Q5VNN5 (DEF1B_ORYSJ) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Peptide deformylase 1B, chloroplastic
Short name=OsPDF1B
Short name=PDF 1B
EC=3.5.1.88

Gene names

Name:	PDF1B
Ordered Locus Names:	Os01g0637600, LOC_Os01g45070
ORF Names:	OsJ_002667, OsJ_02762, P0004A09.6, P0696E01.27

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 › Liliopsida › commelinids › Poales › Poaceae › BEP clade › Ehrhartoideae › Oryzeae › Oryza › Oryza sativa

Protein attributes

Sequence length	269 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 Fe2+ ion By similarity.
Enzyme regulation	Inhibited by actinonin.
Subunit structure	Homodimer By similarity.
Subcellular location	Plastid › chloroplast stroma. Mitochondrion Ref.1.
Tissue specificity	Mainly expressed in mature leaves and sheaths. Ref.1
Disruption phenotype	Chlorina and retarded growth. Ref.1
Sequence similarities	Belongs to the polypeptide deformylase family.
Sequence caution	The sequence EEE55058.1 differs from that shown. Reason: Erroneous gene model prediction.

Ontologies

Keywords
Biological process	Protein biosynthesis
Cellular component	Chloroplast Mitochondrion Plastid
Domain	Transit peptide
Ligand	Iron Metal-binding
Molecular function	Hydrolase
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	translation Inferred from electronic annotation. Source: UniProtKB-KW
Cellular_component	chloroplast stroma Inferred from electronic annotation. Source: UniProtKB-SubCell mitochondrion 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
Complete GO annotation...

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Transit peptide	1 – 51	51	Chloroplast Potential
	Chain	52 – 269	218	Peptide deformylase 1B, chloroplastic		PRO_0000369421
Sites
	Active site	211	1	By similarity
	Metal binding	168	1	Iron By similarity
	Metal binding	210	1	Iron By similarity
	Metal binding	214	1	Iron By similarity

Sequences

	Sequence		Length	Mass (Da)
	Q5VNN5 [UniParc]. Last modified December 7, 2004. Version 1. Checksum: 0E4ED8966241BFF5	FASTA	269	29,676
	10 20 30 40 50 60 MAARLHLRLG PRLRGFASSF APLLAAHPRA LPLSRMGSVA PLAAARARRG FGSAVATAPP 70 80 90 100 110 120 AEDEDFATAA DLQFEPPLKV VKYPDPILRA RNKRINTFDD NLRSLTDEMF DVMYKTDGIG 130 140 150 160 170 180 LSAPQVGVNV QLMVFNPAGV KGEGEEIVLV NPVVYKMSKR LLVYEEGCLS FPGIYANVVR 190 200 210 220 230 240 PDNVKIDAQD VTGAKIKVKL SGLSARVFQH EFDHLQGILF FDRMSLDVLE SVREGLKDLE 250 260 KKYEESTGLV SPESIENYKG RKDLISFSR

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, DISRUPTION PHENOTYPE. Strain: cv. Dongjin.
[2]	"The genome sequence and structure of rice chromosome 1." Sasaki T., Matsumoto T., Yamamoto K., Sakata K., Baba T., Katayose Y., Wu J., Niimura Y., Cheng Z., Nagamura Y., Antonio B.A., Kanamori H., Hosokawa S., Masukawa M., Arikawa K., Chiden Y., Hayashi M., Okamoto M. , Ando T., Aoki H., Arita K., Hamada M., Harada C., Hijishita S., Honda M., Ichikawa Y., Idonuma A., Iijima M., Ikeda M., Ikeno M., Ito S., Ito T., Ito Y., Ito Y., Iwabuchi A., Kamiya K., Karasawa W., Katagiri S., Kikuta A., Kobayashi N., Kono I., Machita K., Maehara T., Mizuno H., Mizubayashi T., Mukai Y., Nagasaki H., Nakashima M., Nakama Y., Nakamichi Y., Nakamura M., Namiki N., Negishi M., Ohta I., Ono N., Saji S., Sakai K., Shibata M., Shimokawa T., Shomura A., Song J., Takazaki Y., Terasawa K., Tsuji K., Waki K., Yamagata H., Yamane H., Yoshiki S., Yoshihara R., Yukawa K., Zhong H., Iwama H., Endo T., Ito H., Hahn J.H., Kim H.-I., Eun M.-Y., Yano M., Jiang J., Gojobori T. Nature 420:312-316(2002) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: cv. Nipponbare.
[3]	"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.
[4]	"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.
[5]	"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.
[6]	"Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice." The rice full-length cDNA consortium Science 301:376-379(2003) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA]. Strain: cv. Nipponbare.

Cross-references

Sequence databases
EMBL GenBank DDBJ	EU213046 mRNA. Translation: ABY64740.1. AP003607 Genomic DNA. Translation: BAD68576.1. AP004367 Genomic DNA. Translation: BAD68940.1. AP008207 Genomic DNA. Translation: BAF05583.1. CM000138 Genomic DNA. Translation: EEE55058.1. Sequence problems. AK106980 mRNA. Translation: BAG97903.1.
RefSeq	NP_001043669.1. NM_001050204.1.
UniGene	Os.27933.
3D structure databases
HSSP	HSSP built from PDB template 1N5N based on UniProtKB Q9I7A8.
ProteinModelPortal	Q5VNN5.
ModBase	Search...
Protein-protein interaction databases
STRING	39947.LOC_Os01g45070.1.
Proteomic databases
PRIDE	Q5VNN5.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblPlants	LOC_Os01g45070.1; LOC_Os01g45070.1; LOC_Os01g45070.
GeneID	4326576.
KEGG	dosa:Os01t0637600-01. osa:4326576.
Organism-specific databases
Gramene	Q5VNN5.
Phylogenomic databases
eggNOG	COG0242.
HOGENOM	HOG000243509.
KO	K01462.
OMA	FFDRMTE.
ProtClustDB	CLSN2919037.
Gene expression databases
ArrayExpress	Q5VNN5.
Family and domain databases
Gene3D	3.90.45.10. 1 hit.
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. Fmet_deformylase. 1 hit.
TIGRFAMs	TIGR00079. pept_deformyl. 1 hit.
ProtoNet	Search...

Entry information

Entry name

DEF1B_ORYSJ

Accession

Primary (citable) accession number: Q5VNN5
Secondary accession number(s): A2ZVU5, B9EY95

Entry history

Integrated into UniProtKB/Swiss-Prot:	April 14, 2009
Last sequence update:	December 7, 2004
Last modified:	April 3, 2013
This is version 57 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Plant Protein Annotation Program