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Q5VNN5

- DEF1B_ORYSJ

UniProt

Q5VNN5 - DEF1B_ORYSJ

Protein

Peptide deformylase 1B, chloroplastic

Gene

PDF1B

Organism
Oryza sativa subsp. japonica (Rice)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at transcript leveli
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    • History
      Entry version 64 (01 Oct 2014)
      Sequence version 1 (07 Dec 2004)
      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 Fe2+ ion.By similarity

    Enzyme regulationi

    Inhibited by actinonin.

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Metal bindingi168 – 1681IronBy similarity
    Metal bindingi210 – 2101IronBy similarity
    Active sitei211 – 2111By similarity
    Metal bindingi214 – 2141IronBy similarity

    GO - Molecular functioni

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

    GO - Biological processi

    1. translation Source: UniProtKB-KW

    Keywords - Molecular functioni

    Hydrolase

    Keywords - Biological processi

    Protein biosynthesis

    Keywords - Ligandi

    Iron, Metal-binding

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Peptide deformylase 1B, chloroplastic (EC:3.5.1.88)
    Short name:
    OsPDF1B
    Short name:
    PDF 1B
    Gene namesi
    Name:PDF1B
    Ordered Locus Names:Os01g0637600, LOC_Os01g45070
    ORF Names:OsJ_002667, OsJ_02762, P0004A09.6, P0696E01.27
    OrganismiOryza sativa subsp. japonica (Rice)
    Taxonomic identifieri39947 [NCBI]
    Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaLiliopsidaPoalesPoaceaeBEP cladeEhrhartoideaeOryzeaeOryza
    ProteomesiUP000000763: Chromosome 1

    Organism-specific databases

    GrameneiQ5VNN5.

    Subcellular locationi

    Plastidchloroplast stroma 1 Publication. Mitochondrion 1 Publication

    GO - Cellular componenti

    1. chloroplast stroma Source: UniProtKB-SubCell
    2. mitochondrion Source: UniProtKB-SubCell

    Keywords - Cellular componenti

    Chloroplast, Mitochondrion, Plastid

    Pathology & Biotechi

    Disruption phenotypei

    Chlorina and retarded growth.1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Transit peptidei1 – 5151ChloroplastSequence AnalysisAdd
    BLAST
    Chaini52 – 269218Peptide deformylase 1B, chloroplasticPRO_0000369421Add
    BLAST

    Proteomic databases

    PRIDEiQ5VNN5.

    Expressioni

    Tissue specificityi

    Mainly expressed in mature leaves and sheaths.1 Publication

    Interactioni

    Subunit structurei

    Homodimer.By similarity

    Protein-protein interaction databases

    STRINGi39947.LOC_Os01g45070.1.

    Structurei

    3D structure databases

    ProteinModelPortaliQ5VNN5.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Sequence similaritiesi

    Belongs to the polypeptide deformylase family.Curated

    Keywords - Domaini

    Transit peptide

    Phylogenomic databases

    eggNOGiCOG0242.
    HOGENOMiHOG000243509.
    KOiK01462.
    OMAiFFDRMTE.

    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.

    Q5VNN5-1 [UniParc]FASTAAdd to Basket

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    MAARLHLRLG PRLRGFASSF APLLAAHPRA LPLSRMGSVA PLAAARARRG    50
    FGSAVATAPP AEDEDFATAA DLQFEPPLKV VKYPDPILRA RNKRINTFDD 100
    NLRSLTDEMF DVMYKTDGIG LSAPQVGVNV QLMVFNPAGV KGEGEEIVLV 150
    NPVVYKMSKR LLVYEEGCLS FPGIYANVVR PDNVKIDAQD VTGAKIKVKL 200
    SGLSARVFQH EFDHLQGILF FDRMSLDVLE SVREGLKDLE KKYEESTGLV 250
    SPESIENYKG RKDLISFSR 269
    Length:269
    Mass (Da):29,676
    Last modified:December 7, 2004 - v1
    Checksum:i0E4ED8966241BFF5
    GO

    Sequence cautioni

    The sequence EEE55058.1 differs from that shown. Reason: Erroneous gene model prediction.

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    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.
    RefSeqiNP_001043669.1. NM_001050204.1.
    UniGeneiOs.27933.

    Genome annotation databases

    EnsemblPlantsiOS01T0637600-01; OS01T0637600-01; OS01G0637600.
    GeneIDi4326576.
    KEGGiosa:4326576.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    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 .
    RefSeqi NP_001043669.1. NM_001050204.1.
    UniGenei Os.27933.

    3D structure databases

    ProteinModelPortali Q5VNN5.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 39947.LOC_Os01g45070.1.

    Proteomic databases

    PRIDEi Q5VNN5.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblPlantsi OS01T0637600-01 ; OS01T0637600-01 ; OS01G0637600 .
    GeneIDi 4326576.
    KEGGi osa:4326576.

    Organism-specific databases

    Gramenei Q5VNN5.

    Phylogenomic databases

    eggNOGi COG0242.
    HOGENOMi HOG000243509.
    KOi K01462.
    OMAi FFDRMTE.

    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, 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. 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.

    Entry informationi

    Entry nameiDEF1B_ORYSJ
    AccessioniPrimary (citable) accession number: Q5VNN5
    Secondary accession number(s): A2ZVU5, B9EY95
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: April 14, 2009
    Last sequence update: December 7, 2004
    Last modified: October 1, 2014
    This is version 64 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