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Q9FV53

- DEF1A_ARATH

UniProt

Q9FV53 - DEF1A_ARATH

Protein

Peptide deformylase 1A, chloroplastic/mitochondrial

Gene

PDF1A

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 108 (01 Oct 2014)
      Sequence version 3 (31 May 2011)
      Previous versions | rss
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    Functioni

    Removes the formyl group from the N-terminal Met of newly synthesized proteins.1 Publication

    Catalytic activityi

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

    Cofactori

    Binds 1 Zinc ion per subunit.1 Publication

    Enzyme regulationi

    Inhibited by actinonin.2 Publications

    Kineticsi

    1. KM=240 µM for N-formyl-Met-Leu-rho-nitroanilide1 Publication
    2. KM=710 µM for N-formyl-Met-Ala-Ser1 Publication

    Vmax=0.11 µmol/min/mg enzyme toward N-formyl-Met-Leu-rho-nitroanilide1 Publication

    Vmax=0.20 µmol/min/mg enzyme toward N-formyl-Met-Ala-Ser1 Publication

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei187 – 1871Substrate; via carbonyl oxygen1 Publication
    Metal bindingi188 – 1881Zinc
    Metal bindingi230 – 2301Zinc
    Active sitei231 – 2311
    Metal bindingi234 – 2341Zinc

    GO - Molecular functioni

    1. iron ion binding Source: InterPro
    2. peptide deformylase activity Source: TAIR

    GO - Biological processi

    1. co-translational protein modification Source: TAIR
    2. translation Source: UniProtKB-KW

    Keywords - Molecular functioni

    Hydrolase

    Keywords - Biological processi

    Protein biosynthesis

    Keywords - Ligandi

    Metal-binding, Zinc

    Enzyme and pathway databases

    BioCyciARA:AT1G15390-MONOMER.
    SABIO-RKQ9FV53.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Peptide deformylase 1A, chloroplastic/mitochondrial (EC:3.5.1.88)
    Short name:
    AtDEF1
    Short name:
    AtPDF1A
    Short name:
    PDF 1A
    Alternative name(s):
    Polypeptide deformylase
    Gene namesi
    Name:PDF1A
    Synonyms:DEF1
    Ordered Locus Names:At1g15390
    ORF Names:F9L1.34, F9L1_34
    OrganismiArabidopsis thaliana (Mouse-ear cress)
    Taxonomic identifieri3702 [NCBI]
    Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
    ProteomesiUP000006548: Chromosome 1

    Organism-specific databases

    TAIRiAT1G15390.

    Subcellular locationi

    Plastidchloroplast stroma. Mitochondrion
    Note: Reported to be localized to mitochondria, based on transient GFP expression in a heterologous system (PubMed:11060042), but also shown to be imported and correctly processed in isolated chloroplast (PubMed:11553738).2 Publications

    GO - Cellular componenti

    1. chloroplast Source: TAIR
    2. chloroplast stroma Source: UniProtKB-SubCell
    3. mitochondrion Source: TAIR
    4. plant-type cell wall Source: TAIR

    Keywords - Cellular componenti

    Chloroplast, Mitochondrion, Plastid

    Pathology & Biotechi

    Disruption phenotypei

    No visible phenotype.1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Transit peptidei1 – 6060Chloroplast and mitochondrionSequence AnalysisAdd
    BLAST
    Chaini61 – 269209Peptide deformylase 1A, chloroplastic/mitochondrialPRO_0000006730Add
    BLAST

    Proteomic databases

    PaxDbiQ9FV53.
    PRIDEiQ9FV53.

    Expressioni

    Tissue specificityi

    Expressed in roots, leaves, flowers and siliques.1 Publication

    Gene expression databases

    GenevestigatoriQ9FV53.

    Interactioni

    Subunit structurei

    Homodimer.1 Publication

    Protein-protein interaction databases

    BioGridi23349. 1 interaction.
    STRINGi3702.AT1G15390.1-P.

    Structurei

    Secondary structure

    1
    269
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi89 – 913
    Helixi100 – 1023
    Helixi106 – 12116
    Beta strandi125 – 1284
    Helixi129 – 1324
    Beta strandi138 – 1436
    Helixi145 – 1484
    Helixi153 – 1597
    Beta strandi164 – 17916
    Beta strandi181 – 1888
    Beta strandi191 – 20919
    Beta strandi215 – 2217
    Helixi222 – 23514
    Helixi240 – 2423
    Helixi252 – 2543

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1ZXZX-ray2.80A/B79-267[»]
    1ZY0X-ray2.90A/B79-267[»]
    1ZY1X-ray3.00A/B79-267[»]
    4JE6X-ray2.00A/B79-267[»]
    4JE7X-ray2.10A/B79-267[»]
    4JE8X-ray2.40A/B79-267[»]
    ProteinModelPortaliQ9FV53.
    SMRiQ9FV53. Positions 79-267.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ9FV53.

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni123 – 1264Substrate binding
    Regioni191 – 1966Dimerization
    Regioni236 – 25419DimerizationAdd
    BLAST

    Sequence similaritiesi

    Belongs to the polypeptide deformylase family.Curated

    Keywords - Domaini

    Transit peptide

    Phylogenomic databases

    eggNOGiCOG0242.
    HOGENOMiHOG000243508.
    InParanoidiQ9FV53.
    KOiK01462.
    OMAiHIDKENP.

    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.

    Q9FV53-1 [UniParc]FASTAAdd to Basket

    « Hide

    MGLHRDEATA METLFRVSLR LLPVSAAVTC RSIRFPVSRP GSSHLLNRKL    50
    YNLPTSSSSS LSTKAGWLLG LGEKKKKVDL PEIVASGDPV LHEKAREVDP 100
    GEIGSERIQK IIDDMIKVMR LAPGVGLAAP QIGVPLRIIV LEDTKEYISY 150
    APKEEILAQE RRHFDLMVMV NPVLKERSNK KALFFEGCLS VDGFRAAVER 200
    YLEVVVTGYD RQGKRIEVNA SGWQARILQH ECDHLDGNLY VDKMVPRTFR 250
    TVDNLDLPLA EGCPKLGPQ 269
    Length:269
    Mass (Da):29,996
    Last modified:May 31, 2011 - v3
    Checksum:iBDDF13CC38F319C3
    GO

    Sequence cautioni

    The sequence AAD39667.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.
    The sequence AAK32873.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AF250959 mRNA. Translation: AAG33973.1.
    AC007591 Genomic DNA. Translation: AAD39667.1. Different initiation.
    CP002684 Genomic DNA. Translation: AEE29315.1.
    AF361861 mRNA. Translation: AAK32873.1. Different initiation.
    AY129485 mRNA. Translation: AAM91071.1.
    PIRiE86288.
    RefSeqiNP_563974.1. NM_101408.2.
    UniGeneiAt.11423.
    At.19791.

    Genome annotation databases

    EnsemblPlantsiAT1G15390.1; AT1G15390.1; AT1G15390.
    GeneIDi838109.
    KEGGiath:AT1G15390.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AF250959 mRNA. Translation: AAG33973.1 .
    AC007591 Genomic DNA. Translation: AAD39667.1 . Different initiation.
    CP002684 Genomic DNA. Translation: AEE29315.1 .
    AF361861 mRNA. Translation: AAK32873.1 . Different initiation.
    AY129485 mRNA. Translation: AAM91071.1 .
    PIRi E86288.
    RefSeqi NP_563974.1. NM_101408.2.
    UniGenei At.11423.
    At.19791.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1ZXZ X-ray 2.80 A/B 79-267 [» ]
    1ZY0 X-ray 2.90 A/B 79-267 [» ]
    1ZY1 X-ray 3.00 A/B 79-267 [» ]
    4JE6 X-ray 2.00 A/B 79-267 [» ]
    4JE7 X-ray 2.10 A/B 79-267 [» ]
    4JE8 X-ray 2.40 A/B 79-267 [» ]
    ProteinModelPortali Q9FV53.
    SMRi Q9FV53. Positions 79-267.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 23349. 1 interaction.
    STRINGi 3702.AT1G15390.1-P.

    Chemistry

    ChEMBLi CHEMBL1075041.

    Proteomic databases

    PaxDbi Q9FV53.
    PRIDEi Q9FV53.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblPlantsi AT1G15390.1 ; AT1G15390.1 ; AT1G15390 .
    GeneIDi 838109.
    KEGGi ath:AT1G15390.

    Organism-specific databases

    TAIRi AT1G15390.

    Phylogenomic databases

    eggNOGi COG0242.
    HOGENOMi HOG000243508.
    InParanoidi Q9FV53.
    KOi K01462.
    OMAi HIDKENP.

    Enzyme and pathway databases

    BioCyci ARA:AT1G15390-MONOMER.
    SABIO-RK Q9FV53.

    Miscellaneous databases

    EvolutionaryTracei Q9FV53.
    PROi Q9FV53.

    Gene expression databases

    Genevestigatori Q9FV53.

    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. "Identification of eukaryotic peptide deformylases reveals universality of N-terminal protein processing mechanisms."
      Giglione C., Serero A., Pierre M., Boisson B., Meinnel T.
      EMBO J. 19:5916-5929(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [MRNA], FUNCTION, TISSUE SPECIFICITY, SUBCELLULAR LOCATION.
    2. "Sequence and analysis of chromosome 1 of the plant Arabidopsis thaliana."
      Theologis A., Ecker J.R., Palm C.J., Federspiel N.A., Kaul S., White O., Alonso J., Altafi H., Araujo R., Bowman C.L., Brooks S.Y., Buehler E., Chan A., Chao Q., Chen H., Cheuk R.F., Chin C.W., Chung M.K.
      , Conn L., Conway A.B., Conway A.R., Creasy T.H., Dewar K., Dunn P., Etgu P., Feldblyum T.V., Feng J.-D., Fong B., Fujii C.Y., Gill J.E., Goldsmith A.D., Haas B., Hansen N.F., Hughes B., Huizar L., Hunter J.L., Jenkins J., Johnson-Hopson C., Khan S., Khaykin E., Kim C.J., Koo H.L., Kremenetskaia I., Kurtz D.B., Kwan A., Lam B., Langin-Hooper S., Lee A., Lee J.M., Lenz C.A., Li J.H., Li Y.-P., Lin X., Liu S.X., Liu Z.A., Luros J.S., Maiti R., Marziali A., Militscher J., Miranda M., Nguyen M., Nierman W.C., Osborne B.I., Pai G., Peterson J., Pham P.K., Rizzo M., Rooney T., Rowley D., Sakano H., Salzberg S.L., Schwartz J.R., Shinn P., Southwick A.M., Sun H., Tallon L.J., Tambunga G., Toriumi M.J., Town C.D., Utterback T., Van Aken S., Vaysberg M., Vysotskaia V.S., Walker M., Wu D., Yu G., Fraser C.M., Venter J.C., Davis R.W.
      Nature 408:816-820(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: cv. Columbia.
    3. The Arabidopsis Information Resource (TAIR)
      Submitted (APR-2011) to the EMBL/GenBank/DDBJ databases
      Cited for: GENOME REANNOTATION.
      Strain: cv. Columbia.
    4. "Empirical analysis of transcriptional activity in the Arabidopsis genome."
      Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M., Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G., Liu S.X., Lam B., Sakano H., Wu T., Yu G.
      , Miranda M., Quach H.L., Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C., Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J., Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A., Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C., Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X., Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M., Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K., Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A., Ecker J.R.
      Science 302:842-846(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 6-269.
      Strain: cv. Columbia.
    5. "Eukaryotic peptide deformylases. Nuclear-encoded and chloroplast-targeted enzymes in Arabidopsis."
      Dirk L.M., Williams M.A., Houtz R.L.
      Plant Physiol. 127:97-107(2001) [PubMed] [Europe PMC] [Abstract]
      Cited for: SUBCELLULAR LOCATION, ENZYME REGULATION, BIOPHYSICOCHEMICAL PROPERTIES.
    6. "Distinctive features of the two classes of eukaryotic peptide deformylases."
      Serero A., Giglione C., Meinnel T.
      J. Mol. Biol. 314:695-708(2001) [PubMed] [Europe PMC] [Abstract]
      Cited for: COFACTOR, ENZYME REGULATION.
    7. "Control of protein life-span by N-terminal methionine excision."
      Giglione C., Vallon O., Meinnel T.
      EMBO J. 22:13-23(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: DISRUPTION PHENOTYPE.
    8. "The crystal structure of mitochondrial (Type 1A) peptide deformylase provides clear guidelines for the design of inhibitors specific for the bacterial forms."
      Fieulaine S., Juillan-Binard C., Serero A., Dardel F., Giglione C., Meinnel T., Ferrer J.-L.
      J. Biol. Chem. 280:42315-42324(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS) OF 79-267 IN COMPLEX WITH ZINC IONS AND SUBSTRATE, HOMODIMERIZATION.

    Entry informationi

    Entry nameiDEF1A_ARATH
    AccessioniPrimary (citable) accession number: Q9FV53
    Secondary accession number(s): Q9XI30
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: December 5, 2001
    Last sequence update: May 31, 2011
    Last modified: October 1, 2014
    This is version 108 of the entry and version 3 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programPlant Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome, Reference proteome

    Documents

    1. Arabidopsis thaliana
      Arabidopsis thaliana: entries and gene names
    2. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    3. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3