DEF_SODGM
ID DEF_SODGM Reviewed; 171 AA.
AC Q2NQQ4;
DT 11-SEP-2007, integrated into UniProtKB/Swiss-Prot.
DT 07-FEB-2006, sequence version 1.
DT 03-AUG-2022, entry version 89.
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=SG2246;
OS Sodalis glossinidius (strain morsitans).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Bruguierivoracaceae; Sodalis.
OX NCBI_TaxID=343509;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=morsitans;
RX PubMed=16365377; DOI=10.1101/gr.4106106;
RA Toh H., Weiss B.L., Perkin S.A.H., Yamashita A., Oshima K., Hattori M.,
RA Aksoy S.;
RT "Massive genome erosion and functional adaptations provide insights into
RT the symbiotic lifestyle of Sodalis glossinidius in the tsetse host.";
RL Genome Res. 16:149-156(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; AP008232; BAE75521.1; -; Genomic_DNA.
DR AlphaFoldDB; Q2NQQ4; -.
DR SMR; Q2NQQ4; -.
DR STRING; 343509.SG2246; -.
DR PRIDE; Q2NQQ4; -.
DR EnsemblBacteria; BAE75521; BAE75521; SG2246.
DR KEGG; sgl:SG2246; -.
DR eggNOG; COG0242; Bacteria.
DR HOGENOM; CLU_061901_2_1_6; -.
DR OMA; VCIQHEI; -.
DR Proteomes; UP000001932; 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..171
FT /note="Peptide deformylase"
FT /id="PRO_0000301100"
FT ACT_SITE 134
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00163"
FT BINDING 91
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00163"
FT BINDING 133
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00163"
FT BINDING 137
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00163"
SQ SEQUENCE 171 AA; 19569 MW; 47D24F57D20FA1F2 CRC64;
MSLLQVLHYP DERLRKVAKP VVDVNDAIRR IVDDMFETMY AEEGIGLAAT QVDIHQRIIV
IDVSESRDQR LVMINPELLE KSGETGIDEG CLSIPDQRGF VPRAEKVKVQ ALDRDGNSFE
LEADDLLAIC IQHEMDHLVG KLFVDYLSPL KRQRIRQKME KLARMTARAE K
