DEF_LEPIN
ID DEF_LEPIN Reviewed; 178 AA.
AC Q93LE9;
DT 19-SEP-2002, integrated into UniProtKB/Swiss-Prot.
DT 01-DEC-2001, sequence version 1.
DT 03-AUG-2022, entry version 128.
DE RecName: Full=Peptide deformylase;
DE Short=PDF;
DE EC=3.5.1.88;
DE AltName: Full=Polypeptide deformylase;
GN Name=def; Synonyms=pdf; OrderedLocusNames=LA_2438;
OS Leptospira interrogans serogroup Icterohaemorrhagiae serovar Lai (strain
OS 56601).
OC Bacteria; Spirochaetes; Leptospirales; Leptospiraceae; Leptospira.
OX NCBI_TaxID=189518;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND CRYSTALLIZATION.
RC STRAIN=Lai / Serogroup Icterohaemorrhagiae / Serovar lai;
RX PubMed=11976499; DOI=10.1107/s0907444902003736;
RA Li Y., Ren S., Gong W.;
RT "Cloning, high-level expression, purification and crystallization of
RT peptide deformylase from Leptospira interrogans.";
RL Acta Crystallogr. D 58:846-848(2002).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=56601;
RX PubMed=12712204; DOI=10.1038/nature01597;
RA Ren S.-X., Fu G., Jiang X.-G., Zeng R., Miao Y.-G., Xu H., Zhang Y.-X.,
RA Xiong H., Lu G., Lu L.-F., Jiang H.-Q., Jia J., Tu Y.-F., Jiang J.-X.,
RA Gu W.-Y., Zhang Y.-Q., Cai Z., Sheng H.-H., Yin H.-F., Zhang Y., Zhu G.-F.,
RA Wan M., Huang H.-L., Qian Z., Wang S.-Y., Ma W., Yao Z.-J., Shen Y.,
RA Qiang B.-Q., Xia Q.-C., Guo X.-K., Danchin A., Saint Girons I.,
RA Somerville R.L., Wen Y.-M., Shi M.-H., Chen Z., Xu J.-G., Zhao G.-P.;
RT "Unique physiological and pathogenic features of Leptospira interrogans
RT revealed by whole-genome sequencing.";
RL Nature 422:888-893(2003).
RN [3]
RP X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS), AND SUBUNIT.
RC STRAIN=Lai / Serogroup Icterohaemorrhagiae / Serovar lai;
RX PubMed=15123432; DOI=10.1016/j.jmb.2004.03.045;
RA Zhou Z., Song X., Li Y., Gong W.;
RT "Unique structural characteristics of peptide deformylase from pathogenic
RT bacterium Leptospira interrogans.";
RL J. Mol. Biol. 339:207-215(2004).
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 -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:15123432}.
CC -!- SIMILARITY: Belongs to the polypeptide deformylase family.
CC {ECO:0000305}.
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DR EMBL; AY040678; AAK70806.1; -; Genomic_DNA.
DR EMBL; AE010300; AAN49637.1; -; Genomic_DNA.
DR RefSeq; NP_712619.1; NC_004342.2.
DR RefSeq; WP_000116243.1; NC_004342.2.
DR PDB; 1SV2; X-ray; 3.00 A; A/B=2-178.
DR PDB; 1SZZ; X-ray; 3.30 A; A/B/C/D/E/F/G/H=2-178.
DR PDB; 1VEV; X-ray; 2.51 A; A/B=2-178.
DR PDB; 1VEY; X-ray; 3.30 A; A/B=2-178.
DR PDB; 1VEZ; X-ray; 2.30 A; A/B=2-178.
DR PDB; 1Y6H; X-ray; 2.20 A; A/B=2-178.
DR PDBsum; 1SV2; -.
DR PDBsum; 1SZZ; -.
DR PDBsum; 1VEV; -.
DR PDBsum; 1VEY; -.
DR PDBsum; 1VEZ; -.
DR PDBsum; 1Y6H; -.
DR AlphaFoldDB; Q93LE9; -.
DR SMR; Q93LE9; -.
DR STRING; 189518.LA_2438; -.
DR DrugBank; DB04310; 2-[(Formyl-Hydroxy-Amino)-Methyl]-Heptanoic Acid [1-(2-Hydroxymethyl-Pyrrolidine-1-Carbonyl)-2-Methyl-Propyl]-Amide.
DR EnsemblBacteria; AAN49637; AAN49637; LA_2438.
DR GeneID; 61144810; -.
DR KEGG; lil:LA_2438; -.
DR PATRIC; fig|189518.3.peg.2418; -.
DR HOGENOM; CLU_061901_5_2_12; -.
DR InParanoid; Q93LE9; -.
DR OMA; VCIQHEI; -.
DR BRENDA; 3.5.1.88; 2986.
DR EvolutionaryTrace; Q93LE9; -.
DR Proteomes; UP000001408; Chromosome I.
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..178
FT /note="Peptide deformylase"
FT /id="PRO_0000082795"
FT ACT_SITE 145
FT /evidence="ECO:0000250"
FT BINDING 102
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /evidence="ECO:0000250"
FT BINDING 144
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /evidence="ECO:0000250"
FT BINDING 148
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /evidence="ECO:0000250"
FT HELIX 12..15
FT /evidence="ECO:0007829|PDB:1Y6H"
FT HELIX 23..25
FT /evidence="ECO:0007829|PDB:1Y6H"
FT HELIX 29..44
FT /evidence="ECO:0007829|PDB:1Y6H"
FT STRAND 48..51
FT /evidence="ECO:0007829|PDB:1Y6H"
FT HELIX 52..55
FT /evidence="ECO:0007829|PDB:1Y6H"
FT STRAND 59..64
FT /evidence="ECO:0007829|PDB:1Y6H"
FT STRAND 70..72
FT /evidence="ECO:0007829|PDB:1VEZ"
FT STRAND 81..90
FT /evidence="ECO:0007829|PDB:1Y6H"
FT STRAND 95..102
FT /evidence="ECO:0007829|PDB:1Y6H"
FT STRAND 105..123
FT /evidence="ECO:0007829|PDB:1Y6H"
FT STRAND 129..135
FT /evidence="ECO:0007829|PDB:1Y6H"
FT HELIX 136..149
FT /evidence="ECO:0007829|PDB:1Y6H"
FT HELIX 154..157
FT /evidence="ECO:0007829|PDB:1Y6H"
FT STRAND 163..166
FT /evidence="ECO:0007829|PDB:1Y6H"
FT HELIX 167..173
FT /evidence="ECO:0007829|PDB:1Y6H"
SQ SEQUENCE 178 AA; 20379 MW; 8F6F3D2449A48B10 CRC64;
MSVRKILRMG DPILRKISEP VTEDEIQTKE FKKLIRDMFD TMRHAEGVGL AAPQIGILKQ
IVVVGSEDNE RYPGTPDVPE RIILNPVITP LTKDTSGFWE GCLSVPGMRG YVERPNQIRM
QWMDEKGNQF DETIDGYKAI VYQHECDHLQ GILYVDRLKD TKLFGFNETL DSSHNVLD
