DEF_ACIBS
ID DEF_ACIBS Reviewed; 176 AA.
AC B0VNL8;
DT 24-MAR-2009, integrated into UniProtKB/Swiss-Prot.
DT 08-APR-2008, sequence version 1.
DT 03-AUG-2022, entry version 85.
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=ABSDF0185;
OS Acinetobacter baumannii (strain SDF).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Moraxellales; Moraxellaceae;
OC Acinetobacter; Acinetobacter calcoaceticus/baumannii complex.
OX NCBI_TaxID=509170;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=SDF;
RX PubMed=18350144; DOI=10.1371/journal.pone.0001805;
RA Vallenet D., Nordmann P., Barbe V., Poirel L., Mangenot S., Bataille E.,
RA Dossat C., Gas S., Kreimeyer A., Lenoble P., Oztas S., Poulain J.,
RA Segurens B., Robert C., Abergel C., Claverie J.-M., Raoult D., Medigue C.,
RA Weissenbach J., Cruveiller S.;
RT "Comparative analysis of Acinetobacters: three genomes for three
RT lifestyles.";
RL PLoS ONE 3:E1805-E1805(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; CU468230; CAO99588.1; -; Genomic_DNA.
DR PDB; 6JER; X-ray; 2.40 A; A/B=3-172.
DR PDB; 6JET; X-ray; 2.60 A; A/B=2-172.
DR PDB; 6JEU; X-ray; 2.10 A; A/B=2-171.
DR PDB; 6JEV; X-ray; 1.90 A; A/B=3-173.
DR PDB; 6JEW; X-ray; 2.00 A; A/B=3-173.
DR PDB; 6JEX; X-ray; 2.11 A; A/B=2-173.
DR PDBsum; 6JER; -.
DR PDBsum; 6JET; -.
DR PDBsum; 6JEU; -.
DR PDBsum; 6JEV; -.
DR PDBsum; 6JEW; -.
DR PDBsum; 6JEX; -.
DR AlphaFoldDB; B0VNL8; -.
DR SMR; B0VNL8; -.
DR EnsemblBacteria; CAO99588; CAO99588; ABSDF0185.
DR KEGG; abm:ABSDF0185; -.
DR HOGENOM; CLU_061901_2_0_6; -.
DR OMA; VCIQHEI; -.
DR Proteomes; UP000001741; 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 1: Evidence at protein level;
KW 3D-structure; Hydrolase; Iron; Metal-binding; Protein biosynthesis.
FT CHAIN 1..176
FT /note="Peptide deformylase"
FT /id="PRO_1000097291"
FT ACT_SITE 135
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00163"
FT BINDING 92
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00163"
FT BINDING 134
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00163"
FT BINDING 138
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00163"
FT HELIX 12..15
FT /evidence="ECO:0007829|PDB:6JEV"
FT HELIX 26..41
FT /evidence="ECO:0007829|PDB:6JEV"
FT STRAND 45..48
FT /evidence="ECO:0007829|PDB:6JEV"
FT HELIX 49..52
FT /evidence="ECO:0007829|PDB:6JEV"
FT STRAND 56..61
FT /evidence="ECO:0007829|PDB:6JEV"
FT STRAND 64..67
FT /evidence="ECO:0007829|PDB:6JER"
FT STRAND 71..81
FT /evidence="ECO:0007829|PDB:6JEV"
FT STRAND 85..90
FT /evidence="ECO:0007829|PDB:6JEV"
FT STRAND 100..113
FT /evidence="ECO:0007829|PDB:6JEV"
FT STRAND 119..125
FT /evidence="ECO:0007829|PDB:6JEV"
FT HELIX 126..139
FT /evidence="ECO:0007829|PDB:6JEV"
FT HELIX 144..147
FT /evidence="ECO:0007829|PDB:6JEV"
FT HELIX 150..172
FT /evidence="ECO:0007829|PDB:6JEV"
SQ SEQUENCE 176 AA; 20095 MW; CBDCA96B5FDA36D0 CRC64;
MALLPILSFP DPRLRTIAKP VEEVTDEIRQ LAADMFETMY AAPGIGLAAS QVDRHIQLIV
MDLSESKDEP MVFINPKVTP LTEETQPYEE GCLSVPQIYD KVDRPSRVKI EAINLEGQAF
EIEADGLLAV CIQHEMDHLN GKLFVDYLSP LKRQRVREKV EKIVRQRERE KVAVKR
