DEF2_BACCR
ID DEF2_BACCR Reviewed; 184 AA.
AC Q819K2;
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 2 {ECO:0000255|HAMAP-Rule:MF_00163};
DE Short=PDF 2 {ECO:0000255|HAMAP-Rule:MF_00163};
DE EC=3.5.1.88 {ECO:0000255|HAMAP-Rule:MF_00163};
DE AltName: Full=Polypeptide deformylase 2 {ECO:0000255|HAMAP-Rule:MF_00163};
GN Name=def2 {ECO:0000255|HAMAP-Rule:MF_00163}; OrderedLocusNames=BC_3974;
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; AAP10894.1; -; Genomic_DNA.
DR RefSeq; NP_833693.1; NC_004722.1.
DR RefSeq; WP_000957048.1; NZ_CP034551.1.
DR PDB; 2OKL; X-ray; 1.70 A; A/B=1-184.
DR PDBsum; 2OKL; -.
DR AlphaFoldDB; Q819K2; -.
DR SMR; Q819K2; -.
DR STRING; 226900.BC_3974; -.
DR DrugBank; DB04310; 2-[(Formyl-Hydroxy-Amino)-Methyl]-Heptanoic Acid [1-(2-Hydroxymethyl-Pyrrolidine-1-Carbonyl)-2-Methyl-Propyl]-Amide.
DR EnsemblBacteria; AAP10894; AAP10894; BC_3974.
DR GeneID; 67468287; -.
DR KEGG; bce:BC3974; -.
DR PATRIC; fig|226900.8.peg.4100; -.
DR HOGENOM; CLU_061901_4_0_9; -.
DR OMA; DMMEYLV; -.
DR BRENDA; 3.5.1.88; 648.
DR EvolutionaryTrace; Q819K2; -.
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..184
FT /note="Peptide deformylase 2"
FT /id="PRO_0000082736"
FT ACT_SITE 154
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00163"
FT BINDING 110
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00163"
FT BINDING 153
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00163"
FT BINDING 157
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00163"
FT HELIX 4..6
FT /evidence="ECO:0007829|PDB:2OKL"
FT HELIX 13..16
FT /evidence="ECO:0007829|PDB:2OKL"
FT HELIX 28..44
FT /evidence="ECO:0007829|PDB:2OKL"
FT HELIX 47..52
FT /evidence="ECO:0007829|PDB:2OKL"
FT STRAND 59..62
FT /evidence="ECO:0007829|PDB:2OKL"
FT HELIX 63..66
FT /evidence="ECO:0007829|PDB:2OKL"
FT STRAND 70..78
FT /evidence="ECO:0007829|PDB:2OKL"
FT STRAND 84..97
FT /evidence="ECO:0007829|PDB:2OKL"
FT STRAND 99..103
FT /evidence="ECO:0007829|PDB:2OKL"
FT STRAND 123..133
FT /evidence="ECO:0007829|PDB:2OKL"
FT STRAND 138..144
FT /evidence="ECO:0007829|PDB:2OKL"
FT HELIX 145..158
FT /evidence="ECO:0007829|PDB:2OKL"
FT HELIX 163..166
FT /evidence="ECO:0007829|PDB:2OKL"
FT STRAND 177..181
FT /evidence="ECO:0007829|PDB:2OKL"
SQ SEQUENCE 184 AA; 20474 MW; 8B4E1CBE1CACA1F1 CRC64;
MLTMKDVIRE GDPILRNVAE EVSLPASEED TTTLKEMIEF VINSQDPEMA EKYSLRPGIG
LAAPQIGVSK KMIAVHVTDA DGTLYSHALF NPKIISHSVE RTYLQGGEGC LSVDREVPGY
VPRYTRITVK ATSINGEEVK LRLKGLPAIV FQHEIDHLNG VMFYDHINKE NPFAAPDDSK
PLER
