ID   DEF1A_ARATH             Reviewed;         269 AA.
AC   Q9FV53; Q9XI30;
DT   05-DEC-2001, integrated into UniProtKB/Swiss-Prot.
DT   31-MAY-2011, sequence version 3.
DT   27-MAR-2024, entry version 160.
DE   RecName: Full=Peptide deformylase 1A, chloroplastic/mitochondrial;
DE            Short=AtDEF1;
DE            Short=AtPDF1A;
DE            Short=PDF 1A;
DE            EC=3.5.1.88 {ECO:0000269|PubMed:11553738, ECO:0000269|PubMed:11733990};
DE   AltName: Full=Polypeptide deformylase;
DE   Flags: Precursor;
GN   Name=PDF1A; Synonyms=DEF1; OrderedLocusNames=At1g15390;
GN   ORFNames=F9L1.34, F9L1_34;
OS   Arabidopsis thaliana (Mouse-ear cress).
OC   Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC   Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC   rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis.
OX   NCBI_TaxID=3702;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [MRNA], FUNCTION, TISSUE SPECIFICITY, AND SUBCELLULAR
RP   LOCATION.
RX   PubMed=11060042; DOI=10.1093/emboj/19.21.5916;
RA   Giglione C., Serero A., Pierre M., Boisson B., Meinnel T.;
RT   "Identification of eukaryotic peptide deformylases reveals universality of
RT   N-terminal protein processing mechanisms.";
RL   EMBO J. 19:5916-5929(2000).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=cv. Columbia;
RX   PubMed=11130712; DOI=10.1038/35048500;
RA   Theologis A., Ecker J.R., Palm C.J., Federspiel N.A., Kaul S., White O.,
RA   Alonso J., Altafi H., Araujo R., Bowman C.L., Brooks S.Y., Buehler E.,
RA   Chan A., Chao Q., Chen H., Cheuk R.F., Chin C.W., Chung M.K., Conn L.,
RA   Conway A.B., Conway A.R., Creasy T.H., Dewar K., Dunn P., Etgu P.,
RA   Feldblyum T.V., Feng J.-D., Fong B., Fujii C.Y., Gill J.E., Goldsmith A.D.,
RA   Haas B., Hansen N.F., Hughes B., Huizar L., Hunter J.L., Jenkins J.,
RA   Johnson-Hopson C., Khan S., Khaykin E., Kim C.J., Koo H.L.,
RA   Kremenetskaia I., Kurtz D.B., Kwan A., Lam B., Langin-Hooper S., Lee A.,
RA   Lee J.M., Lenz C.A., Li J.H., Li Y.-P., Lin X., Liu S.X., Liu Z.A.,
RA   Luros J.S., Maiti R., Marziali A., Militscher J., Miranda M., Nguyen M.,
RA   Nierman W.C., Osborne B.I., Pai G., Peterson J., Pham P.K., Rizzo M.,
RA   Rooney T., Rowley D., Sakano H., Salzberg S.L., Schwartz J.R., Shinn P.,
RA   Southwick A.M., Sun H., Tallon L.J., Tambunga G., Toriumi M.J., Town C.D.,
RA   Utterback T., Van Aken S., Vaysberg M., Vysotskaia V.S., Walker M., Wu D.,
RA   Yu G., Fraser C.M., Venter J.C., Davis R.W.;
RT   "Sequence and analysis of chromosome 1 of the plant Arabidopsis thaliana.";
RL   Nature 408:816-820(2000).
RN   [3]
RP   GENOME REANNOTATION.
RC   STRAIN=cv. Columbia;
RX   PubMed=27862469; DOI=10.1111/tpj.13415;
RA   Cheng C.Y., Krishnakumar V., Chan A.P., Thibaud-Nissen F., Schobel S.,
RA   Town C.D.;
RT   "Araport11: a complete reannotation of the Arabidopsis thaliana reference
RT   genome.";
RL   Plant J. 89:789-804(2017).
RN   [4]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 6-269.
RC   STRAIN=cv. Columbia;
RX   PubMed=14593172; DOI=10.1126/science.1088305;
RA   Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M.,
RA   Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G.,
RA   Liu S.X., Lam B., Sakano H., Wu T., Yu G., Miranda M., Quach H.L.,
RA   Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C.,
RA   Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J.,
RA   Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A.,
RA   Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C.,
RA   Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X.,
RA   Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M.,
RA   Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K.,
RA   Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A.,
RA   Ecker J.R.;
RT   "Empirical analysis of transcriptional activity in the Arabidopsis
RT   genome.";
RL   Science 302:842-846(2003).
RN   [5]
RP   SUBCELLULAR LOCATION, ACTIVITY REGULATION, BIOPHYSICOCHEMICAL PROPERTIES,
RP   FUNCTION, AND CATALYTIC ACTIVITY.
RX   PubMed=11553738; DOI=10.1104/pp.127.1.97;
RA   Dirk L.M., Williams M.A., Houtz R.L.;
RT   "Eukaryotic peptide deformylases. Nuclear-encoded and chloroplast-targeted
RT   enzymes in Arabidopsis.";
RL   Plant Physiol. 127:97-107(2001).
RN   [6]
RP   COFACTOR, AND ACTIVITY REGULATION.
RX   PubMed=11733990; DOI=10.1006/jmbi.2001.5175;
RA   Serero A., Giglione C., Meinnel T.;
RT   "Distinctive features of the two classes of eukaryotic peptide
RT   deformylases.";
RL   J. Mol. Biol. 314:695-708(2001).
RN   [7]
RP   DISRUPTION PHENOTYPE.
RX   PubMed=12505980; DOI=10.1093/emboj/cdg007;
RA   Giglione C., Vallon O., Meinnel T.;
RT   "Control of protein life-span by N-terminal methionine excision.";
RL   EMBO J. 22:13-23(2003).
RN   [8]
RP   X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS) OF 79-267 IN COMPLEX WITH ZINC IONS
RP   AND SUBSTRATE, HOMODIMERIZATION, FUNCTION, AND CATALYTIC ACTIVITY.
RX   PubMed=16192279; DOI=10.1074/jbc.m507155200;
RA   Fieulaine S., Juillan-Binard C., Serero A., Dardel F., Giglione C.,
RA   Meinnel T., Ferrer J.-L.;
RT   "The crystal structure of mitochondrial (Type 1A) peptide deformylase
RT   provides clear guidelines for the design of inhibitors specific for the
RT   bacterial forms.";
RL   J. Biol. Chem. 280:42315-42324(2005).
CC   -!- FUNCTION: Removes the formyl group from the N-terminal Met of newly
CC       synthesized proteins. {ECO:0000269|PubMed:11060042,
CC       ECO:0000269|PubMed:11553738, ECO:0000269|PubMed:11733990}.
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:0000269|PubMed:11553738, ECO:0000269|PubMed:11733990};
CC       PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:24421;
CC         Evidence={ECO:0000305|PubMed:16192279};
CC   -!- COFACTOR:
CC       Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
CC         Evidence={ECO:0000269|PubMed:11733990};
CC       Note=Binds 1 Zn(2+) ion per subunit. {ECO:0000269|PubMed:11733990};
CC   -!- ACTIVITY REGULATION: Inhibited by actinonin.
CC       {ECO:0000269|PubMed:11553738, ECO:0000269|PubMed:11733990}.
CC   -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC       Kinetic parameters:
CC         KM=240 uM for N-formyl-Met-Leu-rho-nitroanilide
CC         {ECO:0000269|PubMed:11553738};
CC         KM=710 uM for N-formyl-Met-Ala-Ser {ECO:0000269|PubMed:11553738};
CC         Vmax=0.11 umol/min/mg enzyme toward N-formyl-Met-Leu-rho-nitroanilide
CC         {ECO:0000269|PubMed:11553738};
CC         Vmax=0.2 umol/min/mg enzyme toward N-formyl-Met-Ala-Ser
CC         {ECO:0000269|PubMed:11553738};
CC   -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:16192279}.
CC   -!- SUBCELLULAR LOCATION: Plastid, chloroplast stroma. Mitochondrion.
CC       Note=Reported to be localized to mitochondria, based on transient GFP
CC       expression in a heterologous system (PubMed:11060042), but also shown
CC       to be imported and correctly processed in isolated chloroplast
CC       (PubMed:11553738). {ECO:0000269|PubMed:11060042,
CC       ECO:0000269|PubMed:11553738}.
CC   -!- TISSUE SPECIFICITY: Expressed in roots, leaves, flowers and siliques.
CC       {ECO:0000269|PubMed:11060042}.
CC   -!- DISRUPTION PHENOTYPE: No visible phenotype.
CC       {ECO:0000269|PubMed:12505980}.
CC   -!- SIMILARITY: Belongs to the polypeptide deformylase family.
CC       {ECO:0000305}.
CC   -!- SEQUENCE CAUTION:
CC       Sequence=AAD39667.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305};
CC       Sequence=AAK32873.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305};
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DR   EMBL; AF250959; AAG33973.1; -; mRNA.
DR   EMBL; AC007591; AAD39667.1; ALT_INIT; Genomic_DNA.
DR   EMBL; CP002684; AEE29315.1; -; Genomic_DNA.
DR   EMBL; AF361861; AAK32873.1; ALT_INIT; mRNA.
DR   EMBL; AY129485; AAM91071.1; -; mRNA.
DR   PIR; E86288; E86288.
DR   RefSeq; NP_563974.1; NM_101408.3.
DR   PDB; 1ZXZ; X-ray; 2.80 A; A/B=79-267.
DR   PDB; 1ZY0; X-ray; 2.90 A; A/B=79-267.
DR   PDB; 1ZY1; X-ray; 3.00 A; A/B=79-267.
DR   PDB; 4JE6; X-ray; 2.00 A; A/B=79-267.
DR   PDB; 4JE7; X-ray; 2.10 A; A/B=79-267.
DR   PDB; 4JE8; X-ray; 2.40 A; A/B=79-267.
DR   PDBsum; 1ZXZ; -.
DR   PDBsum; 1ZY0; -.
DR   PDBsum; 1ZY1; -.
DR   PDBsum; 4JE6; -.
DR   PDBsum; 4JE7; -.
DR   PDBsum; 4JE8; -.
DR   AlphaFoldDB; Q9FV53; -.
DR   SMR; Q9FV53; -.
DR   BioGRID; 23349; 1.
DR   STRING; 3702.Q9FV53; -.
DR   BindingDB; Q9FV53; -.
DR   ChEMBL; CHEMBL1075041; -.
DR   PaxDb; 3702-AT1G15390-1; -.
DR   ProteomicsDB; 224596; -.
DR   EnsemblPlants; AT1G15390.1; AT1G15390.1; AT1G15390.
DR   GeneID; 838109; -.
DR   Gramene; AT1G15390.1; AT1G15390.1; AT1G15390.
DR   KEGG; ath:AT1G15390; -.
DR   Araport; AT1G15390; -.
DR   TAIR; AT1G15390; PDF1A.
DR   eggNOG; KOG3137; Eukaryota.
DR   HOGENOM; CLU_061901_5_0_1; -.
DR   InParanoid; Q9FV53; -.
DR   OMA; HLYYDHI; -.
DR   OrthoDB; 5472512at2759; -.
DR   BRENDA; 3.5.1.88; 399.
DR   SABIO-RK; Q9FV53; -.
DR   EvolutionaryTrace; Q9FV53; -.
DR   PRO; PR:Q9FV53; -.
DR   Proteomes; UP000006548; Chromosome 1.
DR   ExpressionAtlas; Q9FV53; baseline and differential.
DR   GO; GO:0009507; C:chloroplast; HDA:TAIR.
DR   GO; GO:0009570; C:chloroplast stroma; IEA:UniProtKB-SubCell.
DR   GO; GO:0005739; C:mitochondrion; IDA:TAIR.
DR   GO; GO:0009505; C:plant-type cell wall; HDA:TAIR.
DR   GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR   GO; GO:0042586; F:peptide deformylase activity; IDA:TAIR.
DR   GO; GO:0043686; P:co-translational protein modification; IDA:TAIR.
DR   GO; GO:0006412; P:translation; IEA:UniProtKB-KW.
DR   CDD; cd00487; Pep_deformylase; 1.
DR   Gene3D; 3.90.45.10; Peptide deformylase; 1.
DR   HAMAP; MF_00163; Pep_deformylase; 1.
DR   InterPro; IPR023635; Peptide_deformylase.
DR   InterPro; IPR036821; Peptide_deformylase_sf.
DR   NCBIfam; TIGR00079; pept_deformyl; 1.
DR   PANTHER; PTHR10458; PEPTIDE DEFORMYLASE; 1.
DR   PANTHER; PTHR10458:SF2; PEPTIDE DEFORMYLASE, MITOCHONDRIAL; 1.
DR   Pfam; PF01327; Pep_deformylase; 1.
DR   PRINTS; PR01576; PDEFORMYLASE.
DR   SUPFAM; SSF56420; Peptide deformylase; 1.
DR   Genevisible; Q9FV53; AT.
PE   1: Evidence at protein level;
KW   3D-structure; Chloroplast; Hydrolase; Metal-binding; Mitochondrion;
KW   Plastid; Protein biosynthesis; Reference proteome; Transit peptide; Zinc.
FT   TRANSIT         1..60
FT                   /note="Chloroplast and mitochondrion"
FT                   /evidence="ECO:0000255"
FT   CHAIN           61..269
FT                   /note="Peptide deformylase 1A, chloroplastic/mitochondrial"
FT                   /id="PRO_0000006730"
FT   REGION          191..196
FT                   /note="Dimerization"
FT   REGION          236..254
FT                   /note="Dimerization"
FT   ACT_SITE        231
FT   BINDING         123..126
FT                   /ligand="substrate"
FT   BINDING         187
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000269|PubMed:16192279"
FT   BINDING         188
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT   BINDING         230
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT   BINDING         234
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT   HELIX           89..91
FT                   /evidence="ECO:0007829|PDB:4JE6"
FT   HELIX           100..102
FT                   /evidence="ECO:0007829|PDB:4JE6"
FT   HELIX           106..121
FT                   /evidence="ECO:0007829|PDB:4JE6"
FT   STRAND          125..128
FT                   /evidence="ECO:0007829|PDB:4JE6"
FT   HELIX           129..132
FT                   /evidence="ECO:0007829|PDB:4JE6"
FT   STRAND          138..143
FT                   /evidence="ECO:0007829|PDB:4JE6"
FT   HELIX           145..148
FT                   /evidence="ECO:0007829|PDB:4JE6"
FT   HELIX           153..159
FT                   /evidence="ECO:0007829|PDB:4JE6"
FT   STRAND          164..179
FT                   /evidence="ECO:0007829|PDB:4JE6"
FT   STRAND          181..188
FT                   /evidence="ECO:0007829|PDB:4JE6"
FT   STRAND          191..209
FT                   /evidence="ECO:0007829|PDB:4JE6"
FT   STRAND          215..221
FT                   /evidence="ECO:0007829|PDB:4JE6"
FT   HELIX           222..235
FT                   /evidence="ECO:0007829|PDB:4JE6"
FT   HELIX           240..242
FT                   /evidence="ECO:0007829|PDB:4JE6"
FT   HELIX           252..254
FT                   /evidence="ECO:0007829|PDB:4JE6"
SQ   SEQUENCE   269 AA;  29996 MW;  BDDF13CC38F319C3 CRC64;
     MGLHRDEATA METLFRVSLR LLPVSAAVTC RSIRFPVSRP GSSHLLNRKL YNLPTSSSSS
     LSTKAGWLLG LGEKKKKVDL PEIVASGDPV LHEKAREVDP GEIGSERIQK IIDDMIKVMR
     LAPGVGLAAP QIGVPLRIIV LEDTKEYISY APKEEILAQE RRHFDLMVMV NPVLKERSNK
     KALFFEGCLS VDGFRAAVER YLEVVVTGYD RQGKRIEVNA SGWQARILQH ECDHLDGNLY
     VDKMVPRTFR TVDNLDLPLA EGCPKLGPQ
//