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P0A9P0 (DLDH_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Last modified June 11, 2014. Version 91. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (3) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended 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 names
Name:lpdA
Synonyms:lpd
Ordered Locus Names:b0116, JW0112
OrganismEscherichia coli (strain K12) [Reference proteome] [HAMAP]
Taxonomic identifier83333 [NCBI]
Taxonomic lineageBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia

Protein attributes

Sequence length474 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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

Catalytic activity

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

Cofactor

Binds 1 FAD per subunit By similarity.

Subunit structure

Homodimer.

Subcellular location

Cytoplasm. Cell inner membrane; Peripheral membrane protein Ref.8.

Miscellaneous

The active site is a redox-active disulfide bond.

Sequence similarities

Belongs to the class-I pyridine nucleotide-disulfide oxidoreductase family.

Sequence caution

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

Ontologies

Keywords
   Biological processGlycolysis
   Cellular componentCell inner membrane
Cell membrane
Cytoplasm
Membrane
   DomainRedox-active center
   LigandFAD
Flavoprotein
NAD
   Molecular functionOxidoreductase
   PTMAcetylation
Disulfide bond
   Technical term3D-structure
Complete proteome
Direct protein sequencing
Reference proteome
Gene Ontology (GO)
   Biological_process2-oxoglutarate metabolic process

Inferred from mutant phenotype PubMed 4197899. Source: EcoliWiki

cell redox homeostasis

Inferred from electronic annotation. Source: InterPro

glycine decarboxylation via glycine cleavage system

Inferred from mutant phenotype Ref.6. Source: EcoCyc

glycolytic process

Inferred from electronic annotation. Source: UniProtKB-KW

oxidation-reduction process

Inferred from direct assay PubMed 3066354. Source: EcoliWiki

pyruvate metabolic process

Inferred from direct assay PubMed 6311808. Source: EcoliWiki

   Cellular_componentcytoplasm

Inferred from direct assay PubMed 4863745. Source: EcoliWiki

cytosol

Inferred from direct assay PubMed 16858726. Source: UniProtKB

membrane

Inferred from direct assay PubMed 16858726. Source: UniProtKB

plasma membrane

Inferred from electronic annotation. Source: UniProtKB-SubCell

   Molecular_functiondihydrolipoyl dehydrogenase activity

Inferred from direct assay PubMed 3066354. Source: EcoliWiki

disulfide oxidoreductase activity

Inferred from direct assay PubMed 4863745. Source: EcoliWiki

flavin adenine dinucleotide binding

Inferred from direct assay PubMed 4863745. Source: EcoliWiki

identical protein binding

Inferred from physical interaction PubMed 16858726. Source: IntAct

protein binding

Inferred from physical interaction PubMed 15690043PubMed 16606699PubMed 16858726PubMed 24561554. Source: IntAct

zinc ion binding

Inferred from direct assay PubMed 11985624. Source: EcoliWiki

Complete GO annotation...

Binary interactions

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Initiator methionine11Removed Ref.5
Chain2 – 474473Dihydrolipoyl dehydrogenase
PRO_0000068027

Regions

Nucleotide binding36 – 4510FAD By similarity
Nucleotide binding182 – 1865NAD By similarity
Nucleotide binding270 – 2734NAD By similarity

Sites

Active site4451Proton acceptor By similarity
Binding site541FAD By similarity
Binding site1171FAD; via amide nitrogen and carbonyl oxygen By similarity
Binding site2051NAD By similarity
Binding site2381NAD; via amide nitrogen By similarity
Binding site3131FAD By similarity
Binding site3211FAD; via amide nitrogen By similarity

Amino acid modifications

Modified residue2201N6-acetyllysine Ref.9
Disulfide bond45 ↔ 50Redox-active By similarity

Secondary structure

.......................................................................... 474
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P0A9P0 [UniParc].

Last modified January 23, 2007. Version 2.
Checksum: ED16149A3BDF333A

FASTA47450,688
        10         20         30         40         50         60 
MSTEIKTQVV VLGAGPAGYS AAFRCADLGL ETVIVERYNT LGGVCLNVGC IPSKALLHVA 

        70         80         90        100        110        120 
KVIEEAKALA EHGIVFGEPK TDIDKIRTWK EKVINQLTGG LAGMAKGRKV KVVNGLGKFT 

       130        140        150        160        170        180 
GANTLEVEGE NGKTVINFDN AIIAAGSRPI QLPFIPHEDP RIWDSTDALE LKEVPERLLV 

       190        200        210        220        230        240 
MGGGIIGLEM GTVYHALGSQ IDVVEMFDQV IPAADKDIVK VFTKRISKKF NLMLETKVTA 

       250        260        270        280        290        300 
VEAKEDGIYV TMEGKKAPAE PQRYDAVLVA IGRVPNGKNL DAGKAGVEVD DRGFIRVDKQ 

       310        320        330        340        350        360 
LRTNVPHIFA IGDIVGQPML AHKGVHEGHV AAEVIAGKKH YFDPKVIPSI AYTEPEVAWV 

       370        380        390        400        410        420 
GLTEKEAKEK GISYETATFP WAASGRAIAS DCADGMTKLI FDKESHRVIG GAIVGTNGGE 

       430        440        450        460        470 
LLGEIGLAIE MGCDAEDIAL TIHAHPTLHE SVGLAAEVFE GSITDLPNPK AKKK 

« Hide

References

« Hide 'large scale' references
[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]"The complete genome sequence of Escherichia coli K-12."
Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V., Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B., Shao Y.
Science 277:1453-1462(1997) [PubMed] [Europe PMC] [Abstract]
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]"Protein complexes of the Escherichia coli cell envelope."
Stenberg F., Chovanec P., Maslen S.L., Robinson C.V., Ilag L., von Heijne G., Daley D.O.
J. Biol. Chem. 280:34409-34419(2005) [PubMed] [Europe PMC] [Abstract]
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.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
V01498 Genomic DNA. Translation: CAA24742.1. Different initiation.
U00096 Genomic DNA. Translation: AAC73227.1.
AP009048 Genomic DNA. Translation: BAB96686.2.
PIRDEECLP. S45195.
RefSeqNP_414658.1. NC_000913.3.
YP_488419.1. NC_007779.1.

3D structure databases

PDBe
RCSB-PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
4JDRX-ray2.50A/B1-474[»]
ProteinModelPortalP0A9P0.
SMRP0A9P0. Positions 2-472.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

DIPDIP-6854N.
IntActP0A9P0. 90 interactions.
MINTMINT-1242510.
STRING511145.b0116.

2D gel databases

SWISS-2DPAGEP0A9P0.

Proteomic databases

PaxDbP0A9P0.
PRIDEP0A9P0.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaAAC73227; AAC73227; b0116.
BAB96686; BAB96686; BAB96686.
GeneID12932376.
944854.
KEGGecj:Y75_p0113.
eco:b0116.
PATRIC32115333. VBIEscCol129921_0118.

Organism-specific databases

EchoBASEEB0538.
EcoGeneEG10543. lpd.

Phylogenomic databases

eggNOGCOG1249.
HOGENOMHOG000276708.
KOK00382.
OMAIWNSTDA.
OrthoDBEOG6QCD6D.
PhylomeDBP0A9P0.

Enzyme and pathway databases

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

Gene expression databases

GenevestigatorP0A9P0.

Family and domain databases

Gene3D3.30.390.30. 1 hit.
InterProIPR016156. 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]
PfamPF00070. Pyr_redox. 1 hit.
PF07992. Pyr_redox_2. 1 hit.
PF02852. Pyr_redox_dim. 1 hit.
[Graphical view]
PRINTSPR00368. FADPNR.
SUPFAMSSF55424. SSF55424. 1 hit.
TIGRFAMsTIGR01350. lipoamide_DH. 1 hit.
PROSITEPS00076. PYRIDINE_REDOX_1. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

PROP0A9P0.

Entry information

Entry nameDLDH_ECOLI
AccessionPrimary (citable) accession number: P0A9P0
Secondary accession number(s): P00391
Entry history
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 statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

Escherichia coli

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