B6RGY0 (DEF1A_ORYSJ) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

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

Gene names

Name:	PDF1A
Ordered Locus Names:	Os01g0555800, LOC_Os01g37510
ORF Names:	OsJ_002139, OsJ_02204

Organism

Oryza sativa subsp. japonica (Rice) [Reference proteome]

Taxonomic identifier

39947 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Viridiplantae › Streptophyta › Streptophytina › Embryophyta › Tracheophyta › Euphyllophyta › Spermatophyta › Magnoliophyta › Mesangiospermae › Liliopsida › Petrosaviidae › commelinids › Poales › Poaceae › BEP clade › Ehrhartoideae › Oryzeae › Oryza › Oryza sativa

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. HAMAP-Rule MF_00163
Catalytic activity	Formyl-L-methionyl peptide + H2O = formate + methionyl peptide. HAMAP-Rule MF_00163
Cofactor	Binds 1 Zinc ion per subunit By similarity. HAMAP-Rule MF_00163
Enzyme regulation	Inhibited by actinonin. HAMAP-Rule MF_00163
Subunit structure	Homodimer By similarity. HAMAP-Rule MF_00163
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 EEE54799.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.

Ontologies

Keywords
Biological process	Protein biosynthesis
Cellular component	Chloroplast Plastid
Domain	Transit peptide
Ligand	Metal-binding Zinc
Molecular function	Hydrolase
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	co-translational protein modification Inferred from electronic annotation. Source: EnsemblPlants/Gramene translation Inferred from electronic annotation. Source: UniProtKB-KW
Cellular_component	chloroplast stroma Inferred from electronic annotation. Source: UniProtKB-SubCell plant-type cell wall Inferred from electronic annotation. Source: EnsemblPlants/Gramene
Molecular_function	iron ion binding Inferred from electronic annotation. Source: InterPro peptide deformylase activity Inferred from electronic annotation. Source: UniProtKB-EC
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 HAMAP-Rule MF_00163		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 HAMAP-Rule MF_00163
	Compositional bias	57 – 63	7	Poly-Gly HAMAP-Rule MF_00163
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 [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] [Europe PMC] [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] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: cv. Nipponbare.
[3]	"The rice annotation project database (RAP-DB): 2008 update." The rice annotation project (RAP) Nucleic Acids Res. 36:D1028-D1033(2008) [PubMed] [Europe PMC] [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] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: cv. Nipponbare.

Cross-references

Sequence databases
EMBL GenBank DDBJ	EU213045 mRNA. Translation: ABY64739.1. AP008207 Genomic DNA. Translation: BAF05237.1. Sequence problems. CM000138 Genomic DNA. Translation: EEE54799.1. Different initiation.
RefSeq	NP_001043323.1. NM_001049858.1.
UniGene	Os.14593.
3D structure databases
ProteinModelPortal	B6RGY0.
SMR	B6RGY0. Positions 72-259.
ModBase	Search...
MobiDB	Search...
Protein-protein interaction databases
STRING	39947.LOC_Os01g37510.1.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
GeneID	4324565.
KEGG	osa:4324565.
Organism-specific databases
Gramene	B6RGY0.
Phylogenomic databases
eggNOG	COG0242.
KO	K01462.
OMA	RIIAMEF.
Family and domain databases
Gene3D	3.90.45.10. 1 hit.
HAMAP	MF_00163. Pep_deformylase.
InterPro	IPR000181. Fmet_deformylase. IPR023635. Peptide_deformylase. [Graphical view]
PANTHER	PTHR10458. PTHR10458. 1 hit.
Pfam	PF01327. Pep_deformylase. 1 hit. [Graphical view]
PRINTS	PR01576. PDEFORMYLASE.
SUPFAM	SSF56420. SSF56420. 1 hit.
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, B9EXI6, Q0JLZ1

Entry history

Integrated into UniProtKB/Swiss-Prot:	April 14, 2009
Last sequence update:	December 16, 2008
Last modified:	May 14, 2014
This is version 35 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Plant Protein Annotation Program