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Protein

Dihydrolipoyl dehydrogenase

Gene

lpdA

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: 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

FADBy similarityNote: Binds 1 FAD per subunit.By similarity

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei54FADBy similarity1
Binding sitei117FAD; via amide nitrogen and carbonyl oxygenBy similarity1
Binding sitei205NADBy similarity1
Binding sitei238NAD; via amide nitrogenBy similarity1
Binding sitei313FADBy similarity1
Binding sitei321FAD; via amide nitrogenBy similarity1
Active sitei445Proton acceptorBy similarity1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi36 – 45FADBy similarity10
Nucleotide bindingi182 – 186NADBy similarity5
Nucleotide bindingi270 – 273NADBy similarity4

GO - Molecular functioni

  • dihydrolipoyl dehydrogenase activity Source: EcoliWiki
  • disulfide oxidoreductase activity Source: EcoliWiki
  • flavin adenine dinucleotide binding Source: EcoliWiki
  • zinc ion binding Source: EcoliWiki

GO - Biological processi

  • 2-oxoglutarate metabolic process Source: EcoliWiki
  • cell redox homeostasis Source: InterPro
  • glycine decarboxylation via glycine cleavage system Source: EcoCyc
  • glycolytic process Source: UniProtKB-KW
  • oxidation-reduction process Source: EcoliWiki
  • pyruvate metabolic process Source: EcoliWiki
  • response to oxidative stress Source: EcoCyc
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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG10543. lpd.

Subcellular locationi

GO - Cellular componenti

  • cytoplasm Source: EcoliWiki
  • cytosol Source: UniProtKB
  • membrane Source: UniProtKB
  • 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)DescriptionActionsGraphical viewLength
Initiator methionineiRemoved1 Publication
ChainiPRO_00000680272 – 474Dihydrolipoyl dehydrogenaseAdd BLAST473

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Disulfide bondi45 ↔ 50Redox-activeBy similarity
Modified residuei220N6-acetyllysine1 Publication1

Keywords - PTMi

Acetylation, Disulfide bond

Proteomic databases

EPDiP0A9P0.
PaxDbiP0A9P0.
PRIDEiP0A9P0.

2D gel databases

SWISS-2DPAGEP0A9P0.

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

BioGridi4261370. 34 interactors.
DIPiDIP-6854N.
IntActiP0A9P0. 90 interactors.
MINTiMINT-1242510.
STRINGi511145.b0116.

Structurei

Secondary structure

1474
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi3 – 12Combined sources10
Helixi16 – 27Combined sources12
Beta strandi32 – 42Combined sources11
Helixi43 – 47Combined sources5
Helixi50 – 68Combined sources19
Helixi69 – 72Combined sources4
Helixi83 – 107Combined sources25
Beta strandi111 – 121Combined sources11
Beta strandi124 – 128Combined sources5
Beta strandi134 – 143Combined sources10
Beta strandi147 – 149Combined sources3
Beta strandi153 – 155Combined sources3
Helixi165 – 169Combined sources5
Beta strandi176 – 181Combined sources6
Helixi185 – 196Combined sources12
Beta strandi200 – 211Combined sources12
Helixi216 – 226Combined sources11
Turni227 – 229Combined sources3
Beta strandi230 – 244Combined sources15
Beta strandi247 – 254Combined sources8
Beta strandi262 – 269Combined sources8
Beta strandi273 – 275Combined sources3
Helixi277 – 279Combined sources3
Helixi282 – 285Combined sources4
Beta strandi308 – 310Combined sources3
Helixi312 – 315Combined sources4
Helixi321 – 335Combined sources15
Beta strandi349 – 351Combined sources3
Beta strandi353 – 361Combined sources9
Helixi364 – 369Combined sources6
Beta strandi374 – 380Combined sources7
Helixi381 – 383Combined sources3
Helixi385 – 389Combined sources5
Beta strandi396 – 402Combined sources7
Turni403 – 405Combined sources3
Beta strandi407 – 415Combined sources9
Helixi418 – 421Combined sources4
Helixi422 – 430Combined sources9
Helixi435 – 440Combined sources6
Helixi450 – 459Combined sources10

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
4JDRX-ray2.50A/B1-474[»]
ProteinModelPortaliP0A9P0.
SMRiP0A9P0.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Keywords - Domaini

Redox-active center

Phylogenomic databases

eggNOGiENOG4107QN2. Bacteria.
COG1249. LUCA.
HOGENOMiHOG000276708.
InParanoidiP0A9P0.
KOiK00382.
OMAiCSDGMTK.
PhylomeDBiP0A9P0.

Family and domain databases

Gene3Di3.30.390.30. 1 hit.
3.50.50.60. 3 hits.
InterProiIPR023753. FAD/NAD-binding_dom.
IPR016156. FAD/NAD-linked_Rdtase_dimer.
IPR006258. Lipoamide_DH.
IPR004099. Pyr_nucl-diS_OxRdtase_dimer.
IPR012999. Pyr_OxRdtase_I_AS.
[Graphical view]
PfamiPF07992. Pyr_redox_2. 1 hit.
PF02852. Pyr_redox_dim. 1 hit.
[Graphical view]
SUPFAMiSSF51905. SSF51905. 1 hit.
SSF55424. 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

        10         20         30         40         50
MSTEIKTQVV VLGAGPAGYS AAFRCADLGL ETVIVERYNT LGGVCLNVGC
60 70 80 90 100
IPSKALLHVA KVIEEAKALA EHGIVFGEPK TDIDKIRTWK EKVINQLTGG
110 120 130 140 150
LAGMAKGRKV KVVNGLGKFT GANTLEVEGE NGKTVINFDN AIIAAGSRPI
160 170 180 190 200
QLPFIPHEDP RIWDSTDALE LKEVPERLLV MGGGIIGLEM GTVYHALGSQ
210 220 230 240 250
IDVVEMFDQV IPAADKDIVK VFTKRISKKF NLMLETKVTA VEAKEDGIYV
260 270 280 290 300
TMEGKKAPAE PQRYDAVLVA IGRVPNGKNL DAGKAGVEVD DRGFIRVDKQ
310 320 330 340 350
LRTNVPHIFA IGDIVGQPML AHKGVHEGHV AAEVIAGKKH YFDPKVIPSI
360 370 380 390 400
AYTEPEVAWV GLTEKEAKEK GISYETATFP WAASGRAIAS DCADGMTKLI
410 420 430 440 450
FDKESHRVIG GAIVGTNGGE LLGEIGLAIE MGCDAEDIAL TIHAHPTLHE
460 470
SVGLAAEVFE GSITDLPNPK AKKK
Length:474
Mass (Da):50,688
Last modified:January 23, 2007 - v2
Checksum:iED16149A3BDF333A
GO

Sequence cautioni

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

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
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.
WP_000102485.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC73227; AAC73227; b0116.
BAB96686; BAB96686; BAB96686.
GeneIDi944854.
KEGGiecj:JW0112.
eco:b0116.
PATRICi32115333. VBIEscCol129921_0118.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
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.
WP_000102485.1. NZ_LN832404.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
4JDRX-ray2.50A/B1-474[»]
ProteinModelPortaliP0A9P0.
SMRiP0A9P0.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4261370. 34 interactors.
DIPiDIP-6854N.
IntActiP0A9P0. 90 interactors.
MINTiMINT-1242510.
STRINGi511145.b0116.

2D gel databases

SWISS-2DPAGEP0A9P0.

Proteomic databases

EPDiP0A9P0.
PaxDbiP0A9P0.
PRIDEiP0A9P0.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC73227; AAC73227; b0116.
BAB96686; BAB96686; BAB96686.
GeneIDi944854.
KEGGiecj:JW0112.
eco:b0116.
PATRICi32115333. VBIEscCol129921_0118.

Organism-specific databases

EchoBASEiEB0538.
EcoGeneiEG10543. lpd.

Phylogenomic databases

eggNOGiENOG4107QN2. Bacteria.
COG1249. LUCA.
HOGENOMiHOG000276708.
InParanoidiP0A9P0.
KOiK00382.
OMAiCSDGMTK.
PhylomeDBiP0A9P0.

Enzyme and pathway databases

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

Miscellaneous databases

PROiP0A9P0.

Family and domain databases

Gene3Di3.30.390.30. 1 hit.
3.50.50.60. 3 hits.
InterProiIPR023753. FAD/NAD-binding_dom.
IPR016156. FAD/NAD-linked_Rdtase_dimer.
IPR006258. Lipoamide_DH.
IPR004099. Pyr_nucl-diS_OxRdtase_dimer.
IPR012999. Pyr_OxRdtase_I_AS.
[Graphical view]
PfamiPF07992. Pyr_redox_2. 1 hit.
PF02852. Pyr_redox_dim. 1 hit.
[Graphical view]
SUPFAMiSSF51905. SSF51905. 1 hit.
SSF55424. SSF55424. 1 hit.
TIGRFAMsiTIGR01350. lipoamide_DH. 1 hit.
PROSITEiPS00076. PYRIDINE_REDOX_1. 1 hit.
[Graphical view]
ProtoNetiSearch...

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: November 2, 2016
This is version 107 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

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.