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B6RGY0

- DEF1A_ORYSJ

UniProt

B6RGY0 - DEF1A_ORYSJ

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Protein

Peptide deformylase 1A, chloroplastic

Gene
PDF1A, Os01g0555800, LOC_Os01g37510, OsJ_002139, OsJ_02204
Organism
Oryza sativa subsp. japonica (Rice)
Status
Reviewed - Annotation score: 4 out of 5 - Experimental evidence at transcript leveli

Functioni

Removes the formyl group from the N-terminal Met of newly synthesized proteins.UniRule annotation

Catalytic activityi

Formyl-L-methionyl peptide + H2O = formate + methionyl peptide.UniRule annotation

Cofactori

Binds 1 Zinc ion per subunit By similarity.UniRule annotation

Enzyme regulationi

Inhibited by actinonin.UniRule annotation

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei178 – 1781Substrate; via carbonyl oxygen By similarity
Metal bindingi179 – 1791Zinc By similarity
Metal bindingi221 – 2211Zinc By similarity
Active sitei222 – 2221 By similarity
Metal bindingi225 – 2251Zinc By similarity

GO - Molecular functioni

  1. iron ion binding Source: InterPro
  2. peptide deformylase activity Source: UniProtKB-EC

GO - Biological processi

  1. co-translational protein modification Source: EnsemblPlants/Gramene
  2. translation Source: UniProtKB-KW
Complete GO annotation...

Keywords - Molecular functioni

Hydrolase

Keywords - Biological processi

Protein biosynthesis

Keywords - Ligandi

Metal-binding, Zinc

Names & Taxonomyi

Protein namesi
Recommended name:
Peptide deformylase 1A, chloroplastic (EC:3.5.1.88)
Short name:
OsPDF1A
Short name:
PDF 1A
Gene namesi
Name:PDF1A
Ordered Locus Names:Os01g0555800, LOC_Os01g37510
ORF Names:OsJ_002139, OsJ_02204
OrganismiOryza sativa subsp. japonica (Rice)
Taxonomic identifieri39947 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaLiliopsidaPoalesPoaceaeBEP cladeEhrhartoideaeOryzeaeOryza
ProteomesiUP000000763: Chromosome 1

Organism-specific databases

GrameneiB6RGY0.

Subcellular locationi

Plastidchloroplast stroma 1 Publication

GO - Cellular componenti

  1. chloroplast stroma Source: UniProtKB-SubCell
  2. plant-type cell wall Source: EnsemblPlants/Gramene
Complete GO annotation...

Keywords - Cellular componenti

Chloroplast, Plastid

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Transit peptidei1 – 4343Chloroplast Reviewed predictionAdd
BLAST
Chaini44 – 260217Peptide deformylase 1A, chloroplasticUniRule annotationPRO_0000369420Add
BLAST

Expressioni

Tissue specificityi

Mainly expressed in roots. Lower expression in shoots, mature panicles at flowering stages and mature leaves.1 Publication

Interactioni

Subunit structurei

Homodimer By similarity.UniRule annotation

Protein-protein interaction databases

STRINGi39947.LOC_Os01g37510.1.

Structurei

3D structure databases

ProteinModelPortaliB6RGY0.
SMRiB6RGY0. Positions 72-259.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni114 – 1174Substrate binding By similarity
Regioni182 – 1876Dimerization By similarity
Regioni227 – 24519Dimerization By similarityAdd
BLAST

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi47 – 504Poly-GlyUniRule annotation
Compositional biasi57 – 637Poly-GlyUniRule annotation

Sequence similaritiesi

Keywords - Domaini

Transit peptide

Phylogenomic databases

eggNOGiCOG0242.
KOiK01462.
OMAiRIIAMEF.

Family and domain databases

Gene3Di3.90.45.10. 1 hit.
HAMAPiMF_00163. Pep_deformylase.
InterProiIPR000181. Fmet_deformylase.
IPR023635. Peptide_deformylase.
[Graphical view]
PANTHERiPTHR10458. PTHR10458. 1 hit.
PfamiPF01327. Pep_deformylase. 1 hit.
[Graphical view]
PRINTSiPR01576. PDEFORMYLASE.
SUPFAMiSSF56420. SSF56420. 1 hit.
TIGRFAMsiTIGR00079. pept_deformyl. 1 hit.

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

B6RGY0-1 [UniParc]FASTAAdd to Basket

« Hide

MEAHLRPLSA AALLLSPAAP LPTAVAASAR RASPGGRRWS SVRASAGGGG    50
WLSGLLGGKG GGGAPTAMTV TPGTVKAGDP VLHEPAQDVA PGDIPSEKVQ 100
GVIDRMVAVM RKAPGVGLAA PQIGVPLKII VLEDTQEYIS YAPKKDIEAQ 150
DRRPFDLLVI INPKLKTTSK RTALFFEGCL SVDGYRALVE RHLDVEVSGL 200
DRNGRPIKVE ASGWQARILQ HECDHLEGTL YVDTMVPRTF RIVDNLDLPL 250
PVGCPPIGAR 260
Length:260
Mass (Da):27,493
Last modified:December 16, 2008 - v1
Checksum:iA0CEB3C83E884CCE
GO

Sequence cautioni

The sequence EEE54799.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.
The sequence BAF05237.1 differs from that shown. Reason: Erroneous gene model prediction.

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
EU213045 mRNA. Translation: ABY64739.1.
AP008207 Genomic DNA. Translation: BAF05237.1. Sequence problems.
CM000138 Genomic DNA. Translation: EEE54799.1. Different initiation.
RefSeqiNP_001043323.1. NM_001049858.1.
UniGeneiOs.14593.

Genome annotation databases

GeneIDi4324565.
KEGGiosa:4324565.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
EU213045 mRNA. Translation: ABY64739.1 .
AP008207 Genomic DNA. Translation: BAF05237.1 . Sequence problems.
CM000138 Genomic DNA. Translation: EEE54799.1 . Different initiation.
RefSeqi NP_001043323.1. NM_001049858.1.
UniGenei Os.14593.

3D structure databases

ProteinModelPortali B6RGY0.
SMRi B6RGY0. Positions 72-259.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

STRINGi 39947.LOC_Os01g37510.1.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

GeneIDi 4324565.
KEGGi osa:4324565.

Organism-specific databases

Gramenei B6RGY0.

Phylogenomic databases

eggNOGi COG0242.
KOi K01462.
OMAi RIIAMEF.

Family and domain databases

Gene3Di 3.90.45.10. 1 hit.
HAMAPi MF_00163. Pep_deformylase.
InterProi IPR000181. Fmet_deformylase.
IPR023635. Peptide_deformylase.
[Graphical view ]
PANTHERi PTHR10458. PTHR10458. 1 hit.
Pfami PF01327. Pep_deformylase. 1 hit.
[Graphical view ]
PRINTSi PR01576. PDEFORMYLASE.
SUPFAMi SSF56420. SSF56420. 1 hit.
TIGRFAMsi TIGR00079. pept_deformyl. 1 hit.
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  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. 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.

Entry informationi

Entry nameiDEF1A_ORYSJ
AccessioniPrimary (citable) accession number: B6RGY0
Secondary accession number(s): A2ZUB7, B9EXI6, Q0JLZ1
Entry historyi
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 statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Oryza sativa (rice)
    Index of Oryza sativa entries and their corresponding gene designations
  2. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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