DEF1_VIBCH
ID DEF1_VIBCH Reviewed; 169 AA.
AC Q9KVU3;
DT 05-DEC-2001, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-2000, sequence version 1.
DT 03-AUG-2022, entry version 120.
DE RecName: Full=Peptide deformylase 1 {ECO:0000255|HAMAP-Rule:MF_00163};
DE Short=PDF 1 {ECO:0000255|HAMAP-Rule:MF_00163};
DE EC=3.5.1.88 {ECO:0000255|HAMAP-Rule:MF_00163};
DE AltName: Full=Polypeptide deformylase 1 {ECO:0000255|HAMAP-Rule:MF_00163};
GN Name=def1 {ECO:0000255|HAMAP-Rule:MF_00163}; OrderedLocusNames=VC_0046;
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; AE003852; AAF93224.1; -; Genomic_DNA.
DR PIR; A82373; A82373.
DR RefSeq; NP_229705.1; NC_002505.1.
DR RefSeq; WP_000115010.1; NZ_LT906614.1.
DR PDB; 3FWX; X-ray; 2.00 A; A/B=1-169.
DR PDBsum; 3FWX; -.
DR AlphaFoldDB; Q9KVU3; -.
DR SMR; Q9KVU3; -.
DR STRING; 243277.VC_0046; -.
DR PRIDE; Q9KVU3; -.
DR DNASU; 2614445; -.
DR EnsemblBacteria; AAF93224; AAF93224; VC_0046.
DR GeneID; 57741453; -.
DR GeneID; 66938313; -.
DR KEGG; vch:VC_0046; -.
DR PATRIC; fig|243277.26.peg.45; -.
DR eggNOG; COG0242; Bacteria.
DR HOGENOM; CLU_061901_2_1_6; -.
DR OMA; VCIQHEI; -.
DR BioCyc; VCHO:VC0046-MON; -.
DR EvolutionaryTrace; Q9KVU3; -.
DR Proteomes; UP000000584; Chromosome 1.
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..169
FT /note="Peptide deformylase 1"
FT /id="PRO_0000082873"
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:3FWX"
FT HELIX 26..41
FT /evidence="ECO:0007829|PDB:3FWX"
FT STRAND 45..48
FT /evidence="ECO:0007829|PDB:3FWX"
FT HELIX 49..52
FT /evidence="ECO:0007829|PDB:3FWX"
FT STRAND 56..61
FT /evidence="ECO:0007829|PDB:3FWX"
FT STRAND 71..83
FT /evidence="ECO:0007829|PDB:3FWX"
FT STRAND 85..89
FT /evidence="ECO:0007829|PDB:3FWX"
FT STRAND 99..103
FT /evidence="ECO:0007829|PDB:3FWX"
FT STRAND 105..112
FT /evidence="ECO:0007829|PDB:3FWX"
FT STRAND 118..123
FT /evidence="ECO:0007829|PDB:3FWX"
FT HELIX 125..138
FT /evidence="ECO:0007829|PDB:3FWX"
FT HELIX 143..146
FT /evidence="ECO:0007829|PDB:3FWX"
FT HELIX 149..163
FT /evidence="ECO:0007829|PDB:3FWX"
SQ SEQUENCE 169 AA; 19147 MW; 16DB00B08CA40FC7 CRC64;
MSVLQVLTFP DDRLRTVAKP VEQVTPEIQQ IVDDMLETMY AEEGIGLAAT QVDIHQRIVV
IDISETRDQP MVLINPEIIE KRGEDGIEEG CLSVPGARAL VPRAAEVTVK ALDRNGQEYQ
FDADDLLAIC VQHELDHLAG KLFVDYLSPL KRNRIKEKLE KIKRFNEKK
