ID A0A0N9I8C2_9PSEU Unreviewed; 500 AA.
AC A0A0N9I8C2;
DT 20-JAN-2016, integrated into UniProtKB/TrEMBL.
DT 20-JAN-2016, sequence version 1.
DT 27-MAR-2024, entry version 33.
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=AOZ06_32825 {ECO:0000313|EMBL:ALG11037.1};
OS Kibdelosporangium phytohabitans.
OC Bacteria; Actinomycetota; Actinomycetes; Pseudonocardiales;
OC Pseudonocardiaceae; Kibdelosporangium.
OX NCBI_TaxID=860235 {ECO:0000313|EMBL:ALG11037.1, ECO:0000313|Proteomes:UP000063699};
RN [1] {ECO:0000313|EMBL:ALG11037.1, ECO:0000313|Proteomes:UP000063699}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=KLBMP1111 {ECO:0000313|EMBL:ALG11037.1,
RC ECO:0000313|Proteomes:UP000063699};
RA Qin S., Xing K.;
RT "Genome sequencing of Kibdelosporangium phytohabitans.";
RL Submitted (JUL-2015) 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; CP012752; ALG11037.1; -; Genomic_DNA.
DR RefSeq; WP_054292939.1; NZ_JADBEI010000001.1.
DR AlphaFoldDB; A0A0N9I8C2; -.
DR STRING; 860235.AOZ06_32825; -.
DR KEGG; kphy:AOZ06_32825; -.
DR Proteomes; UP000063699; Chromosome.
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:SF22; PEPTIDE DEFORMYLASE; 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|ARBA:ARBA00022801, ECO:0000256|HAMAP-Rule:MF_00163};
KW Iron {ECO:0000256|ARBA:ARBA00023004, ECO:0000256|HAMAP-Rule:MF_00163};
KW Metal-binding {ECO:0000256|HAMAP-Rule:MF_00163};
KW Protein biosynthesis {ECO:0000256|ARBA:ARBA00022917, ECO:0000256|HAMAP-
KW Rule:MF_00163}; Reference proteome {ECO:0000313|Proteomes:UP000063699}.
FT DOMAIN 19..72
FT /note="HTH cro/C1-type"
FT /evidence="ECO:0000259|PROSITE:PS50943"
FT ACT_SITE 466
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00163"
FT BINDING 423
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00163"
FT BINDING 465
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00163"
FT BINDING 469
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00163"
SQ SEQUENCE 500 AA; 57164 MW; 2F89D7481BD5A9A1 CRC64;
MATQDEDSPA HQDVFVGELR RWREVRGMSR TAVAVAMGYS RSYVSKVESG HERPSREFAK
AADDALNAGG ALRRAWREYE ALRPVVVRST PVERTPEPSA RSLFVEHDDA ELRYDGRTYR
AIMRRRLVNN GSDPITRYMI RISVDRFPGD PDLSNQLYRD RPLTWEELDL QAWCGEDRSE
PMRWVAQHDR DAFKEVWLQF ANDSGHFPLY PGQSTWIEYT YTVRDDKWGN WFQRAVRLPT
SLLSVRLDFP EHLDPAVWGL HTSMTAESMP FRTAIDEQRS GNRRVFAWTT EEPPMHARYR
LEWHFRRKPS TQPAEPAEKP SQVMRSLGVV QSDDPILHRP AKPFQLPDEA EDARRVIAEL
VSAAKRVSAA HTFGKGIGLA ANQIGIDRAA AIVFPPGTDD VIMLLNARII ENGGRYDEQY
EGCLSFFDVR GLVPRPMVLH VEHQDLNGAR KITIFERGVA RLVAHEIDHL HGTLYTDRLP
PGAEAIPIEQ YGGSGLNWQY
//
