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B6RGY0

- DEF1A_ORYSJ

UniProt

B6RGY0 - DEF1A_ORYSJ

Protein

Peptide deformylase 1A, chloroplastic

Gene

PDF1A

Organism
Oryza sativa subsp. japonica (Rice)
Status
Reviewed - Annotation score: 4 out of 5- Experimental evidence at transcript leveli
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    • History
      Entry version 36 (01 Oct 2014)
      Sequence version 1 (16 Dec 2008)
      Previous versions | rss
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    Functioni

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

    Catalytic activityi

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

    Cofactori

    Binds 1 Zinc ion per subunit.By similarity

    Enzyme regulationi

    Inhibited by actinonin.

    Sites

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

    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

    Keywords - Cellular componenti

    Chloroplast, Plastid

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Transit peptidei1 – 4343ChloroplastSequence AnalysisAdd
    BLAST
    Chaini44 – 260217Peptide deformylase 1A, chloroplasticPRO_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

    Protein-protein interaction databases

    STRINGi39947.LOC_Os01g37510.1.

    Structurei

    3D structure databases

    ProteinModelPortaliB6RGY0.
    SMRiB6RGY0. Positions 72-259.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni114 – 1174Substrate bindingBy similarity
    Regioni182 – 1876DimerizationBy similarity
    Regioni227 – 24519DimerizationBy similarityAdd
    BLAST

    Compositional bias

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

    Sequence similaritiesi

    Belongs to the polypeptide deformylase family.Curated

    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

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    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

    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: October 1, 2014
    This is version 36 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