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P0A9P0

- DLDH_ECOLI

UniProt

P0A9P0 - DLDH_ECOLI

Protein

Dihydrolipoyl dehydrogenase

Gene

lpdA

Organism
Escherichia coli (strain K12)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 92 (01 Oct 2014)
      Sequence version 2 (23 Jan 2007)
      Previous versions | rss
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    Functioni

    Lipoamide dehydrogenase is a component of the glycine cleavage system as well as of the alpha-ketoacid dehydrogenase complexes.

    Catalytic activityi

    Protein N(6)-(dihydrolipoyl)lysine + NAD+ = protein N(6)-(lipoyl)lysine + NADH.

    Cofactori

    Binds 1 FAD per subunit.By similarity

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei54 – 541FADBy similarity
    Binding sitei117 – 1171FAD; via amide nitrogen and carbonyl oxygenBy similarity
    Binding sitei205 – 2051NADBy similarity
    Binding sitei238 – 2381NAD; via amide nitrogenBy similarity
    Binding sitei313 – 3131FADBy similarity
    Binding sitei321 – 3211FAD; via amide nitrogenBy similarity
    Active sitei445 – 4451Proton acceptorBy similarity

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Nucleotide bindingi36 – 4510FADBy similarity
    Nucleotide bindingi182 – 1865NADBy similarity
    Nucleotide bindingi270 – 2734NADBy similarity

    GO - Molecular functioni

    1. dihydrolipoyl dehydrogenase activity Source: EcoliWiki
    2. disulfide oxidoreductase activity Source: EcoliWiki
    3. flavin adenine dinucleotide binding Source: EcoliWiki
    4. identical protein binding Source: IntAct
    5. protein binding Source: IntAct
    6. zinc ion binding Source: EcoliWiki

    GO - Biological processi

    1. 2-oxoglutarate metabolic process Source: EcoliWiki
    2. cell redox homeostasis Source: InterPro
    3. glycine decarboxylation via glycine cleavage system Source: EcoCyc
    4. glycolytic process Source: UniProtKB-KW
    5. oxidation-reduction process Source: EcoliWiki
    6. pyruvate metabolic process Source: EcoliWiki
    7. response to oxidative stress Source: EcoCyc

    Keywords - Molecular functioni

    Oxidoreductase

    Keywords - Biological processi

    Glycolysis

    Keywords - Ligandi

    FAD, Flavoprotein, NAD

    Enzyme and pathway databases

    BioCyciEcoCyc:E3-MONOMER.
    ECOL316407:JW0112-MONOMER.
    MetaCyc:E3-MONOMER.
    SABIO-RKP0A9P0.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Dihydrolipoyl dehydrogenase (EC:1.8.1.4)
    Alternative name(s):
    Dihydrolipoamide dehydrogenase
    E3 component of pyruvate and 2-oxoglutarate dehydrogenases complexes
    Glycine cleavage system L protein
    Gene namesi
    Name:lpdA
    Synonyms:lpd
    Ordered Locus Names:b0116, JW0112
    OrganismiEscherichia coli (strain K12)
    Taxonomic identifieri83333 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
    ProteomesiUP000000318: Chromosome, UP000000625: Chromosome

    Organism-specific databases

    EcoGeneiEG10543. lpd.

    Subcellular locationi

    Cytoplasm 1 Publication. Cell inner membrane 1 Publication; Peripheral membrane protein 1 Publication

    GO - Cellular componenti

    1. cytoplasm Source: EcoliWiki
    2. cytosol Source: UniProtKB
    3. membrane Source: UniProtKB
    4. plasma membrane Source: UniProtKB-SubCell

    Keywords - Cellular componenti

    Cell inner membrane, Cell membrane, Cytoplasm, Membrane

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Initiator methioninei1 – 11Removed1 Publication
    Chaini2 – 474473Dihydrolipoyl dehydrogenasePRO_0000068027Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Disulfide bondi45 ↔ 50Redox-activeBy similarity
    Modified residuei220 – 2201N6-acetyllysine1 Publication

    Keywords - PTMi

    Acetylation, Disulfide bond

    Proteomic databases

    PaxDbiP0A9P0.
    PRIDEiP0A9P0.

    2D gel databases

    SWISS-2DPAGEP0A9P0.

    Expressioni

    Gene expression databases

    GenevestigatoriP0A9P0.

    Interactioni

    Subunit structurei

    Homodimer.

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    itself2EBI-542856,EBI-542856
    aceFP069593EBI-542856,EBI-542707
    uvrDP030182EBI-542856,EBI-559573

    Protein-protein interaction databases

    DIPiDIP-6854N.
    IntActiP0A9P0. 90 interactions.
    MINTiMINT-1242510.
    STRINGi511145.b0116.

    Structurei

    Secondary structure

    1
    474
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi3 – 1210
    Helixi16 – 2712
    Beta strandi32 – 4211
    Helixi43 – 475
    Helixi50 – 6819
    Helixi69 – 724
    Helixi83 – 10725
    Beta strandi111 – 12111
    Beta strandi124 – 1285
    Beta strandi134 – 14310
    Beta strandi147 – 1493
    Beta strandi153 – 1553
    Helixi165 – 1695
    Beta strandi176 – 1816
    Helixi185 – 19612
    Beta strandi200 – 21112
    Helixi216 – 22611
    Turni227 – 2293
    Beta strandi230 – 24415
    Beta strandi247 – 2548
    Beta strandi262 – 2698
    Beta strandi273 – 2753
    Helixi277 – 2793
    Helixi282 – 2854
    Beta strandi308 – 3103
    Helixi312 – 3154
    Helixi321 – 33515
    Beta strandi349 – 3513
    Beta strandi353 – 3619
    Helixi364 – 3696
    Beta strandi374 – 3807
    Helixi381 – 3833
    Helixi385 – 3895
    Beta strandi396 – 4027
    Turni403 – 4053
    Beta strandi407 – 4159
    Helixi418 – 4214
    Helixi422 – 4309
    Helixi435 – 4406
    Helixi450 – 45910

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    4JDRX-ray2.50A/B1-474[»]
    ProteinModelPortaliP0A9P0.
    SMRiP0A9P0. Positions 2-472.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Sequence similaritiesi

    Keywords - Domaini

    Redox-active center

    Phylogenomic databases

    eggNOGiCOG1249.
    HOGENOMiHOG000276708.
    KOiK00382.
    OMAiIWNSTDA.
    OrthoDBiEOG6QCD6D.
    PhylomeDBiP0A9P0.

    Family and domain databases

    Gene3Di3.30.390.30. 1 hit.
    InterProiIPR016156. FAD/NAD-linked_Rdtase_dimer.
    IPR013027. FAD_pyr_nucl-diS_OxRdtase.
    IPR006258. Lipoamide_DH.
    IPR004099. Pyr_nucl-diS_OxRdtase_dimer.
    IPR023753. Pyr_nucl-diS_OxRdtase_FAD/NAD.
    IPR012999. Pyr_OxRdtase_I_AS.
    IPR001327. Pyr_OxRdtase_NAD-bd_dom.
    [Graphical view]
    PfamiPF00070. Pyr_redox. 1 hit.
    PF07992. Pyr_redox_2. 1 hit.
    PF02852. Pyr_redox_dim. 1 hit.
    [Graphical view]
    PRINTSiPR00368. FADPNR.
    SUPFAMiSSF55424. SSF55424. 1 hit.
    TIGRFAMsiTIGR01350. lipoamide_DH. 1 hit.
    PROSITEiPS00076. PYRIDINE_REDOX_1. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

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

    P0A9P0-1 [UniParc]FASTAAdd to Basket

    « Hide

    MSTEIKTQVV VLGAGPAGYS AAFRCADLGL ETVIVERYNT LGGVCLNVGC    50
    IPSKALLHVA KVIEEAKALA EHGIVFGEPK TDIDKIRTWK EKVINQLTGG 100
    LAGMAKGRKV KVVNGLGKFT GANTLEVEGE NGKTVINFDN AIIAAGSRPI 150
    QLPFIPHEDP RIWDSTDALE LKEVPERLLV MGGGIIGLEM GTVYHALGSQ 200
    IDVVEMFDQV IPAADKDIVK VFTKRISKKF NLMLETKVTA VEAKEDGIYV 250
    TMEGKKAPAE PQRYDAVLVA IGRVPNGKNL DAGKAGVEVD DRGFIRVDKQ 300
    LRTNVPHIFA IGDIVGQPML AHKGVHEGHV AAEVIAGKKH YFDPKVIPSI 350
    AYTEPEVAWV GLTEKEAKEK GISYETATFP WAASGRAIAS DCADGMTKLI 400
    FDKESHRVIG GAIVGTNGGE LLGEIGLAIE MGCDAEDIAL TIHAHPTLHE 450
    SVGLAAEVFE GSITDLPNPK AKKK 474
    Length:474
    Mass (Da):50,688
    Last modified:January 23, 2007 - v2
    Checksum:iED16149A3BDF333A
    GO

    Sequence cautioni

    The sequence CAA24742.1 differs from that shown. Reason: Erroneous initiation.

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    V01498 Genomic DNA. Translation: CAA24742.1. Different initiation.
    U00096 Genomic DNA. Translation: AAC73227.1.
    AP009048 Genomic DNA. Translation: BAB96686.2.
    PIRiS45195. DEECLP.
    RefSeqiNP_414658.1. NC_000913.3.
    YP_488419.1. NC_007779.1.

    Genome annotation databases

    EnsemblBacteriaiAAC73227; AAC73227; b0116.
    BAB96686; BAB96686; BAB96686.
    GeneIDi12932376.
    944854.
    KEGGiecj:Y75_p0113.
    eco:b0116.
    PATRICi32115333. VBIEscCol129921_0118.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    V01498 Genomic DNA. Translation: CAA24742.1 . Different initiation.
    U00096 Genomic DNA. Translation: AAC73227.1 .
    AP009048 Genomic DNA. Translation: BAB96686.2 .
    PIRi S45195. DEECLP.
    RefSeqi NP_414658.1. NC_000913.3.
    YP_488419.1. NC_007779.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    4JDR X-ray 2.50 A/B 1-474 [» ]
    ProteinModelPortali P0A9P0.
    SMRi P0A9P0. Positions 2-472.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    DIPi DIP-6854N.
    IntActi P0A9P0. 90 interactions.
    MINTi MINT-1242510.
    STRINGi 511145.b0116.

    2D gel databases

    SWISS-2DPAGE P0A9P0.

    Proteomic databases

    PaxDbi P0A9P0.
    PRIDEi P0A9P0.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai AAC73227 ; AAC73227 ; b0116 .
    BAB96686 ; BAB96686 ; BAB96686 .
    GeneIDi 12932376.
    944854.
    KEGGi ecj:Y75_p0113.
    eco:b0116.
    PATRICi 32115333. VBIEscCol129921_0118.

    Organism-specific databases

    EchoBASEi EB0538.
    EcoGenei EG10543. lpd.

    Phylogenomic databases

    eggNOGi COG1249.
    HOGENOMi HOG000276708.
    KOi K00382.
    OMAi IWNSTDA.
    OrthoDBi EOG6QCD6D.
    PhylomeDBi P0A9P0.

    Enzyme and pathway databases

    BioCyci EcoCyc:E3-MONOMER.
    ECOL316407:JW0112-MONOMER.
    MetaCyc:E3-MONOMER.
    SABIO-RK P0A9P0.

    Miscellaneous databases

    PROi P0A9P0.

    Gene expression databases

    Genevestigatori P0A9P0.

    Family and domain databases

    Gene3Di 3.30.390.30. 1 hit.
    InterProi IPR016156. FAD/NAD-linked_Rdtase_dimer.
    IPR013027. FAD_pyr_nucl-diS_OxRdtase.
    IPR006258. Lipoamide_DH.
    IPR004099. Pyr_nucl-diS_OxRdtase_dimer.
    IPR023753. Pyr_nucl-diS_OxRdtase_FAD/NAD.
    IPR012999. Pyr_OxRdtase_I_AS.
    IPR001327. Pyr_OxRdtase_NAD-bd_dom.
    [Graphical view ]
    Pfami PF00070. Pyr_redox. 1 hit.
    PF07992. Pyr_redox_2. 1 hit.
    PF02852. Pyr_redox_dim. 1 hit.
    [Graphical view ]
    PRINTSi PR00368. FADPNR.
    SUPFAMi SSF55424. SSF55424. 1 hit.
    TIGRFAMsi TIGR01350. lipoamide_DH. 1 hit.
    PROSITEi PS00076. PYRIDINE_REDOX_1. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "Nucleotide sequence of the lipoamide dehydrogenase gene of Escherichia coli K12."
      Stephens P.E., Lewis H.M., Darlison M.G., Guest J.R.
      Eur. J. Biochem. 135:519-527(1983) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    2. "Systematic sequencing of the Escherichia coli genome: analysis of the 2.4-4.1 min (110,917-193,643 bp) region."
      Fujita N., Mori H., Yura T., Ishihama A.
      Nucleic Acids Res. 22:1637-1639(1994) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
    3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / MG1655 / ATCC 47076.
    4. "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
      Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
      Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
    5. "Comparing the predicted and observed properties of proteins encoded in the genome of Escherichia coli K-12."
      Link A.J., Robison K., Church G.M.
      Electrophoresis 18:1259-1313(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: PROTEIN SEQUENCE OF 2-13.
      Strain: K12 / EMG2.
    6. "The lpd gene product functions as the L protein in the Escherichia coli glycine cleavage enzyme system."
      Steiert P.S., Stauffer L.T., Stauffer G.V.
      J. Bacteriol. 172:6142-6144(1990) [PubMed] [Europe PMC] [Abstract]
      Cited for: INVOLVEMENT IN GLYCINE CLEAVAGE SYSTEM.
    7. "Escherichia coli proteome analysis using the gene-protein database."
      VanBogelen R.A., Abshire K.Z., Moldover B., Olson E.R., Neidhardt F.C.
      Electrophoresis 18:1243-1251(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: IDENTIFICATION BY 2D-GEL.
    8. Cited for: SUBCELLULAR LOCATION.
      Strain: BL21-DE3.
    9. "Lysine acetylation is a highly abundant and evolutionarily conserved modification in Escherichia coli."
      Zhang J., Sprung R., Pei J., Tan X., Kim S., Zhu H., Liu C.F., Grishin N.V., Zhao Y.
      Mol. Cell. Proteomics 8:215-225(2009) [PubMed] [Europe PMC] [Abstract]
      Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT LYS-220, IDENTIFICATION BY MASS SPECTROMETRY.
      Strain: K12 / JW1106 and K12 / MG1655 / ATCC 47076.

    Entry informationi

    Entry nameiDLDH_ECOLI
    AccessioniPrimary (citable) accession number: P0A9P0
    Secondary accession number(s): P00391
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: July 21, 1986
    Last sequence update: January 23, 2007
    Last modified: October 1, 2014
    This is version 92 of the entry and version 2 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    The active site is a redox-active disulfide bond.

    Keywords - Technical termi

    3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

    Documents

    1. Escherichia coli
      Escherichia coli (strain K12): entries and cross-references to EcoGene
    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