Dihydrolipoyl dehydrogenase - Escherichia coli (strain K12)

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P0A9P0 (DLDH_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Last modified May 1, 2013. Version 81. History...

Clusters with 100%, 90%, 50% identity |

Documents (2) |

Third-party data

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Names·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents Customize order

Names and origin

Protein names

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 names

Name:	lpdA
Synonyms:	lpd
Ordered Locus Names:	b0116, JW0112

Organism

Escherichia coli (strain K12) [Reference proteome] [HAMAP]

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia ›

Protein attributes

Sequence length	474 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence 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 process	Glycolysis
Cellular component	Cell inner membrane Cell membrane Cytoplasm Membrane
Domain	Redox-active center
Ligand	FAD Flavoprotein NAD
Molecular function	Oxidoreductase
PTM	Acetylation Disulfide bond
Technical term	Complete proteome Direct protein sequencing Reference proteome
Gene Ontology (GO)
Biological_process	2-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 glycolysis Inferred from electronic annotation. Source: UniProtKB-KW pyruvate metabolic process Inferred from direct assay PubMed 6311808. Source: EcoliWiki
Cellular_component	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_function	dihydrolipoyl 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 zinc ion binding Inferred from direct assay PubMed 11985624. Source: EcoliWiki
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct
itself		2	EBI-542856,EBI-542856
aceF	P06959	2	EBI-542856,EBI-542707
uvrD	P03018	2	EBI-542856,EBI-559573

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Initiator methionine

Removed Ref.5

Chain

2 – 474

473

Dihydrolipoyl dehydrogenase

PRO_0000068027

Regions

Nucleotide binding

36 – 45

FAD By similarity

Nucleotide binding

182 – 186

NAD By similarity

Nucleotide binding

270 – 273

NAD By similarity

Sites

Active site

445

Proton acceptor By similarity

Binding site

FAD By similarity

Binding site

117

FAD; via amide nitrogen and carbonyl oxygen By similarity

Binding site

205

NAD By similarity

Binding site

238

NAD; via amide nitrogen By similarity

Binding site

313

FAD By similarity

Binding site

321

FAD; via amide nitrogen By similarity

Amino acid modifications

Modified residue

220

N6-acetyllysine Ref.9

Disulfide bond

45 ↔ 50

Redox-active By similarity

Sequences

Sequence

Length

Mass (Da)

Tools

P0A9P0 [UniParc].

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

474

50,688

        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' referencesShow '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 277:1453-1474(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, 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.
PIR	DEECLP. S45195.
RefSeq	NP_414658.1. NC_000913.2. YP_488419.1. NC_007779.1.
3D structure databases
ProteinModelPortal	P0A9P0.
SMR	P0A9P0. Positions 19-470.
ModBase	Search...
Protein-protein interaction databases
IntAct	P0A9P0. 90 interactions.
MINT	MINT-1242510.
STRING	511145.b0116.
2D gel databases
SWISS-2DPAGE	P0A9P0.
Proteomic databases
PaxDb	P0A9P0.
PRIDE	P0A9P0.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblBacteria	AAC73227; AAC73227; b0116. BAB96686; BAB96686; BAB96686.
GeneID	12932376. 944854.
KEGG	ecj:Y75_p0113. eco:b0116.
PATRIC	32115333. VBIEscCol129921_0118.
Organism-specific databases
EchoBASE	EB0538.
EcoGene	EG10543. lpd.
Phylogenomic databases
eggNOG	COG1249.
HOGENOM	HOG000276708.
KO	K00382.
OMA	EVAHGTC.
ProtClustDB	PRK06467.
Enzyme and pathway databases
BioCyc	EcoCyc:E3-MONOMER. ECOL316407:JW0112-MONOMER. MetaCyc:E3-MONOMER.
SABIO-RK	P0A9P0.
Gene expression databases
Genevestigator	P0A9P0.
Family and domain databases
Gene3D	3.30.390.30. 1 hit.
InterPro	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]
PANTHER	PTHR22912:SF20. PTHR22912:SF20. 1 hit.
Pfam	PF00070. Pyr_redox. 1 hit. PF07992. Pyr_redox_2. 1 hit. PF02852. Pyr_redox_dim. 1 hit. [Graphical view]
PRINTS	PR00368. FADPNR.
SUPFAM	SSF55424. FAD/NAD-linked_reductase_dimer. 1 hit.
TIGRFAMs	TIGR01350. lipoamide_DH. 1 hit.
PROSITE	PS00076. PYRIDINE_REDOX_1. 1 hit. [Graphical view]
ProtoNet	Search...

Entry information

Entry name

DLDH_ECOLI

Accession

Primary (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:	May 1, 2013
This is version 81 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program

Relevant documents

Escherichia coli

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

SIMILARITY comments

Index of protein domains and families

Names·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents

Preferred order of sections

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Binary interactions

With

Entry

#Exp.

IntAct

Notes

Sequence annotation (Features)

Molecule processing

Regions

Sites

Amino acid modifications

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

2D gel databases

Proteomic databases

Protocols and materials databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Enzyme and pathway databases

Gene expression databases

Family and domain databases

Entry information

Relevant documents