DEF2_VIBCH
ID DEF2_VIBCH Reviewed; 168 AA.
AC Q9KN16;
DT 19-SEP-2002, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-2000, sequence version 1.
DT 03-AUG-2022, entry version 115.
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=VC_A0150;
OS Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Vibrionales; Vibrionaceae;
OC Vibrio.
OX NCBI_TaxID=243277;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 39315 / El Tor Inaba N16961;
RX PubMed=10952301; DOI=10.1038/35020000;
RA Heidelberg J.F., Eisen J.A., Nelson W.C., Clayton R.A., Gwinn M.L.,
RA Dodson R.J., Haft D.H., Hickey E.K., Peterson J.D., Umayam L.A., Gill S.R.,
RA Nelson K.E., Read T.D., Tettelin H., Richardson D.L., Ermolaeva M.D.,
RA Vamathevan J.J., Bass S., Qin H., Dragoi I., Sellers P., McDonald L.A.,
RA Utterback T.R., Fleischmann R.D., Nierman W.C., White O., Salzberg S.L.,
RA Smith H.O., Colwell R.R., Mekalanos J.J., Venter J.C., Fraser C.M.;
RT "DNA sequence of both chromosomes of the cholera pathogen Vibrio
RT cholerae.";
RL Nature 406:477-483(2000).
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; AE003853; AAF96063.1; -; Genomic_DNA.
DR PIR; C82494; C82494.
DR RefSeq; NP_232550.1; NC_002506.1.
DR RefSeq; WP_000279461.1; NZ_LT906615.1.
DR PDB; 3QU1; X-ray; 1.80 A; A/B=1-168.
DR PDBsum; 3QU1; -.
DR AlphaFoldDB; Q9KN16; -.
DR SMR; Q9KN16; -.
DR STRING; 243277.VC_A0150; -.
DR DNASU; 2612555; -.
DR EnsemblBacteria; AAF96063; AAF96063; VC_A0150.
DR GeneID; 57741606; -.
DR KEGG; vch:VC_A0150; -.
DR PATRIC; fig|243277.26.peg.2788; -.
DR eggNOG; COG0242; Bacteria.
DR HOGENOM; CLU_061901_2_1_6; -.
DR OMA; NMHGEPV; -.
DR BioCyc; VCHO:VCA0150-MON; -.
DR EvolutionaryTrace; Q9KN16; -.
DR Proteomes; UP000000584; Chromosome 2.
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..168
FT /note="Peptide deformylase 2"
FT /id="PRO_0000082874"
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..15
FT /evidence="ECO:0007829|PDB:3QU1"
FT HELIX 24..27
FT /evidence="ECO:0007829|PDB:3QU1"
FT HELIX 28..40
FT /evidence="ECO:0007829|PDB:3QU1"
FT STRAND 41..43
FT /evidence="ECO:0007829|PDB:3QU1"
FT STRAND 46..48
FT /evidence="ECO:0007829|PDB:3QU1"
FT HELIX 49..52
FT /evidence="ECO:0007829|PDB:3QU1"
FT STRAND 58..61
FT /evidence="ECO:0007829|PDB:3QU1"
FT STRAND 65..67
FT /evidence="ECO:0007829|PDB:3QU1"
FT STRAND 71..89
FT /evidence="ECO:0007829|PDB:3QU1"
FT STRAND 99..112
FT /evidence="ECO:0007829|PDB:3QU1"
FT STRAND 118..123
FT /evidence="ECO:0007829|PDB:3QU1"
FT HELIX 127..138
FT /evidence="ECO:0007829|PDB:3QU1"
FT HELIX 143..146
FT /evidence="ECO:0007829|PDB:3QU1"
FT HELIX 149..164
FT /evidence="ECO:0007829|PDB:3QU1"
SQ SEQUENCE 168 AA; 18671 MW; F51EDDE3B6C14C59 CRC64;
MAVLEILTAP DPRLRVQSKQ VTDVASVQTL IDDLLDTLYA TDNGIGLAAP QVGREEAIVV
IDLSDNRDQP LVLINPKVVS GSNKEMGQEG CLSVPDYYAD VERYTSVVVE ALDREGKPLR
IETSDFLAIV MQHEIDHLSG NLFIDYLSPL KQQMAMKKVK KHVKNRAR
