DEF_HAEI8
ID DEF_HAEI8 Reviewed; 169 AA.
AC Q4QMV6;
DT 11-SEP-2007, integrated into UniProtKB/Swiss-Prot.
DT 19-JUL-2005, sequence version 1.
DT 03-AUG-2022, entry version 92.
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}; OrderedLocusNames=NTHI0725;
OS Haemophilus influenzae (strain 86-028NP).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Pasteurellales;
OC Pasteurellaceae; Haemophilus.
OX NCBI_TaxID=281310;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=86-028NP;
RX PubMed=15968074; DOI=10.1128/jb.187.13.4627-4636.2005;
RA Harrison A., Dyer D.W., Gillaspy A., Ray W.C., Mungur R., Carson M.B.,
RA Zhong H., Gipson J., Gipson M., Johnson L.S., Lewis L., Bakaletz L.O.,
RA Munson R.S. Jr.;
RT "Genomic sequence of an otitis media isolate of nontypeable Haemophilus
RT influenzae: comparative study with H. influenzae serotype d, strain KW20.";
RL J. Bacteriol. 187:4627-4636(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; CP000057; AAX87641.1; -; Genomic_DNA.
DR RefSeq; WP_005630900.1; NC_007146.2.
DR PDB; 4WXK; X-ray; 2.05 A; A/B/C/D=1-169.
DR PDB; 4WXL; X-ray; 2.33 A; A/B/C/D=1-169.
DR PDBsum; 4WXK; -.
DR PDBsum; 4WXL; -.
DR AlphaFoldDB; Q4QMV6; -.
DR SMR; Q4QMV6; -.
DR EnsemblBacteria; AAX87641; AAX87641; NTHI0725.
DR GeneID; 66615444; -.
DR KEGG; hit:NTHI0725; -.
DR HOGENOM; CLU_061901_2_1_6; -.
DR OMA; VCIQHEI; -.
DR OrthoDB; 1649129at2; -.
DR Proteomes; UP000002525; 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..169
FT /note="Peptide deformylase"
FT /id="PRO_0000301035"
FT ACT_SITE 134
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00163"
FT BINDING 91
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00163"
FT BINDING 133
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00163"
FT BINDING 137
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00163"
FT HELIX 12..14
FT /evidence="ECO:0007829|PDB:4WXK"
FT HELIX 26..41
FT /evidence="ECO:0007829|PDB:4WXK"
FT STRAND 45..48
FT /evidence="ECO:0007829|PDB:4WXK"
FT HELIX 49..52
FT /evidence="ECO:0007829|PDB:4WXK"
FT STRAND 56..61
FT /evidence="ECO:0007829|PDB:4WXK"
FT STRAND 63..69
FT /evidence="ECO:0007829|PDB:4WXK"
FT STRAND 71..82
FT /evidence="ECO:0007829|PDB:4WXK"
FT STRAND 88..91
FT /evidence="ECO:0007829|PDB:4WXL"
FT STRAND 94..100
FT /evidence="ECO:0007829|PDB:4WXL"
FT STRAND 105..112
FT /evidence="ECO:0007829|PDB:4WXK"
FT STRAND 118..123
FT /evidence="ECO:0007829|PDB:4WXK"
FT HELIX 125..138
FT /evidence="ECO:0007829|PDB:4WXK"
FT HELIX 143..146
FT /evidence="ECO:0007829|PDB:4WXK"
FT HELIX 149..165
FT /evidence="ECO:0007829|PDB:4WXK"
SQ SEQUENCE 169 AA; 19058 MW; 7040E05554F738CD CRC64;
MTALNVLIYP DDHLKVVCEP VTEVNDAIRK IVDDMFDTMY QEKGIGLAAP QVDILQRIIT
IDVEGDKQNQ FVLINPEILA SEGETGIEEG CLSIPGFRAL VPRKEKVTVR ALDRDGKEFT
LDADGLLAIC IQHEIDHLNG ILFVDYLSPL KRQRIKEKLI KYKKQIAKS
