ID   DEF1A_ORYSJ             Reviewed;         260 AA.
AC   B6RGY0; A2ZUB7; B9EXI6; Q0JLZ1;
DT   14-APR-2009, integrated into UniProtKB/Swiss-Prot.
DT   16-DEC-2008, sequence version 1.
DT   24-JAN-2024, entry version 88.
DE   RecName: Full=Peptide deformylase 1A, chloroplastic;
DE            Short=OsPDF1A;
DE            Short=PDF 1A;
DE            EC=3.5.1.88;
DE   Flags: Precursor;
GN   Name=PDF1A; OrderedLocusNames=Os01g0555800, LOC_Os01g37510;
GN   ORFNames=OsJ_002139, OsJ_02204;
OS   Oryza sativa subsp. japonica (Rice).
OC   Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC   Spermatophyta; Magnoliopsida; Liliopsida; Poales; Poaceae; BOP clade;
OC   Oryzoideae; Oryzeae; Oryzinae; Oryza; Oryza sativa.
OX   NCBI_TaxID=39947;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [MRNA], TISSUE SPECIFICITY, AND SUBCELLULAR LOCATION.
RC   STRAIN=cv. Dongjin;
RX   PubMed=18718933; DOI=10.1093/pcp/pcn121;
RA   Moon S., Giglione C., Lee D.-Y., An S., Jeong D.-H., Meinnel T., An G.;
RT   "Rice peptide deformylase PDF1B is crucial for development of
RT   chloroplasts.";
RL   Plant Cell Physiol. 49:1536-1546(2008).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=cv. Nipponbare;
RX   PubMed=16100779; DOI=10.1038/nature03895;
RG   International rice genome sequencing project (IRGSP);
RT   "The map-based sequence of the rice genome.";
RL   Nature 436:793-800(2005).
RN   [3]
RP   GENOME REANNOTATION.
RC   STRAIN=cv. Nipponbare;
RX   PubMed=18089549; DOI=10.1093/nar/gkm978;
RG   The rice annotation project (RAP);
RT   "The rice annotation project database (RAP-DB): 2008 update.";
RL   Nucleic Acids Res. 36:D1028-D1033(2008).
RN   [4]
RP   GENOME REANNOTATION.
RC   STRAIN=cv. Nipponbare;
RX   PubMed=24280374; DOI=10.1186/1939-8433-6-4;
RA   Kawahara Y., de la Bastide M., Hamilton J.P., Kanamori H., McCombie W.R.,
RA   Ouyang S., Schwartz D.C., Tanaka T., Wu J., Zhou S., Childs K.L.,
RA   Davidson R.M., Lin H., Quesada-Ocampo L., Vaillancourt B., Sakai H.,
RA   Lee S.S., Kim J., Numa H., Itoh T., Buell C.R., Matsumoto T.;
RT   "Improvement of the Oryza sativa Nipponbare reference genome using next
RT   generation sequence and optical map data.";
RL   Rice 6:4-4(2013).
RN   [5]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=cv. Nipponbare;
RX   PubMed=15685292; DOI=10.1371/journal.pbio.0030038;
RA   Yu J., Wang J., Lin W., Li S., Li H., Zhou J., Ni P., Dong W., Hu S.,
RA   Zeng C., Zhang J., Zhang Y., Li R., Xu Z., Li S., Li X., Zheng H., Cong L.,
RA   Lin L., Yin J., Geng J., Li G., Shi J., Liu J., Lv H., Li J., Wang J.,
RA   Deng Y., Ran L., Shi X., Wang X., Wu Q., Li C., Ren X., Wang J., Wang X.,
RA   Li D., Liu D., Zhang X., Ji Z., Zhao W., Sun Y., Zhang Z., Bao J., Han Y.,
RA   Dong L., Ji J., Chen P., Wu S., Liu J., Xiao Y., Bu D., Tan J., Yang L.,
RA   Ye C., Zhang J., Xu J., Zhou Y., Yu Y., Zhang B., Zhuang S., Wei H.,
RA   Liu B., Lei M., Yu H., Li Y., Xu H., Wei S., He X., Fang L., Zhang Z.,
RA   Zhang Y., Huang X., Su Z., Tong W., Li J., Tong Z., Li S., Ye J., Wang L.,
RA   Fang L., Lei T., Chen C.-S., Chen H.-C., Xu Z., Li H., Huang H., Zhang F.,
RA   Xu H., Li N., Zhao C., Li S., Dong L., Huang Y., Li L., Xi Y., Qi Q.,
RA   Li W., Zhang B., Hu W., Zhang Y., Tian X., Jiao Y., Liang X., Jin J.,
RA   Gao L., Zheng W., Hao B., Liu S.-M., Wang W., Yuan L., Cao M.,
RA   McDermott J., Samudrala R., Wang J., Wong G.K.-S., Yang H.;
RT   "The genomes of Oryza sativa: a history of duplications.";
RL   PLoS Biol. 3:266-281(2005).
CC   -!- FUNCTION: Removes the formyl group from the N-terminal Met of newly
CC       synthesized proteins.
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=Zn(2+); Xref=ChEBI:CHEBI:29105; Evidence={ECO:0000250};
CC       Note=Binds 1 Zn(2+) ion per subunit. {ECO:0000250};
CC   -!- ACTIVITY REGULATION: Inhibited by actinonin.
CC   -!- SUBUNIT: Homodimer. {ECO:0000250}.
CC   -!- SUBCELLULAR LOCATION: Plastid, chloroplast stroma
CC       {ECO:0000269|PubMed:18718933}.
CC   -!- TISSUE SPECIFICITY: Mainly expressed in roots. Lower expression in
CC       shoots, mature panicles at flowering stages and mature leaves.
CC       {ECO:0000269|PubMed:18718933}.
CC   -!- SIMILARITY: Belongs to the polypeptide deformylase family.
CC       {ECO:0000305}.
CC   -!- SEQUENCE CAUTION:
CC       Sequence=BAF05237.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC       Sequence=EEE54799.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305};
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DR   EMBL; EU213045; ABY64739.1; -; mRNA.
DR   EMBL; AP008207; BAF05237.1; ALT_SEQ; Genomic_DNA.
DR   EMBL; AP014957; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR   EMBL; CM000138; EEE54799.1; ALT_INIT; Genomic_DNA.
DR   RefSeq; XP_015621038.1; XM_015765552.1.
DR   AlphaFoldDB; B6RGY0; -.
DR   SMR; B6RGY0; -.
DR   STRING; 39947.B6RGY0; -.
DR   PaxDb; 39947-B6RGY0; -.
DR   EnsemblPlants; Os01t0555800-01; Os01t0555800-01; Os01g0555800.
DR   GeneID; 4324565; -.
DR   Gramene; Os01t0555800-01; Os01t0555800-01; Os01g0555800.
DR   KEGG; osa:4324565; -.
DR   eggNOG; KOG3137; Eukaryota.
DR   HOGENOM; CLU_061901_5_3_1; -.
DR   InParanoid; B6RGY0; -.
DR   OrthoDB; 5472512at2759; -.
DR   BRENDA; 3.5.1.88; 4460.
DR   Proteomes; UP000000763; Chromosome 1.
DR   Proteomes; UP000007752; Chromosome 1.
DR   Proteomes; UP000059680; Chromosome 1.
DR   GO; GO:0009570; C:chloroplast stroma; IEA:UniProtKB-SubCell.
DR   GO; GO:0005739; C:mitochondrion; IBA:GO_Central.
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: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; B6RGY0; OS.
PE   2: Evidence at transcript level;
KW   Chloroplast; Hydrolase; Metal-binding; Plastid; Protein biosynthesis;
KW   Reference proteome; Transit peptide; Zinc.
FT   TRANSIT         1..43
FT                   /note="Chloroplast"
FT                   /evidence="ECO:0000255"
FT   CHAIN           44..260
FT                   /note="Peptide deformylase 1A, chloroplastic"
FT                   /id="PRO_0000369420"
FT   REGION          182..187
FT                   /note="Dimerization"
FT                   /evidence="ECO:0000250"
FT   REGION          227..245
FT                   /note="Dimerization"
FT                   /evidence="ECO:0000250"
FT   ACT_SITE        222
FT                   /evidence="ECO:0000250"
FT   BINDING         114..117
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000250"
FT   BINDING         178
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000250"
FT   BINDING         179
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /evidence="ECO:0000250"
FT   BINDING         221
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /evidence="ECO:0000250"
FT   BINDING         225
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /evidence="ECO:0000250"
SQ   SEQUENCE   260 AA;  27493 MW;  A0CEB3C83E884CCE CRC64;
     MEAHLRPLSA AALLLSPAAP LPTAVAASAR RASPGGRRWS SVRASAGGGG WLSGLLGGKG
     GGGAPTAMTV TPGTVKAGDP VLHEPAQDVA PGDIPSEKVQ GVIDRMVAVM RKAPGVGLAA
     PQIGVPLKII VLEDTQEYIS YAPKKDIEAQ DRRPFDLLVI INPKLKTTSK RTALFFEGCL
     SVDGYRALVE RHLDVEVSGL DRNGRPIKVE ASGWQARILQ HECDHLEGTL YVDTMVPRTF
     RIVDNLDLPL PVGCPPIGAR
//