DEF_DESOH
ID DEF_DESOH Reviewed; 173 AA.
AC A8ZUK5;
DT 24-MAR-2009, integrated into UniProtKB/Swiss-Prot.
DT 15-JAN-2008, sequence version 1.
DT 03-AUG-2022, entry version 74.
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=Dole_2233;
OS Desulfococcus oleovorans (strain DSM 6200 / JCM 39069 / Hxd3).
OC Bacteria; Proteobacteria; Deltaproteobacteria; Desulfobacterales;
OC Desulfosudaceae; Desulfosudis.
OX NCBI_TaxID=96561;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=DSM 6200 / JCM 39069 / Hxd3;
RG US DOE Joint Genome Institute;
RA Copeland A., Lucas S., Lapidus A., Barry K., Glavina del Rio T., Dalin E.,
RA Tice H., Pitluck S., Kiss H., Brettin T., Bruce D., Detter J.C., Han C.,
RA Schmutz J., Larimer F., Land M., Hauser L., Kyrpides N., Kim E., Wawrik B.,
RA Richardson P.;
RT "Complete sequence of Desulfococcus oleovorans Hxd3.";
RL Submitted (OCT-2007) 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: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; CP000859; ABW68037.1; -; Genomic_DNA.
DR RefSeq; WP_012175649.1; NC_009943.1.
DR AlphaFoldDB; A8ZUK5; -.
DR SMR; A8ZUK5; -.
DR STRING; 96561.Dole_2233; -.
DR EnsemblBacteria; ABW68037; ABW68037; Dole_2233.
DR KEGG; dol:Dole_2233; -.
DR eggNOG; COG0242; Bacteria.
DR HOGENOM; CLU_061901_2_0_7; -.
DR OMA; VCIQHEI; -.
DR OrthoDB; 1649129at2; -.
DR Proteomes; UP000008561; 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; Reference proteome.
FT CHAIN 1..173
FT /note="Peptide deformylase"
FT /id="PRO_1000097304"
FT ACT_SITE 137
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00163"
FT BINDING 94
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00163"
FT BINDING 136
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00163"
FT BINDING 140
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00163"
SQ SEQUENCE 173 AA; 19312 MW; F30C037CF7DC9770 CRC64;
MTVLDIVTYP ADVLKDGALP VANIDGKLQQ LIDDMAQTMY AHQGVGLAAV QVDSGLRLVI
YDVSDQREKQ QFRVVINPEV VAVDGECVSE QEGCLSVPEL RTDVKRAATV RVEGVDREGR
PLVIDAEGLE AIVLQHEIDH LNGTLILDRA SRLKRELYKR KVQKRIKQAW QET
