DEF1A_ARATH
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 03-AUG-2022, entry version 153.
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=0.20 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.AT1G15390.1; -.
DR BindingDB; Q9FV53; -.
DR ChEMBL; CHEMBL1075041; -.
DR PaxDb; Q9FV53; -.
DR PRIDE; Q9FV53; -.
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; locus:2037733; AT1G15390.
DR eggNOG; KOG3137; Eukaryota.
DR HOGENOM; CLU_061901_5_0_1; -.
DR InParanoid; Q9FV53; -.
DR OMA; CRSIRFP; -.
DR OrthoDB; 1532656at2759; -.
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 Genevisible; Q9FV53; AT.
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: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-KW.
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 PRINTS; PR01576; PDEFORMYLASE.
DR SUPFAM; SSF56420; SSF56420; 1.
DR TIGRFAMs; TIGR00079; pept_deformyl; 1.
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
