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Q57764

- PDAD_METJA

UniProt

Q57764 - PDAD_METJA

Protein

Pyruvoyl-dependent arginine decarboxylase

Gene

pdaD

Organism
Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) (Methanococcus jannaschii)
Status
Reviewed - Annotation score: 4 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 107 (01 Oct 2014)
      Sequence version 1 (01 Nov 1996)
      Previous versions | rss
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    Functioni

    Catalytic activityi

    L-arginine = agmatine + CO2.

    Cofactori

    Pyruvoyl group.

    Temperature dependencei

    Thermostable.

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sitei52 – 532Cleavage (non-hydrolytic)

    GO - Molecular functioni

    1. arginine decarboxylase activity Source: UniProtKB-HAMAP

    GO - Biological processi

    1. arginine catabolic process Source: InterPro

    Keywords - Molecular functioni

    Decarboxylase, Lyase

    Keywords - Ligandi

    Pyruvate

    Enzyme and pathway databases

    SABIO-RKQ57764.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Pyruvoyl-dependent arginine decarboxylase (EC:4.1.1.19)
    Short name:
    PvlArgDC
    Cleaved into the following 2 chains:
    Gene namesi
    Name:pdaD
    Ordered Locus Names:MJ0316
    OrganismiMethanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) (Methanococcus jannaschii)
    Taxonomic identifieri243232 [NCBI]
    Taxonomic lineageiArchaeaEuryarchaeotaMethanococciMethanococcalesMethanocaldococcaceaeMethanocaldococcus
    ProteomesiUP000000805: Chromosome

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 5252Pyruvoyl-dependent arginine decarboxylase subunit betaPRO_0000023314Add
    BLAST
    Chaini53 – 165113Pyruvoyl-dependent arginine decarboxylase subunit alphaPRO_0000023315Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei53 – 531Pyruvic acid (Ser)

    Interactioni

    Subunit structurei

    Trimer of an alpha-beta dimer.

    Protein-protein interaction databases

    STRINGi243232.MJ0316.

    Structurei

    Secondary structure

    1
    165
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi10 – 123
    Beta strandi17 – 2610
    Helixi30 – 4112
    Beta strandi46 – 516
    Beta strandi53 – 553
    Beta strandi72 – 8211
    Beta strandi88 – 10013
    Beta strandi105 – 11410
    Helixi116 – 13419
    Beta strandi138 – 14912
    Beta strandi151 – 16313

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1MT1X-ray2.20A/C/E/G/I/K1-52[»]
    B/D/F/H/J/L53-165[»]
    1N13X-ray1.40A/C/E/G/I/K1-52[»]
    B/D/F/H/J/L53-165[»]
    1N2MX-ray1.90A/B/C/D/E/F1-165[»]
    2QQCX-ray2.00A/C/E/G/I/K1-52[»]
    B/D/F/H/J/L54-165[»]
    2QQDX-ray2.00A/D1-52[»]
    B/E54-165[»]
    C/F/G/H1-165[»]
    ProteinModelPortaliQ57764.
    SMRiQ57764. Positions 3-165.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ57764.

    Family & Domainsi

    Sequence similaritiesi

    Belongs to the PdaD family.Curated

    Phylogenomic databases

    eggNOGiCOG1945.
    KOiK02626.
    OMAiISSIMPP.
    PhylomeDBiQ57764.

    Family and domain databases

    Gene3Di3.50.20.10. 1 hit.
    HAMAPiMF_01404. PvlArgDC.
    InterProiIPR016104. Pyr-dep_his/arg-deCO2ase.
    IPR016105. Pyr-dep_his/arg-deCO2ase_sand.
    IPR002724. Pyruvoyl-dep_arg_deCO2ase.
    [Graphical view]
    PfamiPF01862. PvlArgDC. 1 hit.
    [Graphical view]
    PIRSFiPIRSF005216. Pyruvoyl-dep_arg_deCO2ase. 1 hit.
    ProDomiPD010449. Pyruvoyl-dep_arg_deCO2ase. 1 hit.
    [Graphical view] [Entries sharing at least one domain]
    SUPFAMiSSF56271. SSF56271. 1 hit.
    TIGRFAMsiTIGR00286. TIGR00286. 1 hit.

    Sequencei

    Sequence statusi: Complete.

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

    Q57764-1 [UniParc]FASTAAdd to Basket

    « Hide

    MNAEINPLHA YFKLPNTVSL VAGSSEGETP LNAFDGALLN AGIGNVNLIR    50
    ISSIMPPEAE IVPLPKLPMG ALVPTAYGYI ISDVPGETIS AAISVAIPKD 100
    KSLCGLIMEY EGKCSKKEAE KTVREMAKIG FEMRGWELDR IESIAVEHTV 150
    EKLGCAFAAA ALWYK 165
    Length:165
    Mass (Da):17,708
    Last modified:November 1, 1996 - v1
    Checksum:i04C7F8AB3AEC2342
    GO

    Mass spectrometryi

    Molecular mass is 5436±11 Da from positions 1 - 52. Determined by MALDI. 1 Publication
    Molecular mass is 12356±57 Da from positions 53 - 165. Determined by MALDI. 1 Publication

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    L77117 Genomic DNA. Translation: AAB98302.1.
    PIRiE64339.
    RefSeqiNP_247289.1. NC_000909.1.
    WP_010869814.1. NC_000909.1.

    Genome annotation databases

    EnsemblBacteriaiAAB98302; AAB98302; MJ_0316.
    GeneIDi1451171.
    KEGGimja:MJ_0316.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    L77117 Genomic DNA. Translation: AAB98302.1 .
    PIRi E64339.
    RefSeqi NP_247289.1. NC_000909.1.
    WP_010869814.1. NC_000909.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1MT1 X-ray 2.20 A/C/E/G/I/K 1-52 [» ]
    B/D/F/H/J/L 53-165 [» ]
    1N13 X-ray 1.40 A/C/E/G/I/K 1-52 [» ]
    B/D/F/H/J/L 53-165 [» ]
    1N2M X-ray 1.90 A/B/C/D/E/F 1-165 [» ]
    2QQC X-ray 2.00 A/C/E/G/I/K 1-52 [» ]
    B/D/F/H/J/L 54-165 [» ]
    2QQD X-ray 2.00 A/D 1-52 [» ]
    B/E 54-165 [» ]
    C/F/G/H 1-165 [» ]
    ProteinModelPortali Q57764.
    SMRi Q57764. Positions 3-165.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 243232.MJ0316.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai AAB98302 ; AAB98302 ; MJ_0316 .
    GeneIDi 1451171.
    KEGGi mja:MJ_0316.

    Phylogenomic databases

    eggNOGi COG1945.
    KOi K02626.
    OMAi ISSIMPP.
    PhylomeDBi Q57764.

    Enzyme and pathway databases

    SABIO-RK Q57764.

    Miscellaneous databases

    EvolutionaryTracei Q57764.

    Family and domain databases

    Gene3Di 3.50.20.10. 1 hit.
    HAMAPi MF_01404. PvlArgDC.
    InterProi IPR016104. Pyr-dep_his/arg-deCO2ase.
    IPR016105. Pyr-dep_his/arg-deCO2ase_sand.
    IPR002724. Pyruvoyl-dep_arg_deCO2ase.
    [Graphical view ]
    Pfami PF01862. PvlArgDC. 1 hit.
    [Graphical view ]
    PIRSFi PIRSF005216. Pyruvoyl-dep_arg_deCO2ase. 1 hit.
    ProDomi PD010449. Pyruvoyl-dep_arg_deCO2ase. 1 hit.
    [Graphical view ] [Entries sharing at least one domain ]
    SUPFAMi SSF56271. SSF56271. 1 hit.
    TIGRFAMsi TIGR00286. TIGR00286. 1 hit.
    ProtoNeti Search...

    Publicationsi

    1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440.
    2. "Methanococcus jannaschii uses a pyruvoyl-dependent arginine decarboxylase in polyamine biosynthesis."
      Graham D.E., Xu H., White R.H.
      J. Biol. Chem. 277:23500-23507(2002) [PubMed] [Europe PMC] [Abstract]
      Cited for: CHARACTERIZATION, MASS SPECTROMETRY.
      Strain: ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440.

    Entry informationi

    Entry nameiPDAD_METJA
    AccessioniPrimary (citable) accession number: Q57764
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: November 1, 1997
    Last sequence update: November 1, 1996
    Last modified: October 1, 2014
    This is version 107 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome, Reference proteome

    Documents

    1. Methanococcus jannaschii
      Methanococcus jannaschii: 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