Reviewed, UniProtKB/Swiss-Prot P0A9P0 (DLDH_ECOLI)

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) [Complete 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.7
Miscellaneous	The active site is a redox-active disulfide bond.
Sequence similarities	Belongs to the class-I pyridine nucleotide-disulfide oxidoreductase family.

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
Gene Ontology (GO)
Biological process	cell redox homeostasis Inferred from electronic annotation. Source: InterPro glycolysis Inferred from electronic annotation. Source: UniProtKB-KW oxidation reduction Inferred from electronic annotation. Source: UniProtKB-KW
Cellular component	cytosol Inferred from direct assay. Source: UniProtKB plasma membrane Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular function	FAD binding Inferred from electronic annotation. Source: InterPro dihydrolipoyl dehydrogenase activity Inferred from electronic annotation. Source: EC protein binding Inferred from physical interaction. Source: IntAct
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
idnD	P39346	1	EBI-542856,EBI-552913
uvrD	P03018	1	EBI-542856,EBI-559573
ybaK	P0AAR3	1	EBI-542856,EBI-559987
ycgE	P75989	1	EBI-542856,EBI-560582
ydjF	P77721	1	EBI-542856,EBI-545197
ygfF	P52037	1	EBI-542856,EBI-561028

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Initiator methionine	1	1	Removed Ref.5
	Chain	2 – 474	473	Dihydrolipoyl dehydrogenase		PRO_0000068027
Regions
	Nucleotide binding	36 – 45	10	FAD By similarity
	Nucleotide binding	182 – 186	5	NAD By similarity
	Nucleotide binding	270 – 273	4	NAD By similarity
Sites
	Active site	445	1	Proton acceptor By similarity
	Binding site	54	1	FAD By similarity
	Binding site	117	1	FAD; via amide nitrogen and carbonyl oxygen By similarity
	Binding site	205	1	NAD By similarity
	Binding site	238	1	NAD; via amide nitrogen By similarity
	Binding site	313	1	FAD By similarity
	Binding site	321	1	FAD; via amide nitrogen By similarity
Amino acid modifications
	Modified residue	220	1	N6-acetyllysine Ref.8
	Disulfide bond	45 ↔ 50		Redox-active By similarity

Sequences

	Sequence		Length	Mass (Da)
	P0A9P0-1 [UniParc]. Last modified January 23, 2007. Version 2. Checksum: ED16149A3BDF333A	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

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: 6352260] [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: 8202364] [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: 9278503] [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: 16738553] [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: 9298646] [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: 2211531] [Abstract] Cited for: INVOLVEMENT IN GLYCINE CLEAVAGE SYSTEM.
[7]	"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: 16079137] [Abstract] Cited for: SUBCELLULAR LOCATION. Strain: BL21-DE3.
[8]	"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: 18723842] [Abstract] Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT LYS-220, MASS SPECTROMETRY.

Cross-references

Sequence databases
EMBLGenBankDDBJ	V01498 Genomic DNA. Translation: CAA24742.1. Different initiation. U00096 Genomic DNA. Translation: AAC73227.1. AP009048 Genomic DNA. Translation: BAB96686.2.
PIR	DEECLP. S45195.
RefSeq	AP_000777.1. NP_414658.1.
3D structure databases
HSSP	HSSP built from PDB template 1OJT based on UniProtKB Q51225.
ModBase	Search...
Protein-protein interaction databases
IntAct	P0A9P0. 90 interactions.
2-D gel databases
SWISS-2DPAGE	P0A9P0.
2DBase-Ecoli	P0A9P0.
ECO2DBASE	G050.5. 6TH EDITION.
Genome annotation databases
GeneID	944854.
GenomeReviews	Gene locus JW0112 in contig AP009048_GR. Gene locus b0116 in contig U00096_GR.
KEGG	ecj:JW0112. eco:b0116.
Organism-specific databases
EchoBASE	EB0538.
EcoGene	EG10543. lpd.
CMR	Search...
Phylogenomic databases
HOGENOM	P0A9P0.
OMA	P0A9P0. MMDGLMA.
Enzyme and pathway databases
BioCyc	EcoCyc:E3-MON. MetaCyc:E3-MON.
Family and domain databases
InterPro	IPR013027. FAD_pyr_nucl-diS_OxRdtase. IPR000815. Hg_reductase. IPR006258. Lipoamide_DH. IPR004099. Pyr_nucl-diS_OxRdtase_dimer. IPR012999. Pyr_OxRdtase_I_AS. IPR001327. Pyr_OxRdtase_NAD_bd. [Graphical view]
Gene3D	G3DSA:3.30.390.30. Pyr_redox_dim. 1 hit.
PANTHER	PTHR22912:SF20. Lipoamide_DH. 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. PR00945. HGRDTASE.
ProDom	PD000139. FAD_pyr_redox. 1 hit. [Graphical view] [Entries sharing at least one domain]
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:	June 16, 2009
This is version 44 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

HAMAP (High-quality Automated and Manual Annotation of microbial Proteomes)