DEF1_BURM1
ID DEF1_BURM1 Reviewed; 181 AA.
AC A0A0H3KB98;
DT 08-JUN-2016, integrated into UniProtKB/Swiss-Prot.
DT 08-JUN-2016, sequence version 2.
DT 03-AUG-2022, entry version 38.
DE RecName: Full=Peptide deformylase 1 {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 1 {ECO:0000255|HAMAP-Rule:MF_00163};
GN Name=def1 {ECO:0000255|HAMAP-Rule:MF_00163}; OrderedLocusNames=BMULJ_00106;
OS Burkholderia multivorans (strain ATCC 17616 / 249).
OC Bacteria; Proteobacteria; Betaproteobacteria; Burkholderiales;
OC Burkholderiaceae; Burkholderia; Burkholderia cepacia complex.
OX NCBI_TaxID=395019;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 17616 / 249;
RA Ohtsubo Y., Yamashita A., Kurokawa K., Takami H., Yuhara S., Nishiyama E.,
RA Endo R., Miyazaki R., Ono A., Yano K., Ito M., Sota M., Yuji N.,
RA Hattori M., Tsuda M.;
RT "Complete genome sequence of Burkholderia multivorans ATCC 17616.";
RL Submitted (APR-2007) to the EMBL/GenBank/DDBJ databases.
RN [2] {ECO:0007744|PDB:5J46}
RP X-RAY CRYSTALLOGRAPHY (1.95 ANGSTROMS) OF 15-181, AND COFACTOR.
RC STRAIN=ATCC 17616 / 249;
RA Potts K.T., Abendroth J., Lorimer D.D., Edwards T.E.;
RT "Crystal structure of a peptide deformylase from Burkholderia
RT multivorans.";
RL Submitted (MAR-2016) to the PDB data bank.
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, ECO:0000305|Ref.2};
CC Note=Binds 1 Fe(2+) ion. {ECO:0000255|HAMAP-Rule:MF_00163};
CC -!- MISCELLANEOUS: The submitted crystal structure binds Zn(+) rather than
CC Fe(2+). {ECO:0000305|Ref.2}.
CC -!- SIMILARITY: Belongs to the polypeptide deformylase family.
CC {ECO:0000255|HAMAP-Rule:MF_00163}.
CC -!- CAUTION: It is uncertain whether Met-1 or Met-15 is the initiator.
CC {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=BAG42085.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305};
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DR EMBL; AP009385; BAG42085.1; ALT_INIT; Genomic_DNA.
DR PDB; 5J46; X-ray; 1.95 A; A=15-181.
DR PDBsum; 5J46; -.
DR AlphaFoldDB; A0A0H3KB98; -.
DR SMR; A0A0H3KB98; -.
DR STRING; 395019.Bmul_3124; -.
DR EnsemblBacteria; BAG42085; BAG42085; BMULJ_00106.
DR KEGG; bmj:BMULJ_00106; -.
DR eggNOG; COG0242; Bacteria.
DR HOGENOM; CLU_061901_2_1_4; -.
DR OMA; VCIQHEI; -.
DR Proteomes; UP000008815; 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 1: Evidence at protein level;
KW 3D-structure; Hydrolase; Iron; Metal-binding; Protein biosynthesis;
KW Reference proteome.
FT CHAIN 1..181
FT /note="Peptide deformylase 1"
FT /id="PRO_0000436380"
FT ACT_SITE 149
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00163"
FT BINDING 106
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00163,
FT ECO:0000305|Ref.2"
FT BINDING 148
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00163,
FT ECO:0000305|Ref.2"
FT BINDING 152
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00163,
FT ECO:0000305|Ref.2"
FT HELIX 26..29
FT /evidence="ECO:0007829|PDB:5J46"
FT HELIX 40..55
FT /evidence="ECO:0007829|PDB:5J46"
FT STRAND 59..62
FT /evidence="ECO:0007829|PDB:5J46"
FT HELIX 63..66
FT /evidence="ECO:0007829|PDB:5J46"
FT STRAND 70..75
FT /evidence="ECO:0007829|PDB:5J46"
FT STRAND 79..81
FT /evidence="ECO:0007829|PDB:5J46"
FT STRAND 85..95
FT /evidence="ECO:0007829|PDB:5J46"
FT STRAND 99..104
FT /evidence="ECO:0007829|PDB:5J46"
FT STRAND 114..127
FT /evidence="ECO:0007829|PDB:5J46"
FT STRAND 133..139
FT /evidence="ECO:0007829|PDB:5J46"
FT HELIX 140..153
FT /evidence="ECO:0007829|PDB:5J46"
FT HELIX 158..161
FT /evidence="ECO:0007829|PDB:5J46"
FT HELIX 164..177
FT /evidence="ECO:0007829|PDB:5J46"
SQ SEQUENCE 181 AA; 20781 MW; AA9FF87CB7C8C1ED CRC64;
MANAAHRFTE YRKTMALLNI LHYPDKRLHK VAKPVDKVDD RIRKLVADMA ETMYAAPGIG
LAATQVDVHE RVIVIDVSED KNELRAFINP EIIWSSDGKQ VYEEGCLSVP GIYDEVERPD
RVRVRALNEQ GETFELDCEG LLAVCIQHEM DHLMGRVFVE YLSPLKQSRI KTKMKKLERA
M
