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Q9FUZ2

- DEF1B_ARATH

UniProt

Q9FUZ2 - DEF1B_ARATH

Protein

Peptide deformylase 1B, chloroplastic/mitochondrial

Gene

PDF1B

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 102 (01 Oct 2014)
      Sequence version 2 (15 Dec 2003)
      Previous versions | rss
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    Functioni

    Removes the formyl group from the N-terminal Met of newly synthesized proteins. Has a preferred substrate specificity towards the photosystem II (PS II) D1 polypeptide.1 Publication

    Catalytic activityi

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

    Cofactori

    Binds 1 Fe2+ ion.1 Publication

    Enzyme regulationi

    Inhibited by actinonin.2 Publications

    Kineticsi

    1. KM=130 µM for N-formyl-Met-Leu-rho-nitroanilide1 Publication
    2. KM=3200 µM for N-formyl-Met-Ala-Ser1 Publication

    Vmax=20 µmol/min/mg enzyme toward N-formyl-Met-Leu-rho-nitroanilide1 Publication

    Vmax=1.3 µmol/min/mg enzyme toward N-formyl-Met-Ala-Ser1 Publication

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Metal bindingi171 – 1711Iron
    Metal bindingi213 – 2131Iron
    Active sitei214 – 2141By similarity
    Metal bindingi217 – 2171Iron

    GO - Molecular functioni

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

    GO - Biological processi

    1. translation Source: UniProtKB-KW

    Keywords - Molecular functioni

    Hydrolase

    Keywords - Biological processi

    Protein biosynthesis

    Keywords - Ligandi

    Iron, Metal-binding

    Enzyme and pathway databases

    BioCyciARA:AT5G14660-MONOMER.
    ARA:GQT-2354-MONOMER.
    SABIO-RKQ9FUZ2.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Peptide deformylase 1B, chloroplastic/mitochondrial (EC:3.5.1.88)
    Short name:
    AtDEF2
    Short name:
    AtPDF1B
    Short name:
    PDF 1B
    Alternative name(s):
    Polypeptide deformylase
    Gene namesi
    Name:PDF1B
    Synonyms:DEF2
    Ordered Locus Names:At5g14660
    ORF Names:T15N1_150
    OrganismiArabidopsis thaliana (Mouse-ear cress)
    Taxonomic identifieri3702 [NCBI]
    Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
    ProteomesiUP000006548: Chromosome 5

    Organism-specific databases

    TAIRiAT5G14660.

    Subcellular locationi

    Plastidchloroplast stroma. Mitochondrion
    Note: Reported to be localized to chloroplast and mitochondria based on transient GFP expression in a heterologous system.1 Publication

    GO - Cellular componenti

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

    Keywords - Cellular componenti

    Chloroplast, Mitochondrion, Plastid

    Pathology & Biotechi

    Disruption phenotypei

    Albino.1 Publication

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi178 – 1781Y → A: Decrease in substrate affinity. 1 Publication
    Mutagenesisi178 – 1781Y → F or R: Increase in substrate affinity. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Transit peptidei1 – 5656Chloroplast and mitochondrionSequence AnalysisAdd
    BLAST
    Chaini57 – 273217Peptide deformylase 1B, chloroplastic/mitochondrialPRO_0000006732Add
    BLAST

    Proteomic databases

    PaxDbiQ9FUZ2.
    PRIDEiQ9FUZ2.

    Expressioni

    Tissue specificityi

    Expressed in leaves and flowers.1 Publication

    Gene expression databases

    GenevestigatoriQ9FUZ2.

    Interactioni

    Subunit structurei

    Homodimer.

    Protein-protein interaction databases

    BioGridi16595. 3 interactions.
    IntActiQ9FUZ2. 2 interactions.

    Structurei

    Secondary structure

    1
    273
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi89 – 913
    Helixi103 – 11816
    Beta strandi122 – 1254
    Helixi126 – 1294
    Beta strandi133 – 1386
    Beta strandi150 – 16011
    Beta strandi164 – 1696
    Beta strandi179 – 1857
    Beta strandi187 – 1926
    Beta strandi194 – 1963
    Beta strandi198 – 2036
    Helixi205 – 21814
    Helixi223 – 2264
    Helixi229 – 2335
    Helixi236 – 25015
    Helixi258 – 2603

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    3CPMX-ray2.40A65-257[»]
    3M6OX-ray2.00A/B83-273[»]
    3M6PX-ray2.00A/B83-273[»]
    3M6QX-ray2.40A83-273[»]
    3M6RX-ray2.40A/B/C/D83-273[»]
    3O3JX-ray3.00A83-273[»]
    3PN2X-ray2.00A83-273[»]
    3PN3X-ray1.30A/B83-273[»]
    3PN4X-ray1.90A83-273[»]
    3PN5X-ray2.30A83-273[»]
    3PN6X-ray2.10A/B83-273[»]
    ProteinModelPortaliQ9FUZ2.
    SMRiQ9FUZ2. Positions 74-257.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ9FUZ2.

    Family & Domainsi

    Sequence similaritiesi

    Belongs to the polypeptide deformylase family.Curated

    Keywords - Domaini

    Transit peptide

    Phylogenomic databases

    eggNOGiCOG0242.
    HOGENOMiHOG000243509.
    InParanoidiQ9FUZ2.
    KOiK01462.
    OMAiTIMYKEG.
    PhylomeDBiQ9FUZ2.

    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.

    Q9FUZ2-1 [UniParc]FASTAAdd to Basket

    « Hide

    MAVCNCFLQA PPLSRILLPV LSRRATTLSA GYGRLKSTVT FCSTVNRTSP    50
    LTSSVRAEVK RVSRKDDKVA SATDVQFETP LKIVEYPDPI LRAKNKRIDI 100
    FDENLKNLVD AMFDVMYKTD GIGLSAPQVG LNVQLMVFNP AGEPGEGKEI 150
    VLVNPKIKKY SDKLVPFDEG CLSFPGIYAE VVRPQSVKID ARDITGERFS 200
    ISLSRLPARI FQHEYDHLEG VLFFDRMTDQ VLDSIREELE ALEKKYEEKT 250
    GLPSPERVEA RQKRKAGVGF GKR 273
    Length:273
    Mass (Da):30,610
    Last modified:December 15, 2003 - v2
    Checksum:i25CDA90ED6D9603E
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti48 – 481T → N in AAM62644. 1 PublicationCurated
    Sequence conflicti205 – 2051R → S in AAG33980. (PubMed:11060042)Curated

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AF269165 mRNA. Translation: AAG33980.1.
    AL163792 Genomic DNA. Translation: CAB87633.1.
    CP002688 Genomic DNA. Translation: AED92059.1.
    CP002688 Genomic DNA. Translation: AED92060.1.
    AY050879 mRNA. Translation: AAK92816.1.
    AY096673 mRNA. Translation: AAM20307.1.
    AY085417 mRNA. Translation: AAM62644.1.
    PIRiT48639.
    RefSeqiNP_196970.1. NM_121470.3.
    NP_850821.1. NM_180490.1.
    UniGeneiAt.5087.

    Genome annotation databases

    EnsemblPlantsiAT5G14660.1; AT5G14660.1; AT5G14660.
    AT5G14660.2; AT5G14660.2; AT5G14660.
    GeneIDi831318.
    KEGGiath:AT5G14660.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AF269165 mRNA. Translation: AAG33980.1 .
    AL163792 Genomic DNA. Translation: CAB87633.1 .
    CP002688 Genomic DNA. Translation: AED92059.1 .
    CP002688 Genomic DNA. Translation: AED92060.1 .
    AY050879 mRNA. Translation: AAK92816.1 .
    AY096673 mRNA. Translation: AAM20307.1 .
    AY085417 mRNA. Translation: AAM62644.1 .
    PIRi T48639.
    RefSeqi NP_196970.1. NM_121470.3.
    NP_850821.1. NM_180490.1.
    UniGenei At.5087.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    3CPM X-ray 2.40 A 65-257 [» ]
    3M6O X-ray 2.00 A/B 83-273 [» ]
    3M6P X-ray 2.00 A/B 83-273 [» ]
    3M6Q X-ray 2.40 A 83-273 [» ]
    3M6R X-ray 2.40 A/B/C/D 83-273 [» ]
    3O3J X-ray 3.00 A 83-273 [» ]
    3PN2 X-ray 2.00 A 83-273 [» ]
    3PN3 X-ray 1.30 A/B 83-273 [» ]
    3PN4 X-ray 1.90 A 83-273 [» ]
    3PN5 X-ray 2.30 A 83-273 [» ]
    3PN6 X-ray 2.10 A/B 83-273 [» ]
    ProteinModelPortali Q9FUZ2.
    SMRi Q9FUZ2. Positions 74-257.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 16595. 3 interactions.
    IntActi Q9FUZ2. 2 interactions.

    Proteomic databases

    PaxDbi Q9FUZ2.
    PRIDEi Q9FUZ2.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblPlantsi AT5G14660.1 ; AT5G14660.1 ; AT5G14660 .
    AT5G14660.2 ; AT5G14660.2 ; AT5G14660 .
    GeneIDi 831318.
    KEGGi ath:AT5G14660.

    Organism-specific databases

    TAIRi AT5G14660.

    Phylogenomic databases

    eggNOGi COG0242.
    HOGENOMi HOG000243509.
    InParanoidi Q9FUZ2.
    KOi K01462.
    OMAi TIMYKEG.
    PhylomeDBi Q9FUZ2.

    Enzyme and pathway databases

    BioCyci ARA:AT5G14660-MONOMER.
    ARA:GQT-2354-MONOMER.
    SABIO-RK Q9FUZ2.

    Miscellaneous databases

    EvolutionaryTracei Q9FUZ2.

    Gene expression databases

    Genevestigatori Q9FUZ2.

    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 5 of the plant Arabidopsis thaliana."
      Tabata S., Kaneko T., Nakamura Y., Kotani H., Kato T., Asamizu E., Miyajima N., Sasamoto S., Kimura T., Hosouchi T., Kawashima K., Kohara M., Matsumoto M., Matsuno A., Muraki A., Nakayama S., Nakazaki N., Naruo K.
      , Okumura S., Shinpo S., Takeuchi C., Wada T., Watanabe A., Yamada M., Yasuda M., Sato S., de la Bastide M., Huang E., Spiegel L., Gnoj L., O'Shaughnessy A., Preston R., Habermann K., Murray J., Johnson D., Rohlfing T., Nelson J., Stoneking T., Pepin K., Spieth J., Sekhon M., Armstrong J., Becker M., Belter E., Cordum H., Cordes M., Courtney L., Courtney W., Dante M., Du H., Edwards J., Fryman J., Haakensen B., Lamar E., Latreille P., Leonard S., Meyer R., Mulvaney E., Ozersky P., Riley A., Strowmatt C., Wagner-McPherson C., Wollam A., Yoakum M., Bell M., Dedhia N., Parnell L., Shah R., Rodriguez M., Hoon See L., Vil D., Baker J., Kirchoff K., Toth K., King L., Bahret A., Miller B., Marra M.A., Martienssen R., McCombie W.R., Wilson R.K., Murphy G., Bancroft I., Volckaert G., Wambutt R., Duesterhoeft A., Stiekema W., Pohl T., Entian K.-D., Terryn N., Hartley N., Bent E., Johnson S., Langham S.-A., McCullagh B., Robben J., Grymonprez B., Zimmermann W., Ramsperger U., Wedler H., Balke K., Wedler E., Peters S., van Staveren M., Dirkse W., Mooijman P., Klein Lankhorst R., Weitzenegger T., Bothe G., Rose M., Hauf J., Berneiser S., Hempel S., Feldpausch M., Lamberth S., Villarroel R., Gielen J., Ardiles W., Bents O., Lemcke K., Kolesov G., Mayer K.F.X., Rudd S., Schoof H., Schueller C., Zaccaria P., Mewes H.-W., Bevan M., Fransz P.F.
      Nature 408:823-826(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].
      Strain: cv. Columbia.
    5. "Full-length cDNA from Arabidopsis thaliana."
      Brover V.V., Troukhan M.E., Alexandrov N.A., Lu Y.-P., Flavell R.B., Feldmann K.A.
      Submitted (MAR-2002) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    6. "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.
    7. "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.
    8. "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.
    9. "Insights into the substrate specificity of plant peptide deformylase, an essential enzyme with potential for the development of novel biotechnology applications in agriculture."
      Dirk L.M., Schmidt J.J., Cai Y., Barnes J.C., Hanger K.M., Nayak N.R., Williams M.A., Grossman R.B., Houtz R.L., Rodgers D.W.
      Biochem. J. 413:417-427(2008) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS) OF 65-257, HOMODIMERIZATION, MUTAGENESIS OF TYR-178.

    Entry informationi

    Entry nameiDEF1B_ARATH
    AccessioniPrimary (citable) accession number: Q9FUZ2
    Secondary accession number(s): Q8LEH0, Q949U8, Q9LYJ4
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: December 5, 2001
    Last sequence update: December 15, 2003
    Last modified: October 1, 2014
    This is version 102 of the entry and version 2 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