DEF_PSEAE
ID DEF_PSEAE Reviewed; 168 AA.
AC Q9I7A8;
DT 05-DEC-2001, integrated into UniProtKB/Swiss-Prot.
DT 01-MAR-2001, sequence version 1.
DT 03-AUG-2022, entry version 137.
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=PA0019;
OS Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM
OS 14847 / LMG 12228 / 1C / PRS 101 / PAO1).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Pseudomonadales;
OC Pseudomonadaceae; Pseudomonas.
OX NCBI_TaxID=208964;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C /
RC PRS 101 / PAO1;
RX PubMed=10984043; DOI=10.1038/35023079;
RA Stover C.K., Pham X.-Q.T., Erwin A.L., Mizoguchi S.D., Warrener P.,
RA Hickey M.J., Brinkman F.S.L., Hufnagle W.O., Kowalik D.J., Lagrou M.,
RA Garber R.L., Goltry L., Tolentino E., Westbrock-Wadman S., Yuan Y.,
RA Brody L.L., Coulter S.N., Folger K.R., Kas A., Larbig K., Lim R.M.,
RA Smith K.A., Spencer D.H., Wong G.K.-S., Wu Z., Paulsen I.T., Reizer J.,
RA Saier M.H. Jr., Hancock R.E.W., Lory S., Olson M.V.;
RT "Complete genome sequence of Pseudomonas aeruginosa PAO1, an opportunistic
RT pathogen.";
RL Nature 406:959-964(2000).
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; AE004091; AAG03409.1; -; Genomic_DNA.
DR PIR; H83643; H83643.
DR RefSeq; NP_248709.1; NC_002516.2.
DR RefSeq; WP_003107059.1; NZ_QZGE01000012.1.
DR PDB; 1IX1; X-ray; 1.85 A; A/B=1-168.
DR PDB; 1LRY; X-ray; 2.60 A; A=2-168.
DR PDB; 1N5N; X-ray; 1.80 A; A/B=1-168.
DR PDB; 1S17; X-ray; 1.95 A; A/B=1-168.
DR PDBsum; 1IX1; -.
DR PDBsum; 1LRY; -.
DR PDBsum; 1N5N; -.
DR PDBsum; 1S17; -.
DR AlphaFoldDB; Q9I7A8; -.
DR SMR; Q9I7A8; -.
DR STRING; 287.DR97_2972; -.
DR BindingDB; Q9I7A8; -.
DR ChEMBL; CHEMBL1649054; -.
DR DrugBank; DB02036; 2-(3,4-Dihydro-3-Oxo-2h-Benzo[B][1,4]Thiazin-2-Yl)-N-Hydroxyacetamide.
DR DrugBank; DB04310; 2-[(Formyl-Hydroxy-Amino)-Methyl]-Heptanoic Acid [1-(2-Hydroxymethyl-Pyrrolidine-1-Carbonyl)-2-Methyl-Propyl]-Amide.
DR DrugBank; DB02810; N-(2-Acetamido)Iminodiacetic Acid.
DR PaxDb; Q9I7A8; -.
DR PRIDE; Q9I7A8; -.
DR DNASU; 879306; -.
DR EnsemblBacteria; AAG03409; AAG03409; PA0019.
DR GeneID; 879306; -.
DR KEGG; pae:PA0019; -.
DR PATRIC; fig|208964.12.peg.18; -.
DR PseudoCAP; PA0019; -.
DR HOGENOM; CLU_061901_2_1_6; -.
DR InParanoid; Q9I7A8; -.
DR OMA; VCIQHEI; -.
DR PhylomeDB; Q9I7A8; -.
DR BioCyc; PAER208964:G1FZ6-19-MON; -.
DR BRENDA; 3.5.1.88; 5087.
DR EvolutionaryTrace; Q9I7A8; -.
DR Proteomes; UP000002438; Chromosome.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0042586; F:peptide deformylase activity; IBA:GO_Central.
DR GO; GO:0043686; P:co-translational protein modification; IBA:GO_Central.
DR GO; GO:0031365; P:N-terminal protein amino acid modification; IBA:GO_Central.
DR GO; GO:0018206; P:peptidyl-methionine modification; IBA:GO_Central.
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;
KW Reference proteome.
FT CHAIN 1..168
FT /note="Peptide deformylase"
FT /id="PRO_0000082819"
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:1N5N"
FT HELIX 26..41
FT /evidence="ECO:0007829|PDB:1N5N"
FT STRAND 45..48
FT /evidence="ECO:0007829|PDB:1N5N"
FT HELIX 49..52
FT /evidence="ECO:0007829|PDB:1N5N"
FT STRAND 56..62
FT /evidence="ECO:0007829|PDB:1N5N"
FT STRAND 64..67
FT /evidence="ECO:0007829|PDB:1IX1"
FT STRAND 70..81
FT /evidence="ECO:0007829|PDB:1N5N"
FT STRAND 85..90
FT /evidence="ECO:0007829|PDB:1N5N"
FT STRAND 100..106
FT /evidence="ECO:0007829|PDB:1N5N"
FT STRAND 108..113
FT /evidence="ECO:0007829|PDB:1N5N"
FT STRAND 119..124
FT /evidence="ECO:0007829|PDB:1N5N"
FT HELIX 126..139
FT /evidence="ECO:0007829|PDB:1N5N"
FT HELIX 144..147
FT /evidence="ECO:0007829|PDB:1N5N"
FT HELIX 150..166
FT /evidence="ECO:0007829|PDB:1N5N"
SQ SEQUENCE 168 AA; 19365 MW; A95F6B921E5F3189 CRC64;
MAILNILEFP DPRLRTIAKP VEVVDDAVRQ LIDDMFETMY EAPGIGLAAT QVNVHKRIVV
MDLSEDKSEP RVFINPEFEP LTEDMDQYQE GCLSVPGFYE NVDRPQKVRI KALDRDGNPF
EEVAEGLLAV CIQHECDHLN GKLFVDYLST LKRDRIRKKL EKQHRQQA
