DEF_STAAU
ID DEF_STAAU Reviewed; 183 AA.
AC P68826; Q9F4L4;
DT 21-DEC-2004, integrated into UniProtKB/Swiss-Prot.
DT 21-DEC-2004, sequence version 1.
DT 03-AUG-2022, entry version 97.
DE RecName: Full=Peptide deformylase;
DE Short=PDF;
DE EC=3.5.1.88;
DE AltName: Full=Polypeptide deformylase;
GN Name=def; Synonyms=def1, pdf1;
OS Staphylococcus aureus.
OC Bacteria; Firmicutes; Bacilli; Bacillales; Staphylococcaceae;
OC Staphylococcus.
OX NCBI_TaxID=1280;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=WCUH29 / NCIMB 40771;
RA Lonetto M.A., Sylvester D.R., Warren R.L.;
RT "Staphylococcus aureus deformylase 1 encoding DNA.";
RL Submitted (AUG-2000) to the EMBL/GenBank/DDBJ databases.
RN [2]
RP MASS SPECTROMETRY.
RC STRAIN=MRSA-M2;
RX PubMed=16714572; DOI=10.1128/iai.00392-06;
RA Brady R.A., Leid J.G., Camper A.K., Costerton J.W., Shirtliff M.E.;
RT "Identification of Staphylococcus aureus proteins recognized by the
RT antibody-mediated immune response to a biofilm infection.";
RL Infect. Immun. 74:3415-3426(2006).
RN [3]
RP X-RAY CRYSTALLOGRAPHY (1.45 ANGSTROMS).
RX PubMed=12823970; DOI=10.1016/s0022-2836(03)00596-5;
RA Kreusch A., Spraggon G., Lee C.C., Klock H., McMullan D., Ng K., Shin T.,
RA Vincent J., Warner I., Ericson C., Lesley S.A.;
RT "Structure analysis of peptide deformylases from Streptococcus pneumoniae,
RT Staphylococcus aureus, Thermotoga maritima and Pseudomonas aeruginosa:
RT snapshots of the oxygen sensitivity of peptide deformylase.";
RL J. Mol. Biol. 330:309-321(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 (By
CC similarity). {ECO:0000250}.
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 -!- COFACTOR:
CC Name=Fe(2+); Xref=ChEBI:CHEBI:29033; Evidence={ECO:0000250};
CC Note=Binds 1 Fe(2+) ion. {ECO:0000250};
CC -!- MASS SPECTROMETRY: Mass=20600; Method=MALDI;
CC Evidence={ECO:0000269|PubMed:16714572};
CC -!- SIMILARITY: Belongs to the polypeptide deformylase family.
CC {ECO:0000305}.
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DR EMBL; AY007227; AAG02249.1; -; Genomic_DNA.
DR RefSeq; WP_000957037.1; NZ_WYDB01000003.1.
DR PDB; 1LM4; X-ray; 1.45 A; A/B=1-183.
DR PDB; 1LMH; X-ray; 1.90 A; A=1-183.
DR PDB; 1LQW; X-ray; 1.87 A; A/B=1-183.
DR PDB; 1Q1Y; X-ray; 1.90 A; A=1-183.
DR PDB; 2AI9; X-ray; 2.50 A; A/B=1-183.
DR PDB; 6JFG; X-ray; 2.60 A; A=1-183.
DR PDB; 6JFO; X-ray; 1.60 A; A=1-183.
DR PDB; 6JFQ; X-ray; 2.20 A; A=1-183.
DR PDB; 6JFR; X-ray; 2.40 A; A=1-183.
DR PDB; 6JFS; X-ray; 2.25 A; A=1-183.
DR PDBsum; 1LM4; -.
DR PDBsum; 1LMH; -.
DR PDBsum; 1LQW; -.
DR PDBsum; 1Q1Y; -.
DR PDBsum; 2AI9; -.
DR PDBsum; 6JFG; -.
DR PDBsum; 6JFO; -.
DR PDBsum; 6JFQ; -.
DR PDBsum; 6JFR; -.
DR PDBsum; 6JFS; -.
DR AlphaFoldDB; P68826; -.
DR BMRB; P68826; -.
DR SMR; P68826; -.
DR BindingDB; P68826; -.
DR ChEMBL; CHEMBL2010635; -.
DR DrugBank; DB04310; 2-[(Formyl-Hydroxy-Amino)-Methyl]-Heptanoic Acid [1-(2-Hydroxymethyl-Pyrrolidine-1-Carbonyl)-2-Methyl-Propyl]-Amide.
DR OMA; DMMEYLV; -.
DR BRENDA; 3.5.1.88; 3352.
DR EvolutionaryTrace; P68826; -.
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_0000082843"
FT ACT_SITE 155
FT /evidence="ECO:0000250"
FT BINDING 111
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT BINDING 154
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT BINDING 158
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT HELIX 4..6
FT /evidence="ECO:0007829|PDB:1LM4"
FT HELIX 13..16
FT /evidence="ECO:0007829|PDB:1LM4"
FT HELIX 28..45
FT /evidence="ECO:0007829|PDB:1LM4"
FT HELIX 47..53
FT /evidence="ECO:0007829|PDB:1LM4"
FT STRAND 58..62
FT /evidence="ECO:0007829|PDB:1LM4"
FT HELIX 63..66
FT /evidence="ECO:0007829|PDB:1LM4"
FT STRAND 70..77
FT /evidence="ECO:0007829|PDB:1LM4"
FT STRAND 81..83
FT /evidence="ECO:0007829|PDB:1LM4"
FT STRAND 86..98
FT /evidence="ECO:0007829|PDB:1LM4"
FT STRAND 100..104
FT /evidence="ECO:0007829|PDB:1LM4"
FT STRAND 124..133
FT /evidence="ECO:0007829|PDB:1LM4"
FT STRAND 139..145
FT /evidence="ECO:0007829|PDB:1LM4"
FT HELIX 146..159
FT /evidence="ECO:0007829|PDB:1LM4"
FT HELIX 164..167
FT /evidence="ECO:0007829|PDB:1LM4"
FT STRAND 170..172
FT /evidence="ECO:0007829|PDB:1LM4"
SQ SEQUENCE 183 AA; 20559 MW; 32A64066A6FEAB0E CRC64;
MLTMKDIIRD GHPTLRQKAA ELELPLTKEE KETLIAMREF LVNSQDEEIA KRYGLRSGVG
LAAPQINISK RMIAVLIPDD GSGKSYDYML VNPKIVSHSV QEAYLPTGEG CLSVDDNVAG
LVHRHNRITI KAKDIEGNDI QLRLKGYPAI VFQHEIDHLN GVMFYDHIDK NHPLQPHTDA
VEV
