DEF1A_ORYSJ
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 03-AUG-2022, entry version 82.
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; 4530.OS01T0555800-01; -.
DR PaxDb; B6RGY0; -.
DR PRIDE; B6RGY0; -.
DR GeneID; 4324565; -.
DR KEGG; osa:4324565; -.
DR eggNOG; KOG3137; Eukaryota.
DR HOGENOM; CLU_061901_5_3_1; -.
DR InParanoid; B6RGY0; -.
DR OrthoDB; 1532656at2759; -.
DR BRENDA; 3.5.1.88; 4460.
DR Proteomes; UP000000763; Chromosome 1.
DR Proteomes; UP000007752; Chromosome 1.
DR Proteomes; UP000059680; Chromosome 1.
DR Genevisible; B6RGY0; OS.
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: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 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
