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P0A9P0

- DLDH_ECOLI

UniProt

P0A9P0 - DLDH_ECOLI

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Protein

Dihydrolipoyl dehydrogenase

Gene
lpdA, lpd, b0116, JW0112
Organism
Escherichia coli (strain K12)
Status
Reviewed - Annotation score: 5 out of 5 - Experimental evidence at protein leveli

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 – 541FAD By similarity
Binding sitei117 – 1171FAD; via amide nitrogen and carbonyl oxygen By similarity
Binding sitei205 – 2051NAD By similarity
Binding sitei238 – 2381NAD; via amide nitrogen By similarity
Binding sitei313 – 3131FAD By similarity
Binding sitei321 – 3211FAD; via amide nitrogen By similarity
Active sitei445 – 4451Proton acceptor By similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi36 – 4510FAD By similarity
Nucleotide bindingi182 – 1865NAD By similarity
Nucleotide bindingi270 – 2734NAD By 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
Complete GO annotation...

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. Cell inner membrane; 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
Complete GO annotation...

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-active By 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.

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

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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

« Hide 'large scale' publications
  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: June 11, 2014
This is version 91 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

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