DEF1B_ORYSJ
ID DEF1B_ORYSJ Reviewed; 269 AA.
AC Q5VNN5; A0A0P0V5R4; A2ZVU5; B9EY95;
DT 14-APR-2009, integrated into UniProtKB/Swiss-Prot.
DT 07-DEC-2004, sequence version 1.
DT 03-AUG-2022, entry version 103.
DE RecName: Full=Peptide deformylase 1B, chloroplastic;
DE Short=OsPDF1B;
DE Short=PDF 1B;
DE EC=3.5.1.88;
DE Flags: Precursor;
GN Name=PDF1B; OrderedLocusNames=Os01g0637600, LOC_Os01g45070;
GN ORFNames=OsJ_002667, OsJ_02762, P0004A09.6, P0696E01.27;
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, SUBCELLULAR LOCATION, AND
RP DISRUPTION PHENOTYPE.
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=12447438; DOI=10.1038/nature01184;
RA Sasaki T., Matsumoto T., Yamamoto K., Sakata K., Baba T., Katayose Y.,
RA Wu J., Niimura Y., Cheng Z., Nagamura Y., Antonio B.A., Kanamori H.,
RA Hosokawa S., Masukawa M., Arikawa K., Chiden Y., Hayashi M., Okamoto M.,
RA Ando T., Aoki H., Arita K., Hamada M., Harada C., Hijishita S., Honda M.,
RA Ichikawa Y., Idonuma A., Iijima M., Ikeda M., Ikeno M., Ito S., Ito T.,
RA Ito Y., Ito Y., Iwabuchi A., Kamiya K., Karasawa W., Katagiri S.,
RA Kikuta A., Kobayashi N., Kono I., Machita K., Maehara T., Mizuno H.,
RA Mizubayashi T., Mukai Y., Nagasaki H., Nakashima M., Nakama Y.,
RA Nakamichi Y., Nakamura M., Namiki N., Negishi M., Ohta I., Ono N., Saji S.,
RA Sakai K., Shibata M., Shimokawa T., Shomura A., Song J., Takazaki Y.,
RA Terasawa K., Tsuji K., Waki K., Yamagata H., Yamane H., Yoshiki S.,
RA Yoshihara R., Yukawa K., Zhong H., Iwama H., Endo T., Ito H., Hahn J.H.,
RA Kim H.-I., Eun M.-Y., Yano M., Jiang J., Gojobori T.;
RT "The genome sequence and structure of rice chromosome 1.";
RL Nature 420:312-316(2002).
RN [3]
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 [4]
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 [5]
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 [6]
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).
RN [7]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=12869764; DOI=10.1126/science.1081288;
RG The rice full-length cDNA consortium;
RT "Collection, mapping, and annotation of over 28,000 cDNA clones from
RT japonica rice.";
RL Science 301:376-379(2003).
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=Fe(2+); Xref=ChEBI:CHEBI:29033; Evidence={ECO:0000250};
CC Note=Binds 1 Fe(2+) ion. {ECO:0000250};
CC -!- ACTIVITY REGULATION: Inhibited by actinonin.
CC -!- SUBUNIT: Homodimer. {ECO:0000250}.
CC -!- SUBCELLULAR LOCATION: Plastid, chloroplast stroma
CC {ECO:0000269|PubMed:18718933}. Mitochondrion
CC {ECO:0000269|PubMed:18718933}.
CC -!- TISSUE SPECIFICITY: Mainly expressed in mature leaves and sheaths.
CC {ECO:0000269|PubMed:18718933}.
CC -!- DISRUPTION PHENOTYPE: Chlorina and retarded growth.
CC {ECO:0000269|PubMed:18718933}.
CC -!- SIMILARITY: Belongs to the polypeptide deformylase family.
CC {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=EEE55058.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; EU213046; ABY64740.1; -; mRNA.
DR EMBL; AP003607; BAD68576.1; -; Genomic_DNA.
DR EMBL; AP004367; BAD68940.1; -; Genomic_DNA.
DR EMBL; AP008207; BAF05583.1; -; Genomic_DNA.
DR EMBL; AP014957; BAS73349.1; -; Genomic_DNA.
DR EMBL; CM000138; EEE55058.1; ALT_SEQ; Genomic_DNA.
DR EMBL; AK106980; BAG97903.1; -; mRNA.
DR RefSeq; XP_015612309.1; XM_015756823.1.
DR AlphaFoldDB; Q5VNN5; -.
DR SMR; Q5VNN5; -.
DR STRING; 4530.OS01T0637600-01; -.
DR PaxDb; Q5VNN5; -.
DR PRIDE; Q5VNN5; -.
DR EnsemblPlants; Os01t0637600-01; Os01t0637600-01; Os01g0637600.
DR GeneID; 4326576; -.
DR Gramene; Os01t0637600-01; Os01t0637600-01; Os01g0637600.
DR KEGG; osa:4326576; -.
DR eggNOG; KOG3137; Eukaryota.
DR HOGENOM; CLU_061901_0_0_1; -.
DR InParanoid; Q5VNN5; -.
DR OMA; CAAWLQP; -.
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; Q5VNN5; 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; IEA:UniProtKB-EC.
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; Iron; Metal-binding; Mitochondrion; Plastid;
KW Protein biosynthesis; Reference proteome; Transit peptide.
FT TRANSIT 1..51
FT /note="Chloroplast"
FT /evidence="ECO:0000255"
FT CHAIN 52..269
FT /note="Peptide deformylase 1B, chloroplastic"
FT /id="PRO_0000369421"
FT ACT_SITE 211
FT /evidence="ECO:0000250"
FT BINDING 168
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /evidence="ECO:0000250"
FT BINDING 210
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /evidence="ECO:0000250"
FT BINDING 214
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /evidence="ECO:0000250"
SQ SEQUENCE 269 AA; 29676 MW; 0E4ED8966241BFF5 CRC64;
MAARLHLRLG PRLRGFASSF APLLAAHPRA LPLSRMGSVA PLAAARARRG FGSAVATAPP
AEDEDFATAA DLQFEPPLKV VKYPDPILRA RNKRINTFDD NLRSLTDEMF DVMYKTDGIG
LSAPQVGVNV QLMVFNPAGV KGEGEEIVLV NPVVYKMSKR LLVYEEGCLS FPGIYANVVR
PDNVKIDAQD VTGAKIKVKL SGLSARVFQH EFDHLQGILF FDRMSLDVLE SVREGLKDLE
KKYEESTGLV SPESIENYKG RKDLISFSR
