DEF1_BACCR
ID DEF1_BACCR Reviewed; 156 AA.
AC Q819U0;
DT 15-DEC-2003, integrated into UniProtKB/Swiss-Prot.
DT 01-JUN-2003, sequence version 1.
DT 03-AUG-2022, entry version 116.
DE RecName: Full=Peptide deformylase 1 {ECO:0000255|HAMAP-Rule:MF_00163};
DE Short=PDF 1 {ECO:0000255|HAMAP-Rule:MF_00163};
DE EC=3.5.1.88 {ECO:0000255|HAMAP-Rule:MF_00163};
DE AltName: Full=Polypeptide deformylase 1 {ECO:0000255|HAMAP-Rule:MF_00163};
GN Name=def1 {ECO:0000255|HAMAP-Rule:MF_00163}; OrderedLocusNames=BC_3865;
OS Bacillus cereus (strain ATCC 14579 / DSM 31 / CCUG 7414 / JCM 2152 / NBRC
OS 15305 / NCIMB 9373 / NCTC 2599 / NRRL B-3711).
OC Bacteria; Firmicutes; Bacilli; Bacillales; Bacillaceae; Bacillus;
OC Bacillus cereus group.
OX NCBI_TaxID=226900;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 14579 / DSM 31 / CCUG 7414 / JCM 2152 / NBRC 15305 / NCIMB 9373
RC / NCTC 2599 / NRRL B-3711;
RX PubMed=12721630; DOI=10.1038/nature01582;
RA Ivanova N., Sorokin A., Anderson I., Galleron N., Candelon B., Kapatral V.,
RA Bhattacharyya A., Reznik G., Mikhailova N., Lapidus A., Chu L., Mazur M.,
RA Goltsman E., Larsen N., D'Souza M., Walunas T., Grechkin Y., Pusch G.,
RA Haselkorn R., Fonstein M., Ehrlich S.D., Overbeek R., Kyrpides N.C.;
RT "Genome sequence of Bacillus cereus and comparative analysis with Bacillus
RT anthracis.";
RL Nature 423:87-91(2003).
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; AE016877; AAP10787.1; -; Genomic_DNA.
DR RefSeq; NP_833586.1; NC_004722.1.
DR RefSeq; WP_000279455.1; NZ_CP034551.1.
DR PDB; 1WS0; X-ray; 1.70 A; A=1-156.
DR PDB; 1WS1; X-ray; 2.00 A; A=1-156.
DR PDBsum; 1WS0; -.
DR PDBsum; 1WS1; -.
DR AlphaFoldDB; Q819U0; -.
DR SMR; Q819U0; -.
DR STRING; 226900.BC_3865; -.
DR DrugBank; DB04310; 2-[(Formyl-Hydroxy-Amino)-Methyl]-Heptanoic Acid [1-(2-Hydroxymethyl-Pyrrolidine-1-Carbonyl)-2-Methyl-Propyl]-Amide.
DR EnsemblBacteria; AAP10787; AAP10787; BC_3865.
DR GeneID; 67508502; -.
DR KEGG; bce:BC3865; -.
DR PATRIC; fig|226900.8.peg.3984; -.
DR HOGENOM; CLU_061901_4_2_9; -.
DR OMA; VCIQHEI; -.
DR EvolutionaryTrace; Q819U0; -.
DR Proteomes; UP000001417; 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..156
FT /note="Peptide deformylase 1"
FT /id="PRO_0000082735"
FT ACT_SITE 133
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00163"
FT BINDING 90
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00163"
FT BINDING 132
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 HELIX 12..15
FT /evidence="ECO:0007829|PDB:1WS0"
FT HELIX 26..41
FT /evidence="ECO:0007829|PDB:1WS0"
FT STRAND 45..48
FT /evidence="ECO:0007829|PDB:1WS0"
FT HELIX 49..52
FT /evidence="ECO:0007829|PDB:1WS0"
FT STRAND 56..62
FT /evidence="ECO:0007829|PDB:1WS0"
FT TURN 65..67
FT /evidence="ECO:0007829|PDB:1WS0"
FT STRAND 69..88
FT /evidence="ECO:0007829|PDB:1WS0"
FT STRAND 98..111
FT /evidence="ECO:0007829|PDB:1WS0"
FT STRAND 117..123
FT /evidence="ECO:0007829|PDB:1WS0"
FT HELIX 124..137
FT /evidence="ECO:0007829|PDB:1WS0"
FT HELIX 142..144
FT /evidence="ECO:0007829|PDB:1WS0"
FT STRAND 146..149
FT /evidence="ECO:0007829|PDB:1WS0"
SQ SEQUENCE 156 AA; 17480 MW; 0B68AB39485C4D8A CRC64;
MAVLEIIKHP NEVLETPCER VINFDKKLVK LLKDMHETML IADGVGLAAP QVGVSLQVAV
VDVDDDTGKI ELINPSILEK RGEQVGPEGC LSFPGLYGEV ERADYIKVRA QNRRGKVFLL
EAEGFLARAI QHEIDHLHGV LFTSKVTRYY EENELE
