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B6RGY0 (DEF1A_ORYSJ) Reviewed, UniProtKB/Swiss-Prot

Last modified March 19, 2014. Version 34. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (2) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended 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
OrganismOryza sativa subsp. japonica (Rice) [Reference proteome]
Taxonomic identifier39947 [NCBI]
Taxonomic lineageEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaLiliopsidaPoalesPoaceaeBEP cladeEhrhartoideaeOryzeaeOryza

Protein attributes

Sequence length260 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence 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

Plastidchloroplast 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 processProtein biosynthesis
   Cellular componentChloroplast
Plastid
   DomainTransit peptide
   LigandMetal-binding
Zinc
   Molecular functionHydrolase
   Technical termComplete proteome
Reference proteome
Gene Ontology (GO)
   Biological_processco-translational protein modification

Inferred from electronic annotation. Source: EnsemblPlants/Gramene

translation

Inferred from electronic annotation. Source: UniProtKB-KW

   Cellular_componentchloroplast stroma

Inferred from electronic annotation. Source: UniProtKB-SubCell

plant-type cell wall

Inferred from electronic annotation. Source: EnsemblPlants/Gramene

   Molecular_functioniron 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 keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Transit peptide1 – 4343Chloroplast Potential
Chain44 – 260217Peptide deformylase 1A, chloroplastic HAMAP-Rule MF_00163
PRO_0000369420

Regions

Region114 – 1174Substrate binding By similarity
Region182 – 1876Dimerization By similarity
Region227 – 24519Dimerization By similarity
Compositional bias47 – 504Poly-Gly HAMAP-Rule MF_00163
Compositional bias57 – 637Poly-Gly HAMAP-Rule MF_00163

Sites

Active site2221 By similarity
Metal binding1791Zinc By similarity
Metal binding2211Zinc By similarity
Metal binding2251Zinc By similarity
Binding site1781Substrate; via carbonyl oxygen By similarity

Sequences

Sequence LengthMass (Da)Tools
B6RGY0 [UniParc].

Last modified December 16, 2008. Version 1.
Checksum: A0CEB3C83E884CCE

FASTA26027,493
        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 

« Hide

References

« Hide '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. expand/collapse author list , 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.
RefSeqNP_001043323.1. NM_001049858.1.
UniGeneOs.14593.

3D structure databases

ProteinModelPortalB6RGY0.
SMRB6RGY0. Positions 72-259.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

STRING39947.LOC_Os01g37510.1.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

GeneID4324565.
KEGGosa:4324565.

Organism-specific databases

GrameneB6RGY0.

Phylogenomic databases

eggNOGCOG0242.
KOK01462.
OMAAFFFEGC.

Family and domain databases

Gene3D3.90.45.10. 1 hit.
HAMAPMF_00163. Pep_deformylase.
InterProIPR000181. Fmet_deformylase.
IPR023635. Peptide_deformylase.
[Graphical view]
PANTHERPTHR10458. PTHR10458. 1 hit.
PfamPF01327. Pep_deformylase. 1 hit.
[Graphical view]
PRINTSPR01576. PDEFORMYLASE.
SUPFAMSSF56420. SSF56420. 1 hit.
TIGRFAMsTIGR00079. pept_deformyl. 1 hit.
ProtoNetSearch...

Entry information

Entry nameDEF1A_ORYSJ
AccessionPrimary (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: March 19, 2014
This is version 34 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

Oryza sativa (rice)

Index of Oryza sativa entries and their corresponding gene designations