DEF_THEMA
ID DEF_THEMA Reviewed; 164 AA.
AC P96113;
DT 15-JUL-1998, integrated into UniProtKB/Swiss-Prot.
DT 01-MAY-1997, sequence version 1.
DT 03-AUG-2022, entry version 144.
DE RecName: Full=Peptide deformylase;
DE Short=PDF;
DE EC=3.5.1.88;
DE AltName: Full=Polypeptide deformylase;
GN Name=def; OrderedLocusNames=TM_1661;
OS Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826
OS / MSB8).
OC Bacteria; Thermotogae; Thermotogales; Thermotogaceae; Thermotoga.
OX NCBI_TaxID=243274;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=9086272; DOI=10.1006/jmbi.1996.0835;
RA Mazel D., Coic E., Blanchard S., Saurin W., Marliere P.;
RT "A survey of polypeptide deformylase function throughout the eubacterial
RT lineage.";
RL J. Mol. Biol. 266:939-949(1997).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8;
RX PubMed=10360571; DOI=10.1038/20601;
RA Nelson K.E., Clayton R.A., Gill S.R., Gwinn M.L., Dodson R.J., Haft D.H.,
RA Hickey E.K., Peterson J.D., Nelson W.C., Ketchum K.A., McDonald L.A.,
RA Utterback T.R., Malek J.A., Linher K.D., Garrett M.M., Stewart A.M.,
RA Cotton M.D., Pratt M.S., Phillips C.A., Richardson D.L., Heidelberg J.F.,
RA Sutton G.G., Fleischmann R.D., Eisen J.A., White O., Salzberg S.L.,
RA Smith H.O., Venter J.C., Fraser C.M.;
RT "Evidence for lateral gene transfer between Archaea and Bacteria from
RT genome sequence of Thermotoga maritima.";
RL Nature 399:323-329(1999).
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 (By
CC similarity). {ECO:0000250}.
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 -!- COFACTOR:
CC Name=Fe(2+); Xref=ChEBI:CHEBI:29033; Evidence={ECO:0000250};
CC Note=Binds 1 Fe(2+) ion. {ECO:0000250};
CC -!- SIMILARITY: Belongs to the polypeptide deformylase family.
CC {ECO:0000305}.
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DR EMBL; Y10306; CAA71356.1; -; Genomic_DNA.
DR EMBL; AE000512; AAD36728.1; -; Genomic_DNA.
DR PIR; C72224; C72224.
DR RefSeq; NP_229461.1; NC_000853.1.
DR RefSeq; WP_004082176.1; NZ_CP011107.1.
DR PDB; 1LME; X-ray; 2.20 A; A/B=1-164.
DR PDBsum; 1LME; -.
DR AlphaFoldDB; P96113; -.
DR SMR; P96113; -.
DR STRING; 243274.THEMA_05940; -.
DR DrugBank; DB03661; L-cysteic acid.
DR EnsemblBacteria; AAD36728; AAD36728; TM_1661.
DR KEGG; tma:TM1661; -.
DR eggNOG; COG0242; Bacteria.
DR InParanoid; P96113; -.
DR OMA; VCIQHEI; -.
DR OrthoDB; 1649129at2; -.
DR BRENDA; 3.5.1.88; 6331.
DR EvolutionaryTrace; P96113; -.
DR Proteomes; UP000008183; 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..164
FT /note="Peptide deformylase"
FT /id="PRO_0000082866"
FT ACT_SITE 130
FT /evidence="ECO:0000250"
FT BINDING 87
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /evidence="ECO:0000250"
FT BINDING 129
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /evidence="ECO:0000250"
FT BINDING 133
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /evidence="ECO:0000250"
FT HELIX 10..12
FT /evidence="ECO:0007829|PDB:1LME"
FT HELIX 24..39
FT /evidence="ECO:0007829|PDB:1LME"
FT STRAND 43..46
FT /evidence="ECO:0007829|PDB:1LME"
FT HELIX 47..50
FT /evidence="ECO:0007829|PDB:1LME"
FT STRAND 54..59
FT /evidence="ECO:0007829|PDB:1LME"
FT STRAND 61..63
FT /evidence="ECO:0007829|PDB:1LME"
FT STRAND 66..76
FT /evidence="ECO:0007829|PDB:1LME"
FT STRAND 80..85
FT /evidence="ECO:0007829|PDB:1LME"
FT STRAND 95..108
FT /evidence="ECO:0007829|PDB:1LME"
FT STRAND 114..120
FT /evidence="ECO:0007829|PDB:1LME"
FT HELIX 121..134
FT /evidence="ECO:0007829|PDB:1LME"
FT HELIX 139..142
FT /evidence="ECO:0007829|PDB:1LME"
SQ SEQUENCE 164 AA; 19024 MW; 9FE94A206DE50842 CRC64;
MYRIRVFGDP VLRKRAKPVT KFDENLKKTI ERMIETMYHY DGVGLAAPQV GISQRFFVMD
VGNGPVAVIN PEILEIDPET EVAEEGCLSF PEIFVEIERS KRIKVKYQNT RGEYVEEELE
GYAARVFQHE FDHLNGVLII DRISPAKRLL LRKKLMDIAR TVKR
