Reviewed, UniProtKB/Swiss-Prot B6RGY0 (DEF1A_ORYSJ)

Names and origin

Protein names

Recommended name:
    Peptide deformylase 1A, chloroplastic
      Short name=PDF 1A
      Short name=OsPDF1A
    EC=3.5.1.88

Gene names

Name:	PDF1A
Ordered Locus Names:	Os01g0555800, LOC_Os01g37510
ORF Names:	OsJ_002139

Organism

Oryza sativa subsp. japonica (Rice)

Taxonomic identifier

39947 [NCBI]

Taxonomic lineage

Eukaryota › Viridiplantae › Streptophyta › Embryophyta › Tracheophyta › Spermatophyta › Magnoliophyta › Liliopsida › Poales › Poaceae › BEP clade › Ehrhartoideae › Oryzeae › Oryza

Protein attributes

Sequence length	260 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at transcript level.

General annotation (Comments)

Function	Removes the formyl group from the N-terminal Met of newly synthesized proteins.
Catalytic activity	Formyl-L-methionyl peptide + H2O = formate + methionyl peptide.
Cofactor	Binds 1 Zinc ion per subunit By similarity.
Enzyme regulation	Inhibited by actinonin.
Subunit structure	Homodimer By similarity.
Subcellular location	Plastid › chloroplast stroma. Ref.1
Tissue specificity	Mainly expressed in roots. Lower expression in shoots, mature panicles at flowering stages and mature leaves. Ref.1
Sequence similarities	Belongs to the polypeptide deformylase family.
Sequence caution	The sequence BAF05237.1 differs from that shown. Reason: Erroneous gene model prediction. The sequence EAZ12314.1 differs from that shown. Reason: Erroneous gene model prediction.

Ontologies

Keywords
Biological process	Protein biosynthesis
Cellular component	Chloroplast Plastid
Domain	Transit peptide
Ligand	Metal-binding Zinc
Molecular function	Hydrolase
Gene Ontology (GO)
Biological process	translation Inferred from electronic annotation. Source: UniProtKB-KW
Cellular component	chloroplast stroma Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular function	iron ion binding Inferred from electronic annotation. Source: InterPro peptide deformylase activity Inferred from electronic annotation. Source: EC zinc ion binding Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Transit peptide	1 – 43	43	Chloroplast Potential
	Chain	44 – 260	217	Peptide deformylase 1A, chloroplastic		PRO_0000369420
Regions
	Region	114 – 117	4	Substrate binding By similarity
	Region	182 – 187	6	Dimerization By similarity
	Region	227 – 245	19	Dimerization By similarity
	Compositional bias	47 – 50	4	Poly-Gly
	Compositional bias	57 – 63	7	Poly-Gly
Sites
	Active site	222	1	By similarity
	Metal binding	179	1	Zinc By similarity
	Metal binding	221	1	Zinc By similarity
	Metal binding	225	1	Zinc By similarity
	Binding site	178	1	Substrate; via carbonyl oxygen By similarity

Sequences

	Sequence		Length	Mass (Da)
	B6RGY0-1 [UniParc]. Last modified December 16, 2008. Version 1. Checksum: A0CEB3C83E884CCE	FASTA	260	27,493
	10 20 30 40 50 60 MEAHLRPLSA AALLLSPAAP LPTAVAASAR RASPGGRRWS SVRASAGGGG WLSGLLGGKG 70 80 90 100 110 120 GGGAPTAMTV TPGTVKAGDP VLHEPAQDVA PGDIPSEKVQ GVIDRMVAVM RKAPGVGLAA 130 140 150 160 170 180 PQIGVPLKII VLEDTQEYIS YAPKKDIEAQ DRRPFDLLVI INPKLKTTSK RTALFFEGCL 190 200 210 220 230 240 SVDGYRALVE RHLDVEVSGL DRNGRPIKVE ASGWQARILQ HECDHLEGTL YVDTMVPRTF 250 260 RIVDNLDLPL PVGCPPIGAR

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Rice peptide deformylase PDF1B is crucial for development of chloroplasts." Moon S., Giglione C., Lee D.-Y., An S., Jeong D.-H., Meinnel T., An G. Plant Cell Physiol. 49:1536-1546(2008) [PubMed: 18718933] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA], TISSUE SPECIFICITY, SUBCELLULAR LOCATION. Strain: cv. Dongjin.
[2]	"The map-based sequence of the rice genome." International rice genome sequencing project (IRGSP) Nature 436:793-800(2005) [PubMed: 16100779] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: cv. Nipponbare.
[3]	"Curated genome annotation of Oryza sativa ssp. japonica and comparative genome analysis with Arabidopsis thaliana." The rice annotation project (RAP) Genome Res. 17:175-183(2007) [PubMed: 17210932] [Abstract] Cited for: GENOME REANNOTATION. Strain: cv. Nipponbare.
[4]	"The genomes of Oryza sativa: a history of duplications." Yu J., Wang J., Lin W., Li S., Li H., Zhou J., Ni P., Dong W., Hu S., Zeng C., Zhang J., Zhang Y., Li R., Xu Z., Li S., Li X., Zheng H., Cong L. , Lin L., Yin J., Geng J., Li G., Shi J., Liu J., Lv H., Li J., Wang J., Deng Y., Ran L., Shi X., Wang X., Wu Q., Li C., Ren X., Wang J., Wang X., Li D., Liu D., Zhang X., Ji Z., Zhao W., Sun Y., Zhang Z., Bao J., Han Y., Dong L., Ji J., Chen P., Wu S., Liu J., Xiao Y., Bu D., Tan J., Yang L., Ye C., Zhang J., Xu J., Zhou Y., Yu Y., Zhang B., Zhuang S., Wei H., Liu B., Lei M., Yu H., Li Y., Xu H., Wei S., He X., Fang L., Zhang Z., Zhang Y., Huang X., Su Z., Tong W., Li J., Tong Z., Li S., Ye J., Wang L., Fang L., Lei T., Chen C.-S., Chen H.-C., Xu Z., Li H., Huang H., Zhang F., Xu H., Li N., Zhao C., Li S., Dong L., Huang Y., Li L., Xi Y., Qi Q., Li W., Zhang B., Hu W., Zhang Y., Tian X., Jiao Y., Liang X., Jin J., Gao L., Zheng W., Hao B., Liu S.-M., Wang W., Yuan L., Cao M., McDermott J., Samudrala R., Wang J., Wong G.K.-S., Yang H. PLoS Biol. 3:266-281(2005) [PubMed: 15685292] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: cv. Nipponbare.

Cross-references

Sequence databases
EMBLGenBankDDBJ	EU213045 mRNA. Translation: ABY64739.1. AP008207 Genomic DNA. Translation: BAF05237.1. Sequence problems. CM000138 Genomic DNA. Translation: EAZ12314.1. Sequence problems.
RefSeq	NP_001043323.1.
3D structure databases
ModBase	Search...
Genome annotation databases
GeneID	4324565.
GenomeReviews	Gene locus PDF1A in contig AP008207_GR.
KEGG	osa:4324565.
Family and domain databases
InterPro	IPR000181. Fmet_deformylase. [Graphical view]
Gene3D	G3DSA:3.90.45.10. Fmet_deformylase. 1 hit.
PANTHER	PTHR10458. Fmet_deformylase. 1 hit.
Pfam	PF01327. Pep_deformylase. 1 hit. [Graphical view]
PRINTS	PR01576. PDEFORMYLASE.
TIGRFAMs	TIGR00079. pept_deformyl. 1 hit.
ProtoNet	Search...

Entry information

Entry name

DEF1A_ORYSJ

Accession

Primary (citable) accession number: B6RGY0
Secondary accession number(s): A2ZUB7, Q0JLZ1

Entry history

Integrated into UniProtKB/Swiss-Prot:	April 14, 2009
Last sequence update:	December 16, 2008
Last modified:	October 13, 2009
This is version 8 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

PPAP (Plant Proteome Annotation Project)