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P16932

- DGDA_BURCE

UniProt

P16932 - DGDA_BURCE

Protein

2,2-dialkylglycine decarboxylase

Gene

dgdA

Organism
Burkholderia cepacia (Pseudomonas cepacia)
Status
Reviewed - Annotation score: 4 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 94 (01 Oct 2014)
      Sequence version 3 (23 Jan 2007)
      Previous versions | rss
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    Functioni

    The dialkylglycine decarboxylase is of interest because it normally catalyzes both decarboxylation and amino transfer. It may be more properly described as a decarboxylating aminotransferase rather than an aminotransferring decarboxylase.

    Catalytic activityi

    2,2-dialkylglycine + pyruvate = dialkyl ketone + CO2 + L-alanine.

    Cofactori

    Pyridoxal phosphate.

    GO - Molecular functioni

    1. 2,2-dialkylglycine decarboxylase (pyruvate) activity Source: UniProtKB-EC
    2. pyridoxal phosphate binding Source: InterPro
    3. transaminase activity Source: InterPro

    Keywords - Molecular functioni

    Decarboxylase, Lyase

    Keywords - Ligandi

    Pyridoxal phosphate

    Enzyme and pathway databases

    SABIO-RKP16932.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    2,2-dialkylglycine decarboxylase (EC:4.1.1.64)
    Short name:
    DGD
    Gene namesi
    Name:dgdA
    OrganismiBurkholderia cepacia (Pseudomonas cepacia)
    Taxonomic identifieri292 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaBetaproteobacteriaBurkholderialesBurkholderiaceaeBurkholderiaBurkholderia cepacia complex

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Initiator methioninei1 – 11Removed1 Publication
    Chaini2 – 4334322,2-dialkylglycine decarboxylasePRO_0000120509Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei272 – 2721N6-(pyridoxal phosphate)lysine

    Interactioni

    Subunit structurei

    Homotetramer.

    Structurei

    Secondary structure

    1
    433
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi7 – 1610
    Beta strandi31 – 344
    Beta strandi36 – 383
    Beta strandi44 – 474
    Helixi50 – 534
    Helixi62 – 7413
    Helixi85 – 9713
    Beta strandi104 – 1096
    Helixi111 – 12616
    Beta strandi130 – 1345
    Helixi143 – 1475
    Beta strandi151 – 1533
    Beta strandi155 – 1573
    Beta strandi164 – 1674
    Beta strandi172 – 1743
    Beta strandi178 – 1836
    Helixi185 – 19915
    Beta strandi204 – 2096
    Beta strandi211 – 2133
    Turni214 – 2174
    Beta strandi218 – 2203
    Helixi225 – 23511
    Beta strandi239 – 2435
    Turni245 – 2528
    Beta strandi253 – 2564
    Helixi258 – 2614
    Beta strandi266 – 2705
    Helixi272 – 2754
    Beta strandi281 – 2855
    Helixi287 – 2959
    Turni303 – 3064
    Helixi308 – 32316
    Helixi326 – 34722
    Beta strandi351 – 3577
    Beta strandi360 – 3689
    Turni369 – 3724
    Helixi378 – 38811
    Beta strandi395 – 3973
    Beta strandi404 – 4074
    Helixi415 – 43218

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1D7RX-ray2.00A1-433[»]
    1D7SX-ray2.05A1-433[»]
    1D7UX-ray1.95A1-433[»]
    1D7VX-ray2.80A1-433[»]
    1DGDX-ray2.80A2-433[»]
    1DGEX-ray2.80A2-433[»]
    1DKAX-ray2.60A1-433[»]
    1M0NX-ray2.20A1-433[»]
    1M0OX-ray2.40A1-433[»]
    1M0PX-ray2.60A1-433[»]
    1M0QX-ray2.00A1-433[»]
    1Z3ZX-ray2.90A3-433[»]
    1ZC9X-ray2.00A1-433[»]
    1ZOBX-ray2.75A1-433[»]
    1ZODX-ray1.80A1-433[»]
    2DKBX-ray2.10A1-433[»]
    ProteinModelPortaliP16932.
    SMRiP16932. Positions 3-433.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP16932.

    Family & Domainsi

    Sequence similaritiesi

    Family and domain databases

    Gene3Di3.40.640.10. 1 hit.
    3.90.1150.10. 1 hit.
    InterProiIPR005814. Aminotrans_3.
    IPR015424. PyrdxlP-dep_Trfase.
    IPR015421. PyrdxlP-dep_Trfase_major_sub1.
    IPR015422. PyrdxlP-dep_Trfase_major_sub2.
    [Graphical view]
    PANTHERiPTHR11986. PTHR11986. 1 hit.
    PfamiPF00202. Aminotran_3. 1 hit.
    [Graphical view]
    PIRSFiPIRSF000521. Transaminase_4ab_Lys_Orn. 1 hit.
    SUPFAMiSSF53383. SSF53383. 1 hit.
    PROSITEiPS00600. AA_TRANSFER_CLASS_3. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

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

    P16932-1 [UniParc]FASTAAdd to Basket

    « Hide

    MSLNDDATFW RNARQHLVRY GGTFEPMIIE RAKGSFVYDA DGRAILDFTS    50
    GQMSAVLGHC HPEIVSVIGE YAGKLDHLFS GMLSRPVVDL ATRLANITPP 100
    GLDRALLLST GAESNEAAIR MAKLVTGKYE IVGFAQSWHG MTGAAASATY 150
    SAGRKGVGPA AVGSFAIPAP FTYRPRFERN GAYDYLAELD YAFDLIDRQS 200
    SGNLAAFIAE PILSSGGIIE LPDGYMAALK RKCEARGMLL ILDEAQTGVG 250
    RTGTMFACQR DGVTPDILTL SKTLGAGLPL AAIVTSAAIE ERAHELGYLF 300
    YTTHVSDPLP AAVGLRVLDV VQRDGLVARA NVMGDRLRRG LLDLMERFDC 350
    IGDVRGRGLL LGVEIVKDRR TKEPADGLGA KITRECMNLG LSMNIVQLPG 400
    MGGVFRIAPP LTVSEDEIDL GLSLLGQAIE RAL 433
    Length:433
    Mass (Da):46,444
    Last modified:January 23, 2007 - v3
    Checksum:iEF441EC8DF8C37FE
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    J05282 Genomic DNA. Translation: AAA50844.1.
    PIRiA35173.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    J05282 Genomic DNA. Translation: AAA50844.1 .
    PIRi A35173.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1D7R X-ray 2.00 A 1-433 [» ]
    1D7S X-ray 2.05 A 1-433 [» ]
    1D7U X-ray 1.95 A 1-433 [» ]
    1D7V X-ray 2.80 A 1-433 [» ]
    1DGD X-ray 2.80 A 2-433 [» ]
    1DGE X-ray 2.80 A 2-433 [» ]
    1DKA X-ray 2.60 A 1-433 [» ]
    1M0N X-ray 2.20 A 1-433 [» ]
    1M0O X-ray 2.40 A 1-433 [» ]
    1M0P X-ray 2.60 A 1-433 [» ]
    1M0Q X-ray 2.00 A 1-433 [» ]
    1Z3Z X-ray 2.90 A 3-433 [» ]
    1ZC9 X-ray 2.00 A 1-433 [» ]
    1ZOB X-ray 2.75 A 1-433 [» ]
    1ZOD X-ray 1.80 A 1-433 [» ]
    2DKB X-ray 2.10 A 1-433 [» ]
    ProteinModelPortali P16932.
    SMRi P16932. Positions 3-433.
    ModBasei Search...
    MobiDBi Search...

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Enzyme and pathway databases

    SABIO-RK P16932.

    Miscellaneous databases

    EvolutionaryTracei P16932.

    Family and domain databases

    Gene3Di 3.40.640.10. 1 hit.
    3.90.1150.10. 1 hit.
    InterProi IPR005814. Aminotrans_3.
    IPR015424. PyrdxlP-dep_Trfase.
    IPR015421. PyrdxlP-dep_Trfase_major_sub1.
    IPR015422. PyrdxlP-dep_Trfase_major_sub2.
    [Graphical view ]
    PANTHERi PTHR11986. PTHR11986. 1 hit.
    Pfami PF00202. Aminotran_3. 1 hit.
    [Graphical view ]
    PIRSFi PIRSF000521. Transaminase_4ab_Lys_Orn. 1 hit.
    SUPFAMi SSF53383. SSF53383. 1 hit.
    PROSITEi PS00600. AA_TRANSFER_CLASS_3. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "Pseudomonas cepacia 2,2-dialkylglycine decarboxylase. Sequence and expression in Escherichia coli of structural and repressor genes."
      Keller J.W., Baurick K.B., Rutt G.C., O'Malley M.V., Sonafrank N.L., Reynolds R.A., Ebbesson L.O.E., Vajdos F.F.
      J. Biol. Chem. 265:5531-5539(1990) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 2-20 AND 261-276.
    2. "Dialkylglycine decarboxylase structure: bifunctional active site and alkali metal sites."
      Toney M.D., Hohenester E., Cowan S.W., Jansonius J.N.
      Science 261:756-759(1993) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS).
    3. "An alkali metal ion size-dependent switch in the active site structure of dialkylglycine decarboxylase."
      Hohenester E., Keller J.W., Jansonius J.N.
      Biochemistry 33:13561-13570(1994) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS), SEQUENCE REVISION TO 52; 82-83 AND 308-312.
    4. "Structural and mechanistic analysis of two refined crystal structures of the pyridoxal phosphate-dependent enzyme dialkylglycine decarboxylase."
      Toney M.D., Hohenester E., Keller J.W., Jansonius J.N.
      J. Mol. Biol. 245:151-179(1995) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS).
    5. "Crystal structures of dialkylglycine decarboxylase inhibitor complexes."
      Malashkevich V.N., Strop P., Keller J.W., Jansonius J.N., Toney M.D.
      J. Mol. Biol. 294:193-200(1999) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS).

    Entry informationi

    Entry nameiDGDA_BURCE
    AccessioniPrimary (citable) accession number: P16932
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: August 1, 1990
    Last sequence update: January 23, 2007
    Last modified: October 1, 2014
    This is version 94 of the entry and version 3 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    The enzyme may have evolved to use the rare dialkylglycines of cosmic origin, or it may be part of a metabolic pathway for breaking down cytotoxic peptides and the constituent amino acids.

    Keywords - Technical termi

    3D-structure, Direct protein sequencing

    Documents

    1. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    2. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3