DLDH_ECOLI
ID DLDH_ECOLI Reviewed; 474 AA.
AC P0A9P0; P00391;
DT 21-JUL-1986, integrated into UniProtKB/Swiss-Prot.
DT 23-JAN-2007, sequence version 2.
DT 03-AUG-2022, entry version 144.
DE RecName: Full=Dihydrolipoyl dehydrogenase;
DE EC=1.8.1.4;
DE AltName: Full=Dihydrolipoamide dehydrogenase;
DE AltName: Full=E3 component of pyruvate and 2-oxoglutarate dehydrogenases complexes;
DE AltName: Full=Glycine cleavage system L protein;
GN Name=lpdA; Synonyms=lpd; OrderedLocusNames=b0116, JW0112;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=6352260; DOI=10.1111/j.1432-1033.1983.tb07683.x;
RA Stephens P.E., Lewis H.M., Darlison M.G., Guest J.R.;
RT "Nucleotide sequence of the lipoamide dehydrogenase gene of Escherichia
RT coli K12.";
RL Eur. J. Biochem. 135:519-527(1983).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=8202364; DOI=10.1093/nar/22.9.1637;
RA Fujita N., Mori H., Yura T., Ishihama A.;
RT "Systematic sequencing of the Escherichia coli genome: analysis of the 2.4-
RT 4.1 min (110,917-193,643 bp) region.";
RL Nucleic Acids Res. 22:1637-1639(1994).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=9278503; DOI=10.1126/science.277.5331.1453;
RA Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
RA Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
RA Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B.,
RA Shao Y.;
RT "The complete genome sequence of Escherichia coli K-12.";
RL Science 277:1453-1462(1997).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=16738553; DOI=10.1038/msb4100049;
RA Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
RA Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
RT "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655
RT and W3110.";
RL Mol. Syst. Biol. 2:E1-E5(2006).
RN [5]
RP PROTEIN SEQUENCE OF 2-13.
RC STRAIN=K12 / EMG2;
RX PubMed=9298646; DOI=10.1002/elps.1150180807;
RA Link A.J., Robison K., Church G.M.;
RT "Comparing the predicted and observed properties of proteins encoded in the
RT genome of Escherichia coli K-12.";
RL Electrophoresis 18:1259-1313(1997).
RN [6]
RP INVOLVEMENT IN GLYCINE CLEAVAGE SYSTEM.
RX PubMed=2211531; DOI=10.1128/jb.172.10.6142-6144.1990;
RA Steiert P.S., Stauffer L.T., Stauffer G.V.;
RT "The lpd gene product functions as the L protein in the Escherichia coli
RT glycine cleavage enzyme system.";
RL J. Bacteriol. 172:6142-6144(1990).
RN [7]
RP IDENTIFICATION BY 2D-GEL.
RX PubMed=9298644; DOI=10.1002/elps.1150180805;
RA VanBogelen R.A., Abshire K.Z., Moldover B., Olson E.R., Neidhardt F.C.;
RT "Escherichia coli proteome analysis using the gene-protein database.";
RL Electrophoresis 18:1243-1251(1997).
RN [8]
RP SUBCELLULAR LOCATION.
RC STRAIN=BL21-DE3;
RX PubMed=16079137; DOI=10.1074/jbc.m506479200;
RA Stenberg F., Chovanec P., Maslen S.L., Robinson C.V., Ilag L.,
RA von Heijne G., Daley D.O.;
RT "Protein complexes of the Escherichia coli cell envelope.";
RL J. Biol. Chem. 280:34409-34419(2005).
RN [9]
RP ACETYLATION [LARGE SCALE ANALYSIS] AT LYS-220, AND IDENTIFICATION BY MASS
RP SPECTROMETRY.
RC STRAIN=K12 / JW1106, and K12 / MG1655 / ATCC 47076;
RX PubMed=18723842; DOI=10.1074/mcp.m800187-mcp200;
RA Zhang J., Sprung R., Pei J., Tan X., Kim S., Zhu H., Liu C.F.,
RA Grishin N.V., Zhao Y.;
RT "Lysine acetylation is a highly abundant and evolutionarily conserved
RT modification in Escherichia coli.";
RL Mol. Cell. Proteomics 8:215-225(2009).
CC -!- FUNCTION: Lipoamide dehydrogenase is a component of the glycine
CC cleavage system as well as of the alpha-ketoacid dehydrogenase
CC complexes.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=(R)-N(6)-dihydrolipoyl-L-lysyl-[protein] + NAD(+) = (R)-N(6)-
CC lipoyl-L-lysyl-[protein] + H(+) + NADH; Xref=Rhea:RHEA:15045,
CC Rhea:RHEA-COMP:10474, Rhea:RHEA-COMP:10475, ChEBI:CHEBI:15378,
CC ChEBI:CHEBI:57540, ChEBI:CHEBI:57945, ChEBI:CHEBI:83099,
CC ChEBI:CHEBI:83100; EC=1.8.1.4;
CC -!- COFACTOR:
CC Name=FAD; Xref=ChEBI:CHEBI:57692; Evidence={ECO:0000250};
CC Note=Binds 1 FAD per subunit. {ECO:0000250};
CC -!- SUBUNIT: Homodimer.
CC -!- INTERACTION:
CC P0A9P0; P06959: aceF; NbExp=3; IntAct=EBI-542856, EBI-542707;
CC P0A9P0; P75989: bluR; NbExp=2; IntAct=EBI-542856, EBI-560582;
CC P0A9P0; P39346: idnD; NbExp=2; IntAct=EBI-542856, EBI-552913;
CC P0A9P0; P0A9P0: lpdA; NbExp=2; IntAct=EBI-542856, EBI-542856;
CC P0A9P0; P0AFG6: sucB; NbExp=3; IntAct=EBI-542856, EBI-558621;
CC P0A9P0; P03018: uvrD; NbExp=3; IntAct=EBI-542856, EBI-559573;
CC P0A9P0; P0AAR3: ybaK; NbExp=2; IntAct=EBI-542856, EBI-559987;
CC P0A9P0; P77721: ydjF; NbExp=2; IntAct=EBI-542856, EBI-545197;
CC P0A9P0; P52037: ygfF; NbExp=2; IntAct=EBI-542856, EBI-561028;
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:16079137}. Cell
CC inner membrane {ECO:0000269|PubMed:16079137}; Peripheral membrane
CC protein {ECO:0000269|PubMed:16079137}.
CC -!- MISCELLANEOUS: The active site is a redox-active disulfide bond.
CC -!- SIMILARITY: Belongs to the class-I pyridine nucleotide-disulfide
CC oxidoreductase family. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=CAA24742.1; Type=Erroneous initiation; Evidence={ECO:0000305};
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DR EMBL; V01498; CAA24742.1; ALT_INIT; Genomic_DNA.
DR EMBL; U00096; AAC73227.1; -; Genomic_DNA.
DR EMBL; AP009048; BAB96686.2; -; Genomic_DNA.
DR PIR; S45195; DEECLP.
DR RefSeq; NP_414658.1; NC_000913.3.
DR RefSeq; WP_000102485.1; NZ_STEB01000010.1.
DR PDB; 4JDR; X-ray; 2.50 A; A/B=1-474.
DR PDBsum; 4JDR; -.
DR AlphaFoldDB; P0A9P0; -.
DR SMR; P0A9P0; -.
DR BioGRID; 4261370; 34.
DR BioGRID; 849254; 2.
DR ComplexPortal; CPX-3921; 2-oxoglutarate dehydrogenase complex.
DR ComplexPortal; CPX-3943; Pyruvate dehydrogenase complex.
DR ComplexPortal; CPX-3949; Glycine cleavage system complex.
DR DIP; DIP-6854N; -.
DR IntAct; P0A9P0; 92.
DR STRING; 511145.b0116; -.
DR iPTMnet; P0A9P0; -.
DR SWISS-2DPAGE; P0A9P0; -.
DR jPOST; P0A9P0; -.
DR PaxDb; P0A9P0; -.
DR PRIDE; P0A9P0; -.
DR EnsemblBacteria; AAC73227; AAC73227; b0116.
DR EnsemblBacteria; BAB96686; BAB96686; BAB96686.
DR GeneID; 66671596; -.
DR GeneID; 944854; -.
DR KEGG; ecj:JW0112; -.
DR KEGG; eco:b0116; -.
DR PATRIC; fig|1411691.4.peg.2166; -.
DR EchoBASE; EB0538; -.
DR eggNOG; COG1249; Bacteria.
DR HOGENOM; CLU_016755_0_3_6; -.
DR InParanoid; P0A9P0; -.
DR OMA; HMVGDRM; -.
DR PhylomeDB; P0A9P0; -.
DR BioCyc; EcoCyc:E3-MON; -.
DR BioCyc; MetaCyc:E3-MON; -.
DR BRENDA; 1.2.1.104; 2026.
DR BRENDA; 1.4.1.27; 2026.
DR BRENDA; 1.8.1.4; 2026.
DR SABIO-RK; P0A9P0; -.
DR PRO; PR:P0A9P0; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IDA:ComplexPortal.
DR GO; GO:0005829; C:cytosol; IDA:EcoCyc.
DR GO; GO:0045250; C:cytosolic pyruvate dehydrogenase complex; IDA:EcoCyc.
DR GO; GO:0005960; C:glycine cleavage complex; IC:ComplexPortal.
DR GO; GO:0016020; C:membrane; HDA:UniProtKB.
DR GO; GO:0045252; C:oxoglutarate dehydrogenase complex; IPI:ComplexPortal.
DR GO; GO:0005886; C:plasma membrane; IEA:UniProtKB-SubCell.
DR GO; GO:0045254; C:pyruvate dehydrogenase complex; IC:ComplexPortal.
DR GO; GO:0004148; F:dihydrolipoyl dehydrogenase activity; IDA:EcoCyc.
DR GO; GO:0015036; F:disulfide oxidoreductase activity; IDA:EcoliWiki.
DR GO; GO:0050660; F:flavin adenine dinucleotide binding; IDA:EcoliWiki.
DR GO; GO:0042802; F:identical protein binding; IPI:IntAct.
DR GO; GO:0008270; F:zinc ion binding; IDA:EcoliWiki.
DR GO; GO:0006103; P:2-oxoglutarate metabolic process; IMP:EcoliWiki.
DR GO; GO:0045454; P:cell redox homeostasis; IEA:InterPro.
DR GO; GO:0019464; P:glycine decarboxylation via glycine cleavage system; IMP:EcoCyc.
DR GO; GO:0006096; P:glycolytic process; IEA:UniProtKB-KW.
DR GO; GO:0006730; P:one-carbon metabolic process; IC:ComplexPortal.
DR GO; GO:0042867; P:pyruvate catabolic process; IC:ComplexPortal.
DR GO; GO:0006090; P:pyruvate metabolic process; IDA:EcoliWiki.
DR GO; GO:0006979; P:response to oxidative stress; IMP:EcoCyc.
DR GO; GO:0006099; P:tricarboxylic acid cycle; IDA:ComplexPortal.
DR Gene3D; 3.30.390.30; -; 1.
DR Gene3D; 3.50.50.60; -; 2.
DR InterPro; IPR036188; FAD/NAD-bd_sf.
DR InterPro; IPR023753; FAD/NAD-binding_dom.
DR InterPro; IPR016156; FAD/NAD-linked_Rdtase_dimer_sf.
DR InterPro; IPR006258; Lipoamide_DH.
DR InterPro; IPR001100; Pyr_nuc-diS_OxRdtase.
DR InterPro; IPR004099; Pyr_nucl-diS_OxRdtase_dimer.
DR InterPro; IPR012999; Pyr_OxRdtase_I_AS.
DR Pfam; PF07992; Pyr_redox_2; 1.
DR Pfam; PF02852; Pyr_redox_dim; 1.
DR PIRSF; PIRSF000350; Mercury_reductase_MerA; 1.
DR SUPFAM; SSF51905; SSF51905; 1.
DR SUPFAM; SSF55424; SSF55424; 1.
DR TIGRFAMs; TIGR01350; lipoamide_DH; 1.
DR PROSITE; PS00076; PYRIDINE_REDOX_1; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Acetylation; Cell inner membrane; Cell membrane; Cytoplasm;
KW Direct protein sequencing; Disulfide bond; FAD; Flavoprotein; Glycolysis;
KW Membrane; NAD; Oxidoreductase; Redox-active center; Reference proteome.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0000269|PubMed:9298646"
FT CHAIN 2..474
FT /note="Dihydrolipoyl dehydrogenase"
FT /id="PRO_0000068027"
FT ACT_SITE 445
FT /note="Proton acceptor"
FT /evidence="ECO:0000250"
FT BINDING 36..45
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000250"
FT BINDING 54
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000250"
FT BINDING 117
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000250"
FT BINDING 182..186
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000250"
FT BINDING 205
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000250"
FT BINDING 238
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000250"
FT BINDING 270..273
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000250"
FT BINDING 313
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000250"
FT BINDING 321
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000250"
FT MOD_RES 220
FT /note="N6-acetyllysine"
FT /evidence="ECO:0000269|PubMed:18723842"
FT DISULFID 45..50
FT /note="Redox-active"
FT /evidence="ECO:0000250"
FT STRAND 3..12
FT /evidence="ECO:0007829|PDB:4JDR"
FT HELIX 16..27
FT /evidence="ECO:0007829|PDB:4JDR"
FT STRAND 32..42
FT /evidence="ECO:0007829|PDB:4JDR"
FT HELIX 43..47
FT /evidence="ECO:0007829|PDB:4JDR"
FT HELIX 50..68
FT /evidence="ECO:0007829|PDB:4JDR"
FT HELIX 69..72
FT /evidence="ECO:0007829|PDB:4JDR"
FT HELIX 83..107
FT /evidence="ECO:0007829|PDB:4JDR"
FT STRAND 111..121
FT /evidence="ECO:0007829|PDB:4JDR"
FT STRAND 124..128
FT /evidence="ECO:0007829|PDB:4JDR"
FT STRAND 134..143
FT /evidence="ECO:0007829|PDB:4JDR"
FT STRAND 147..149
FT /evidence="ECO:0007829|PDB:4JDR"
FT STRAND 153..155
FT /evidence="ECO:0007829|PDB:4JDR"
FT HELIX 165..169
FT /evidence="ECO:0007829|PDB:4JDR"
FT STRAND 176..181
FT /evidence="ECO:0007829|PDB:4JDR"
FT HELIX 185..196
FT /evidence="ECO:0007829|PDB:4JDR"
FT STRAND 200..211
FT /evidence="ECO:0007829|PDB:4JDR"
FT HELIX 216..226
FT /evidence="ECO:0007829|PDB:4JDR"
FT TURN 227..229
FT /evidence="ECO:0007829|PDB:4JDR"
FT STRAND 230..244
FT /evidence="ECO:0007829|PDB:4JDR"
FT STRAND 247..254
FT /evidence="ECO:0007829|PDB:4JDR"
FT STRAND 262..269
FT /evidence="ECO:0007829|PDB:4JDR"
FT STRAND 273..275
FT /evidence="ECO:0007829|PDB:4JDR"
FT HELIX 277..279
FT /evidence="ECO:0007829|PDB:4JDR"
FT HELIX 282..285
FT /evidence="ECO:0007829|PDB:4JDR"
FT STRAND 308..310
FT /evidence="ECO:0007829|PDB:4JDR"
FT HELIX 312..315
FT /evidence="ECO:0007829|PDB:4JDR"
FT HELIX 321..335
FT /evidence="ECO:0007829|PDB:4JDR"
FT STRAND 349..351
FT /evidence="ECO:0007829|PDB:4JDR"
FT STRAND 353..361
FT /evidence="ECO:0007829|PDB:4JDR"
FT HELIX 364..369
FT /evidence="ECO:0007829|PDB:4JDR"
FT STRAND 374..380
FT /evidence="ECO:0007829|PDB:4JDR"
FT HELIX 381..383
FT /evidence="ECO:0007829|PDB:4JDR"
FT HELIX 385..389
FT /evidence="ECO:0007829|PDB:4JDR"
FT STRAND 396..402
FT /evidence="ECO:0007829|PDB:4JDR"
FT TURN 403..405
FT /evidence="ECO:0007829|PDB:4JDR"
FT STRAND 407..415
FT /evidence="ECO:0007829|PDB:4JDR"
FT HELIX 418..421
FT /evidence="ECO:0007829|PDB:4JDR"
FT HELIX 422..430
FT /evidence="ECO:0007829|PDB:4JDR"
FT HELIX 435..440
FT /evidence="ECO:0007829|PDB:4JDR"
FT HELIX 450..459
FT /evidence="ECO:0007829|PDB:4JDR"
SQ 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
