaseibacillus.
OX NCBI_TaxID=321967;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 334 / BCRC 17002 / CCUG 31169 / CIP 107868 / KCTC 3260 / NRRL
RC B-441;
RX PubMed=17030793; DOI=10.1073/pnas.0607117103;
RA Makarova K.S., Slesarev A., Wolf Y.I., Sorokin A., Mirkin B., Koonin E.V.,
RA Pavlov A., Pavlova N., Karamychev V., Polouchine N., Shakhova V.,
RA Grigoriev I., Lou Y., Rohksar D., Lucas S., Huang K., Goodstein D.M.,
RA Hawkins T., Plengvidhya V., Welker D., Hughes J., Goh Y., Benson A.,
RA Baldwin K., Lee J.-H., Diaz-Muniz I., Dosti B., Smeianov V., Wechter W.,
RA Barabote R., Lorca G., Altermann E., Barrangou R., Ganesan B., Xie Y.,
RA Rawsthorne H., Tamir D., Parker C., Breidt F., Broadbent J.R., Hutkins R.,
RA O'Sullivan D., Steele J., Unlu G., Saier M.H. Jr., Klaenhammer T.,
RA Richardson P., Kozyavkin S., Weimer B.C., Mills D.A.;
RT "Comparative genomics of the lactic acid bacteria.";
RL Proc. Natl. Acad. Sci. U.S.A. 103:15611-15616(2006).
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; CP000423; ABJ70085.1; -; Genomic_DNA.
DR RefSeq; WP_003565220.1; NC_008526.1.
DR RefSeq; YP_806527.1; NC_008526.1.
DR AlphaFoldDB; Q039N7; -.
DR SMR; Q039N7; -.
DR STRING; 321967.LSEI_1303; -.
DR EnsemblBacteria; ABJ70085; ABJ70085; LSEI_1303.
DR GeneID; 61269528; -.
DR KEGG; lca:LSEI_1303; -.
DR PATRIC; fig|321967.11.peg.1282; -.
DR HOGENOM; CLU_061901_4_0_9; -.
DR OMA; DMMEYLV; -.
DR Proteomes; UP000001651; 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 3: Inferred from homology;
KW Hydrolase; Iron; Metal-binding; Protein biosynthesis.
FT CHAIN 1..184
FT /note="Peptide deformylase"
FT /id="PRO_0000301043"
FT ACT_SITE 155
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00163"
FT BINDING 111
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00163"
FT BINDING 154
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00163"
FT BINDING 158
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00163"
SQ SEQUENCE 184 AA; 20586 MW; 381BAEB784D5DA15 CRC64;
MYLMKDITRD GAKVLRETAK PVTFPLSDED KQLAHDMMAY LVISQDEEQN EKYHLRPGVG
LAAPQVGQSK AMAAVLVPGD DNEILFKEVL INPRIISNSV QHAALAEGEG CLSVDKDVPG
YVVRADRITI SYQNEAGEHK KIRLKNYPAI VCQHEIDHLN GVLFYDHINK EHPFTIDPDA
VIIK
