ID A0A1C5GSD3_9ACTN Unreviewed; 506 AA.
AC A0A1C5GSD3;
DT 02-NOV-2016, integrated into UniProtKB/TrEMBL.
DT 02-NOV-2016, sequence version 1.
DT 27-MAR-2024, entry version 27.
DE RecName: Full=Peptide deformylase {ECO:0000256|HAMAP-Rule:MF_00163};
DE Short=PDF {ECO:0000256|HAMAP-Rule:MF_00163};
DE EC=3.5.1.88 {ECO:0000256|HAMAP-Rule:MF_00163};
DE AltName: Full=Polypeptide deformylase {ECO:0000256|HAMAP-Rule:MF_00163};
GN Name=def {ECO:0000256|HAMAP-Rule:MF_00163};
GN ORFNames=GA0074704_0413 {ECO:0000313|EMBL:SCG36664.1};
OS Micromonospora siamensis.
OC Bacteria; Actinomycetota; Actinomycetes; Micromonosporales;
OC Micromonosporaceae; Micromonospora.
OX NCBI_TaxID=299152 {ECO:0000313|EMBL:SCG36664.1, ECO:0000313|Proteomes:UP000198210};
RN [1] {ECO:0000313|EMBL:SCG36664.1, ECO:0000313|Proteomes:UP000198210}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=DSM 45097 {ECO:0000313|EMBL:SCG36664.1,
RC ECO:0000313|Proteomes:UP000198210};
RA Kjaerup R.B., Dalgaard T.S., Juul-Madsen H.R.;
RL Submitted (JUN-2016) to the EMBL/GenBank/DDBJ databases.
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:0000256|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:0000256|HAMAP-Rule:MF_00163};
CC -!- COFACTOR:
CC Name=Fe(2+); Xref=ChEBI:CHEBI:29033;
CC Evidence={ECO:0000256|HAMAP-Rule:MF_00163};
CC Note=Binds 1 Fe(2+) ion. {ECO:0000256|HAMAP-Rule:MF_00163};
CC -!- SIMILARITY: Belongs to the polypeptide deformylase family.
CC {ECO:0000256|ARBA:ARBA00010759, ECO:0000256|HAMAP-Rule:MF_00163}.
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DR EMBL; LT607751; SCG36664.1; -; Genomic_DNA.
DR AlphaFoldDB; A0A1C5GSD3; -.
DR Proteomes; UP000198210; Chromosome i.
DR GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
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; cd00093; HTH_XRE; 1.
DR Gene3D; 1.10.260.40; lambda repressor-like DNA-binding domains; 1.
DR Gene3D; 3.90.45.10; Peptide deformylase; 1.
DR HAMAP; MF_00163; Pep_deformylase; 1.
DR InterPro; IPR001387; Cro/C1-type_HTH.
DR InterPro; IPR010982; Lambda_DNA-bd_dom_sf.
DR InterPro; IPR023635; Peptide_deformylase.
DR InterPro; IPR036821; Peptide_deformylase_sf.
DR PANTHER; PTHR10458; PEPTIDE DEFORMYLASE; 1.
DR PANTHER; PTHR10458:SF2; PEPTIDE DEFORMYLASE, MITOCHONDRIAL; 1.
DR Pfam; PF13560; HTH_31; 1.
DR Pfam; PF01327; Pep_deformylase; 1.
DR PRINTS; PR01576; PDEFORMYLASE.
DR SMART; SM00530; HTH_XRE; 1.
DR SUPFAM; SSF47413; lambda repressor-like DNA-binding domains; 1.
DR SUPFAM; SSF56420; Peptide deformylase; 1.
DR PROSITE; PS50943; HTH_CROC1; 1.
PE 3: Inferred from homology;
KW DNA-binding {ECO:0000256|ARBA:ARBA00023125};
KW Hydrolase {ECO:0000256|HAMAP-Rule:MF_00163};
KW Iron {ECO:0000256|HAMAP-Rule:MF_00163};
KW Metal-binding {ECO:0000256|HAMAP-Rule:MF_00163};
KW Protein biosynthesis {ECO:0000256|HAMAP-Rule:MF_00163};
KW Reference proteome {ECO:0000313|Proteomes:UP000198210}.
FT DOMAIN 17..71
FT /note="HTH cro/C1-type"
FT /evidence="ECO:0000259|PROSITE:PS50943"
FT ACT_SITE 472
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00163"
FT BINDING 429
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00163"
FT BINDING 471
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00163"
FT BINDING 475
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00163"
SQ SEQUENCE 506 AA; 57906 MW; 083F0A3C89F2A4A2 CRC64;
MTTSPIERAA DSFAAELARH RTGRGLSKKQ LATLMGFDPS YVSHVEGRRH RPTEDFARRA
EAVLEASGAI WQRFREYDEI RHARSAAPHR EPPPPGQWMP PGTGLIVERE QARLRYADDA
YHCVIRRELY NAGTEPVTRY LVRVAVDRYP NDPGRSNRHH REHPLSFAEL RLRAYREDDG
EQEPLHWRAK HDRDAFKEIW LLFENGDGRF PLYPGDRATI EYAYQVGREK WGPWFQRAVR
VPTRRLEVRL DLPATLEPQV WGVETSLSAE EGPLRTPVAR HDDGDRAIFD WGTDEPPLNA
RYRLQWRFRG GPPDDPADRP GDVRASDRMR AIGIVQRGAD LLRQPARQFD LPREERTARE
VVARLGGMLA RLDELHPFSK GVGIAAPQLG IGWAAALVRP ADRGAEPVVL LNPRVVDAAG
ETDEQYEGCL SFFDHRGLVP RPLRIDVEHT QWDGSRVITS FEYAMARLVA HEIDHLEGRL
YVDRMAPGVP LVPVEEYRQT GSPWRY
//
