DEF_MYCTU
ID DEF_MYCTU Reviewed; 197 AA.
AC P9WIJ3; L0T3J0; P96275;
DT 16-APR-2014, integrated into UniProtKB/Swiss-Prot.
DT 16-APR-2014, sequence version 1.
DT 03-AUG-2022, entry version 44.
DE RecName: Full=Peptide deformylase;
DE Short=PDF;
DE EC=3.5.1.88;
DE AltName: Full=Polypeptide deformylase;
GN Name=def; OrderedLocusNames=Rv0429c; ORFNames=MTCY22G10.26c;
OS Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv).
OC Bacteria; Actinobacteria; Corynebacteriales; Mycobacteriaceae;
OC Mycobacterium; Mycobacterium tuberculosis complex.
OX NCBI_TaxID=83332;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 25618 / H37Rv;
RX PubMed=9634230; DOI=10.1038/31159;
RA Cole S.T., Brosch R., Parkhill J., Garnier T., Churcher C.M., Harris D.E.,
RA Gordon S.V., Eiglmeier K., Gas S., Barry C.E. III, Tekaia F., Badcock K.,
RA Basham D., Brown D., Chillingworth T., Connor R., Davies R.M., Devlin K.,
RA Feltwell T., Gentles S., Hamlin N., Holroyd S., Hornsby T., Jagels K.,
RA Krogh A., McLean J., Moule S., Murphy L.D., Oliver S., Osborne J.,
RA Quail M.A., Rajandream M.A., Rogers J., Rutter S., Seeger K., Skelton S.,
RA Squares S., Squares R., Sulston J.E., Taylor K., Whitehead S.,
RA Barrell B.G.;
RT "Deciphering the biology of Mycobacterium tuberculosis from the complete
RT genome sequence.";
RL Nature 393:537-544(1998).
RN [2]
RP IDENTIFICATION AS A DRUG TARGET [LARGE SCALE ANALYSIS].
RX PubMed=19099550; DOI=10.1186/1752-0509-2-109;
RA Raman K., Yeturu K., Chandra N.;
RT "targetTB: a target identification pipeline for Mycobacterium tuberculosis
RT through an interactome, reactome and genome-scale structural analysis.";
RL BMC Syst. Biol. 2:109-109(2008).
RN [3]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC STRAIN=ATCC 25618 / H37Rv;
RX PubMed=21969609; DOI=10.1074/mcp.m111.011627;
RA Kelkar D.S., Kumar D., Kumar P., Balakrishnan L., Muthusamy B., Yadav A.K.,
RA Shrivastava P., Marimuthu A., Anand S., Sundaram H., Kingsbury R.,
RA Harsha H.C., Nair B., Prasad T.S., Chauhan D.S., Katoch K., Katoch V.M.,
RA Kumar P., Chaerkady R., Ramachandran S., Dash D., Pandey A.;
RT "Proteogenomic analysis of Mycobacterium tuberculosis by high resolution
RT mass spectrometry.";
RL Mol. Cell. Proteomics 10:M111.011627-M111.011627(2011).
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 -!- MISCELLANEOUS: Was identified as a high-confidence drug target.
CC -!- SIMILARITY: Belongs to the polypeptide deformylase family.
CC {ECO:0000305}.
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DR EMBL; AL123456; CCP43160.1; -; Genomic_DNA.
DR PIR; C70631; C70631.
DR RefSeq; NP_214943.1; NC_000962.3.
DR RefSeq; WP_003402185.1; NZ_NVQJ01000002.1.
DR PDB; 3E3U; X-ray; 1.56 A; A=1-197.
DR PDBsum; 3E3U; -.
DR AlphaFoldDB; P9WIJ3; -.
DR SMR; P9WIJ3; -.
DR STRING; 83332.Rv0429c; -.
DR BindingDB; P9WIJ3; -.
DR ChEMBL; CHEMBL5765; -.
DR DrugBank; DB08310; N-[(2R)-2-{[(2S)-2-(1,3-benzoxazol-2-yl)pyrrolidin-1-yl]carbonyl}hexyl]-N-hydroxyformamide.
DR PaxDb; P9WIJ3; -.
DR GeneID; 45424390; -.
DR GeneID; 886366; -.
DR KEGG; mtu:Rv0429c; -.
DR TubercuList; Rv0429c; -.
DR eggNOG; COG0242; Bacteria.
DR OMA; VCIQHEI; -.
DR PhylomeDB; P9WIJ3; -.
DR BRENDA; 3.5.1.88; 3445.
DR Proteomes; UP000001584; Chromosome.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0042586; F:peptide deformylase activity; IDA:MTBBASE.
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:0035601; P:protein deacylation; IDA:MTBBASE.
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..197
FT /note="Peptide deformylase"
FT /id="PRO_0000082806"
FT ACT_SITE 149
FT /evidence="ECO:0000250"
FT BINDING 106
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 BINDING 152
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /evidence="ECO:0000250"
FT HELIX 12..14
FT /evidence="ECO:0007829|PDB:3E3U"
FT HELIX 33..46
FT /evidence="ECO:0007829|PDB:3E3U"
FT STRAND 50..53
FT /evidence="ECO:0007829|PDB:3E3U"
FT HELIX 54..57
FT /evidence="ECO:0007829|PDB:3E3U"
FT STRAND 61..67
FT /evidence="ECO:0007829|PDB:3E3U"
FT STRAND 78..90
FT /evidence="ECO:0007829|PDB:3E3U"
FT TURN 99..101
FT /evidence="ECO:0007829|PDB:3E3U"
FT STRAND 103..105
FT /evidence="ECO:0007829|PDB:3E3U"
FT STRAND 113..115
FT /evidence="ECO:0007829|PDB:3E3U"
FT STRAND 120..127
FT /evidence="ECO:0007829|PDB:3E3U"
FT STRAND 133..139
FT /evidence="ECO:0007829|PDB:3E3U"
FT HELIX 140..153
FT /evidence="ECO:0007829|PDB:3E3U"
FT HELIX 158..161
FT /evidence="ECO:0007829|PDB:3E3U"
FT HELIX 164..177
FT /evidence="ECO:0007829|PDB:3E3U"
SQ SEQUENCE 197 AA; 20939 MW; 14F2F655EDF01C93 CRC64;
MAVVPIRIVG DPVLHTATTP VTVAADGSLP ADLAQLIATM YDTMDAANGV GLAANQIGCS
LRLFVYDCAA DRAMTARRRG VVINPVLETS EIPETMPDPD TDDEGCLSVP GESFPTGRAK
WARVTGLDAD GSPVSIEGTG LFARMLQHET GHLDGFLYLD RLIGRYARNA KRAVKSHGWG
VPGLSWLPGE DPDPFGH
