DEF_ALISL
ID DEF_ALISL Reviewed; 169 AA.
AC B6EP21;
DT 24-MAR-2009, integrated into UniProtKB/Swiss-Prot.
DT 25-NOV-2008, sequence version 1.
DT 03-AUG-2022, entry version 67.
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=VSAL_I0075;
OS Aliivibrio salmonicida (strain LFI1238) (Vibrio salmonicida (strain
OS LFI1238)).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Vibrionales; Vibrionaceae;
OC Aliivibrio.
OX NCBI_TaxID=316275;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=LFI1238;
RX PubMed=19099551; DOI=10.1186/1471-2164-9-616;
RA Hjerde E., Lorentzen M.S., Holden M.T., Seeger K., Paulsen S., Bason N.,
RA Churcher C., Harris D., Norbertczak H., Quail M.A., Sanders S.,
RA Thurston S., Parkhill J., Willassen N.P., Thomson N.R.;
RT "The genome sequence of the fish pathogen Aliivibrio salmonicida strain
RT LFI1238 shows extensive evidence of gene decay.";
RL BMC Genomics 9:616-616(2008).
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; FM178379; CAQ77760.1; -; Genomic_DNA.
DR RefSeq; WP_012548971.1; NC_011312.1.
DR AlphaFoldDB; B6EP21; -.
DR SMR; B6EP21; -.
DR STRING; 316275.VSAL_I0075; -.
DR EnsemblBacteria; CAQ77760; CAQ77760; VSAL_I0075.
DR KEGG; vsa:VSAL_I0075; -.
DR eggNOG; COG0242; Bacteria.
DR HOGENOM; CLU_061901_2_1_6; -.
DR OMA; VCIQHEI; -.
DR OrthoDB; 1649129at2; -.
DR Proteomes; UP000001730; Chromosome 1.
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..169
FT /note="Peptide deformylase"
FT /id="PRO_1000097293"
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 169 AA; 18975 MW; D5A5D2B7584C76DC CRC64;
MAVLEVLTFP DDRLRTVAKP VKTVTPEIQT FIDDMIETMY DEEGIGLAAT QVDFHQRIVV
IDVSETRDEP MVLINPVITQ KSGDDGIEEG CLSVPGAKGM VPRSAEVSVT ALDRDGNEFS
FDADDLLAIC VQHELDHLEG KLFVDYLSPL KRKRIKEKLE KIKKFNEKN
