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Dihydrolipoyl dehydrogenase (EC 1.8.1.4) (Dihydrolipoamide dehydrogenase) (E3 component of pyruvate and 2-oxoglutarate dehydrogenases complexes) (Glycine cleavage system L protein)

 DLDH_ECOLI              Reviewed;         474 AA.
P0A9P0; P00391;
21-JUL-1986, integrated into UniProtKB/Swiss-Prot.
23-JAN-2007, sequence version 2.
25-OCT-2017, entry version 117.
RecName: Full=Dihydrolipoyl dehydrogenase;
EC=1.8.1.4;
AltName: Full=Dihydrolipoamide dehydrogenase;
AltName: Full=E3 component of pyruvate and 2-oxoglutarate dehydrogenases complexes;
AltName: Full=Glycine cleavage system L protein;
Name=lpdA; Synonyms=lpd; OrderedLocusNames=b0116, JW0112;
Escherichia coli (strain K12).
Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
Enterobacteriaceae; Escherichia.
NCBI_TaxID=83333;
[1]
NUCLEOTIDE SEQUENCE [GENOMIC DNA].
PubMed=6352260; DOI=10.1111/j.1432-1033.1983.tb07683.x;
Stephens P.E., Lewis H.M., Darlison M.G., Guest J.R.;
"Nucleotide sequence of the lipoamide dehydrogenase gene of
Escherichia coli K12.";
Eur. J. Biochem. 135:519-527(1983).
[2]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
PubMed=8202364; DOI=10.1093/nar/22.9.1637;
Fujita N., Mori H., Yura T., Ishihama A.;
"Systematic sequencing of the Escherichia coli genome: analysis of the
2.4-4.1 min (110,917-193,643 bp) region.";
Nucleic Acids Res. 22:1637-1639(1994).
[3]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=K12 / MG1655 / ATCC 47076;
PubMed=9278503; DOI=10.1126/science.277.5331.1453;
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.;
"The complete genome sequence of Escherichia coli K-12.";
Science 277:1453-1462(1997).
[4]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
PubMed=16738553; DOI=10.1038/msb4100049;
Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
"Highly accurate genome sequences of Escherichia coli K-12 strains
MG1655 and W3110.";
Mol. Syst. Biol. 2:E1-E5(2006).
[5]
PROTEIN SEQUENCE OF 2-13.
STRAIN=K12 / EMG2;
PubMed=9298646; DOI=10.1002/elps.1150180807;
Link A.J., Robison K., Church G.M.;
"Comparing the predicted and observed properties of proteins encoded
in the genome of Escherichia coli K-12.";
Electrophoresis 18:1259-1313(1997).
[6]
INVOLVEMENT IN GLYCINE CLEAVAGE SYSTEM.
PubMed=2211531; DOI=10.1128/jb.172.10.6142-6144.1990;
Steiert P.S., Stauffer L.T., Stauffer G.V.;
"The lpd gene product functions as the L protein in the Escherichia
coli glycine cleavage enzyme system.";
J. Bacteriol. 172:6142-6144(1990).
[7]
IDENTIFICATION BY 2D-GEL.
PubMed=9298644; DOI=10.1002/elps.1150180805;
VanBogelen R.A., Abshire K.Z., Moldover B., Olson E.R.,
Neidhardt F.C.;
"Escherichia coli proteome analysis using the gene-protein database.";
Electrophoresis 18:1243-1251(1997).
[8]
SUBCELLULAR LOCATION.
STRAIN=BL21-DE3;
PubMed=16079137; DOI=10.1074/jbc.M506479200;
Stenberg F., Chovanec P., Maslen S.L., Robinson C.V., Ilag L.,
von Heijne G., Daley D.O.;
"Protein complexes of the Escherichia coli cell envelope.";
J. Biol. Chem. 280:34409-34419(2005).
[9]
ACETYLATION [LARGE SCALE ANALYSIS] AT LYS-220, AND IDENTIFICATION BY
MASS SPECTROMETRY.
STRAIN=K12 / JW1106, and K12 / MG1655 / ATCC 47076;
PubMed=18723842; DOI=10.1074/mcp.M800187-MCP200;
Zhang J., Sprung R., Pei J., Tan X., Kim S., Zhu H., Liu C.F.,
Grishin N.V., Zhao Y.;
"Lysine acetylation is a highly abundant and evolutionarily conserved
modification in Escherichia coli.";
Mol. Cell. Proteomics 8:215-225(2009).
-!- 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:
Name=FAD; Xref=ChEBI:CHEBI:57692; Evidence={ECO:0000250};
Note=Binds 1 FAD per subunit. {ECO:0000250};
-!- SUBUNIT: Homodimer.
-!- INTERACTION:
Self; NbExp=2; IntAct=EBI-542856, EBI-542856;
P06959:aceF; NbExp=3; IntAct=EBI-542856, EBI-542707;
P75989:bluR; NbExp=2; IntAct=EBI-542856, EBI-560582;
P39346:idnD; NbExp=2; IntAct=EBI-542856, EBI-552913;
P0AFG6:sucB; NbExp=3; IntAct=EBI-542856, EBI-558621;
P03018:uvrD; NbExp=3; IntAct=EBI-542856, EBI-559573;
P0AAR3:ybaK; NbExp=2; IntAct=EBI-542856, EBI-559987;
P77721:ydjF; NbExp=2; IntAct=EBI-542856, EBI-545197;
P52037:ygfF; NbExp=2; IntAct=EBI-542856, EBI-561028;
-!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:16079137}.
Cell inner membrane {ECO:0000269|PubMed:16079137}; Peripheral
membrane protein {ECO:0000269|PubMed:16079137}.
-!- MISCELLANEOUS: The active site is a redox-active disulfide bond.
-!- SIMILARITY: Belongs to the class-I pyridine nucleotide-disulfide
oxidoreductase family. {ECO:0000305}.
-!- SEQUENCE CAUTION:
Sequence=CAA24742.1; Type=Erroneous initiation; Evidence={ECO:0000305};
-----------------------------------------------------------------------
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EMBL; V01498; CAA24742.1; ALT_INIT; Genomic_DNA.
EMBL; U00096; AAC73227.1; -; Genomic_DNA.
EMBL; AP009048; BAB96686.2; -; Genomic_DNA.
PIR; S45195; DEECLP.
RefSeq; NP_414658.1; NC_000913.3.
RefSeq; WP_000102485.1; NZ_LN832404.1.
PDB; 4JDR; X-ray; 2.50 A; A/B=1-474.
PDBsum; 4JDR; -.
ProteinModelPortal; P0A9P0; -.
SMR; P0A9P0; -.
BioGrid; 4261370; 34.
DIP; DIP-6854N; -.
IntAct; P0A9P0; 92.
MINT; MINT-1242510; -.
STRING; 316385.ECDH10B_0096; -.
iPTMnet; P0A9P0; -.
SWISS-2DPAGE; P0A9P0; -.
PaxDb; P0A9P0; -.
PRIDE; P0A9P0; -.
EnsemblBacteria; AAC73227; AAC73227; b0116.
EnsemblBacteria; BAB96686; BAB96686; BAB96686.
GeneID; 944854; -.
KEGG; ecj:JW0112; -.
KEGG; eco:b0116; -.
PATRIC; fig|1411691.4.peg.2166; -.
EchoBASE; EB0538; -.
EcoGene; EG10543; lpd.
eggNOG; ENOG4107QN2; Bacteria.
eggNOG; COG1249; LUCA.
HOGENOM; HOG000276708; -.
InParanoid; P0A9P0; -.
KO; K00382; -.
PhylomeDB; P0A9P0; -.
BioCyc; EcoCyc:E3-MONOMER; -.
BioCyc; MetaCyc:E3-MONOMER; -.
SABIO-RK; P0A9P0; -.
PRO; PR:P0A9P0; -.
Proteomes; UP000000318; Chromosome.
Proteomes; UP000000625; Chromosome.
GO; GO:0005737; C:cytoplasm; IDA:EcoliWiki.
GO; GO:0005829; C:cytosol; IDA:UniProtKB.
GO; GO:0016020; C:membrane; IDA:UniProtKB.
GO; GO:0005886; C:plasma membrane; IEA:UniProtKB-SubCell.
GO; GO:0004148; F:dihydrolipoyl dehydrogenase activity; IDA:EcoliWiki.
GO; GO:0015036; F:disulfide oxidoreductase activity; IDA:EcoliWiki.
GO; GO:0009055; F:electron carrier activity; IEA:InterPro.
GO; GO:0050660; F:flavin adenine dinucleotide binding; IDA:EcoliWiki.
GO; GO:0042802; F:identical protein binding; IPI:IntAct.
GO; GO:0008270; F:zinc ion binding; IDA:EcoliWiki.
GO; GO:0006103; P:2-oxoglutarate metabolic process; IMP:EcoliWiki.
GO; GO:0045454; P:cell redox homeostasis; IEA:InterPro.
GO; GO:0019464; P:glycine decarboxylation via glycine cleavage system; IMP:EcoCyc.
GO; GO:0006096; P:glycolytic process; IEA:UniProtKB-KW.
GO; GO:0055114; P:oxidation-reduction process; IDA:EcoliWiki.
GO; GO:0006090; P:pyruvate metabolic process; IDA:EcoliWiki.
GO; GO:0006979; P:response to oxidative stress; IMP:EcoCyc.
Gene3D; 3.30.390.30; -; 1.
Gene3D; 3.50.50.60; -; 2.
InterPro; IPR036188; FAD/NAD-bd_sf.
InterPro; IPR023753; FAD/NAD-binding_dom.
InterPro; IPR016156; FAD/NAD-linked_Rdtase_dimer.
InterPro; IPR006258; Lipoamide_DH.
InterPro; IPR001100; Pyr_nuc-diS_OxRdtase.
InterPro; IPR004099; Pyr_nucl-diS_OxRdtase_dimer.
InterPro; IPR012999; Pyr_OxRdtase_I_AS.
Pfam; PF07992; Pyr_redox_2; 1.
Pfam; PF02852; Pyr_redox_dim; 1.
PIRSF; PIRSF000350; Mercury_reductase_MerA; 1.
SUPFAM; SSF51905; SSF51905; 1.
SUPFAM; SSF55424; SSF55424; 1.
TIGRFAMs; TIGR01350; lipoamide_DH; 1.
PROSITE; PS00076; PYRIDINE_REDOX_1; 1.
1: Evidence at protein level;
3D-structure; Acetylation; Cell inner membrane; Cell membrane;
Complete proteome; Cytoplasm; Direct protein sequencing;
Disulfide bond; FAD; Flavoprotein; Glycolysis; Membrane; NAD;
Oxidoreductase; Redox-active center; Reference proteome.
INIT_MET 1 1 Removed. {ECO:0000269|PubMed:9298646}.
CHAIN 2 474 Dihydrolipoyl dehydrogenase.
/FTId=PRO_0000068027.
NP_BIND 36 45 FAD. {ECO:0000250}.
NP_BIND 182 186 NAD. {ECO:0000250}.
NP_BIND 270 273 NAD. {ECO:0000250}.
ACT_SITE 445 445 Proton acceptor. {ECO:0000250}.
BINDING 54 54 FAD. {ECO:0000250}.
BINDING 117 117 FAD; via amide nitrogen and carbonyl
oxygen. {ECO:0000250}.
BINDING 205 205 NAD. {ECO:0000250}.
BINDING 238 238 NAD; via amide nitrogen. {ECO:0000250}.
BINDING 313 313 FAD. {ECO:0000250}.
BINDING 321 321 FAD; via amide nitrogen. {ECO:0000250}.
MOD_RES 220 220 N6-acetyllysine.
{ECO:0000269|PubMed:18723842}.
DISULFID 45 50 Redox-active. {ECO:0000250}.
STRAND 3 12 {ECO:0000244|PDB:4JDR}.
HELIX 16 27 {ECO:0000244|PDB:4JDR}.
STRAND 32 42 {ECO:0000244|PDB:4JDR}.
HELIX 43 47 {ECO:0000244|PDB:4JDR}.
HELIX 50 68 {ECO:0000244|PDB:4JDR}.
HELIX 69 72 {ECO:0000244|PDB:4JDR}.
HELIX 83 107 {ECO:0000244|PDB:4JDR}.
STRAND 111 121 {ECO:0000244|PDB:4JDR}.
STRAND 124 128 {ECO:0000244|PDB:4JDR}.
STRAND 134 143 {ECO:0000244|PDB:4JDR}.
STRAND 147 149 {ECO:0000244|PDB:4JDR}.
STRAND 153 155 {ECO:0000244|PDB:4JDR}.
HELIX 165 169 {ECO:0000244|PDB:4JDR}.
STRAND 176 181 {ECO:0000244|PDB:4JDR}.
HELIX 185 196 {ECO:0000244|PDB:4JDR}.
STRAND 200 211 {ECO:0000244|PDB:4JDR}.
HELIX 216 226 {ECO:0000244|PDB:4JDR}.
TURN 227 229 {ECO:0000244|PDB:4JDR}.
STRAND 230 244 {ECO:0000244|PDB:4JDR}.
STRAND 247 254 {ECO:0000244|PDB:4JDR}.
STRAND 262 269 {ECO:0000244|PDB:4JDR}.
STRAND 273 275 {ECO:0000244|PDB:4JDR}.
HELIX 277 279 {ECO:0000244|PDB:4JDR}.
HELIX 282 285 {ECO:0000244|PDB:4JDR}.
STRAND 308 310 {ECO:0000244|PDB:4JDR}.
HELIX 312 315 {ECO:0000244|PDB:4JDR}.
HELIX 321 335 {ECO:0000244|PDB:4JDR}.
STRAND 349 351 {ECO:0000244|PDB:4JDR}.
STRAND 353 361 {ECO:0000244|PDB:4JDR}.
HELIX 364 369 {ECO:0000244|PDB:4JDR}.
STRAND 374 380 {ECO:0000244|PDB:4JDR}.
HELIX 381 383 {ECO:0000244|PDB:4JDR}.
HELIX 385 389 {ECO:0000244|PDB:4JDR}.
STRAND 396 402 {ECO:0000244|PDB:4JDR}.
TURN 403 405 {ECO:0000244|PDB:4JDR}.
STRAND 407 415 {ECO:0000244|PDB:4JDR}.
HELIX 418 421 {ECO:0000244|PDB:4JDR}.
HELIX 422 430 {ECO:0000244|PDB:4JDR}.
HELIX 435 440 {ECO:0000244|PDB:4JDR}.
HELIX 450 459 {ECO:0000244|PDB:4JDR}.
SEQUENCE 474 AA; 50688 MW; ED16149A3BDF333A CRC64;
MSTEIKTQVV VLGAGPAGYS AAFRCADLGL ETVIVERYNT LGGVCLNVGC IPSKALLHVA
KVIEEAKALA EHGIVFGEPK TDIDKIRTWK EKVINQLTGG LAGMAKGRKV KVVNGLGKFT
GANTLEVEGE NGKTVINFDN AIIAAGSRPI QLPFIPHEDP RIWDSTDALE LKEVPERLLV
MGGGIIGLEM GTVYHALGSQ IDVVEMFDQV IPAADKDIVK VFTKRISKKF NLMLETKVTA
VEAKEDGIYV TMEGKKAPAE PQRYDAVLVA IGRVPNGKNL DAGKAGVEVD DRGFIRVDKQ
LRTNVPHIFA IGDIVGQPML AHKGVHEGHV AAEVIAGKKH YFDPKVIPSI AYTEPEVAWV
GLTEKEAKEK GISYETATFP WAASGRAIAS DCADGMTKLI FDKESHRVIG GAIVGTNGGE
LLGEIGLAIE MGCDAEDIAL TIHAHPTLHE SVGLAAEVFE GSITDLPNPK AKKK


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