DEF_STAAC
ID DEF_STAAC Reviewed; 183 AA.
AC Q5HGZ3;
DT 19-JUL-2005, integrated into UniProtKB/Swiss-Prot.
DT 15-FEB-2005, sequence version 1.
DT 03-AUG-2022, entry version 95.
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}; Synonyms=def1, pdf1;
GN OrderedLocusNames=SACOL1100;
OS Staphylococcus aureus (strain COL).
OC Bacteria; Firmicutes; Bacilli; Bacillales; Staphylococcaceae;
OC Staphylococcus.
OX NCBI_TaxID=93062;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=COL;
RX PubMed=15774886; DOI=10.1128/jb.187.7.2426-2438.2005;
RA Gill S.R., Fouts D.E., Archer G.L., Mongodin E.F., DeBoy R.T., Ravel J.,
RA Paulsen I.T., Kolonay J.F., Brinkac L.M., Beanan M.J., Dodson R.J.,
RA Daugherty S.C., Madupu R., Angiuoli S.V., Durkin A.S., Haft D.H.,
RA Vamathevan J.J., Khouri H., Utterback T.R., Lee C., Dimitrov G., Jiang L.,
RA Qin H., Weidman J., Tran K., Kang K.H., Hance I.R., Nelson K.E.,
RA Fraser C.M.;
RT "Insights on evolution of virulence and resistance from the complete genome
RT analysis of an early methicillin-resistant Staphylococcus aureus strain and
RT a biofilm-producing methicillin-resistant Staphylococcus epidermidis
RT strain.";
RL J. Bacteriol. 187:2426-2438(2005).
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; CP000046; AAW37980.1; -; Genomic_DNA.
DR RefSeq; WP_000957036.1; NC_002951.2.
DR PDB; 3U7K; X-ray; 1.90 A; A=1-183.
DR PDB; 3U7L; X-ray; 2.01 A; A=1-183.
DR PDB; 3U7M; X-ray; 2.15 A; A=1-183.
DR PDB; 3U7N; X-ray; 2.30 A; A=1-183.
DR PDBsum; 3U7K; -.
DR PDBsum; 3U7L; -.
DR PDBsum; 3U7M; -.
DR PDBsum; 3U7N; -.
DR AlphaFoldDB; Q5HGZ3; -.
DR BMRB; Q5HGZ3; -.
DR SMR; Q5HGZ3; -.
DR EnsemblBacteria; AAW37980; AAW37980; SACOL1100.
DR KEGG; sac:SACOL1100; -.
DR HOGENOM; CLU_061901_4_0_9; -.
DR OMA; DMMEYLV; -.
DR Proteomes; UP000000530; 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..183
FT /note="Peptide deformylase"
FT /id="PRO_0000082838"
FT ACT_SITE 155
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00163"
FT BINDING 111
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00163"
FT BINDING 154
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00163"
FT BINDING 158
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:3U7K"
FT HELIX 13..16
FT /evidence="ECO:0007829|PDB:3U7K"
FT HELIX 28..44
FT /evidence="ECO:0007829|PDB:3U7K"
FT HELIX 47..52
FT /evidence="ECO:0007829|PDB:3U7K"
FT STRAND 59..62
FT /evidence="ECO:0007829|PDB:3U7K"
FT HELIX 63..66
FT /evidence="ECO:0007829|PDB:3U7K"
FT STRAND 70..77
FT /evidence="ECO:0007829|PDB:3U7K"
FT STRAND 81..83
FT /evidence="ECO:0007829|PDB:3U7K"
FT STRAND 86..98
FT /evidence="ECO:0007829|PDB:3U7K"
FT STRAND 100..104
FT /evidence="ECO:0007829|PDB:3U7K"
FT STRAND 124..133
FT /evidence="ECO:0007829|PDB:3U7K"
FT STRAND 139..146
FT /evidence="ECO:0007829|PDB:3U7K"
FT HELIX 147..159
FT /evidence="ECO:0007829|PDB:3U7K"
FT HELIX 164..167
FT /evidence="ECO:0007829|PDB:3U7K"
FT STRAND 170..172
FT /evidence="ECO:0007829|PDB:3U7K"
SQ SEQUENCE 183 AA; 20560 MW; 32A64066AE5CAB0E CRC64;
MLTMKDIIRD GHPTLRQKAA ELELPLTKEE KETLIAMREF LVNSQDEEIA KRYGLRSGVG
LAAPQINISK RMIAVLIPDD GSGKSYDYML VNPKIVSHSV QEAYLPTGEG CLSVDDNVAG
LVHRHNRITI KAKDIEGNDI QLRLKGYPAI VFQHEIDHLN GVMFYDHIDK DHPLQPHTDA
VEV
