DLDH_MYCTU
ID DLDH_MYCTU Reviewed; 464 AA.
AC P9WHH9; L0T3N4; O53747; P66004;
DT 16-APR-2014, integrated into UniProtKB/Swiss-Prot.
DT 16-APR-2014, sequence version 1.
DT 03-AUG-2022, entry version 52.
DE RecName: Full=Dihydrolipoyl dehydrogenase;
DE Short=LPD;
DE EC=1.8.1.4;
DE AltName: Full=Component of peroxynitrite reductase/peroxidase complex;
DE Short=Component of PNR/P;
DE AltName: Full=Dihydrolipoamide dehydrogenase;
DE AltName: Full=E3 component of alpha-ketoacid dehydrogenase complexes;
GN Name=lpdC; Synonyms=lpd; OrderedLocusNames=Rv0462; ORFNames=MTV038.06;
OS Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv).
OC Bacteria; Actinobacteria; Corynebacteriales; Mycobacteriaceae;
OC Mycobacterium; Mycobacterium tuberculosis complex.
OX NCBI_TaxID=83332;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 25618 / H37Rv;
RX PubMed=9634230; DOI=10.1038/31159;
RA Cole S.T., Brosch R., Parkhill J., Garnier T., Churcher C.M., Harris D.E.,
RA Gordon S.V., Eiglmeier K., Gas S., Barry C.E. III, Tekaia F., Badcock K.,
RA Basham D., Brown D., Chillingworth T., Connor R., Davies R.M., Devlin K.,
RA Feltwell T., Gentles S., Hamlin N., Holroyd S., Hornsby T., Jagels K.,
RA Krogh A., McLean J., Moule S., Murphy L.D., Oliver S., Osborne J.,
RA Quail M.A., Rajandream M.A., Rogers J., Rutter S., Seeger K., Skelton S.,
RA Squares S., Squares R., Sulston J.E., Taylor K., Whitehead S.,
RA Barrell B.G.;
RT "Deciphering the biology of Mycobacterium tuberculosis from the complete
RT genome sequence.";
RL Nature 393:537-544(1998).
RN [2]
RP FUNCTION, CATALYTIC ACTIVITY, SUBSTRATE SPECIFICITY, KINETIC PARAMETERS,
RP COFACTOR, GENE NAME, SUBUNIT, AND REACTION MECHANISM.
RC STRAIN=ATCC 25618 / H37Rv;
RX PubMed=11560483; DOI=10.1021/bi010575o;
RA Argyrou A., Blanchard J.S.;
RT "Mycobacterium tuberculosis lipoamide dehydrogenase is encoded by Rv0462
RT and not by the lpdA or lpdB genes.";
RL Biochemistry 40:11353-11363(2001).
RN [3]
RP FUNCTION AS AN ANTIOXIDANT, AND SUBUNIT.
RC STRAIN=ATCC 25618 / H37Rv;
RX PubMed=11799204; DOI=10.1126/science.1067798;
RA Bryk R., Lima C.D., Erdjument-Bromage H., Tempst P., Nathan C.;
RT "Metabolic enzymes of mycobacteria linked to antioxidant defense by a
RT thioredoxin-like protein.";
RL Science 295:1073-1077(2002).
RN [4]
RP FUNCTION AS A PDH COMPONENT, BIOPHYSICOCHEMICAL PROPERTIES, AND
RP IDENTIFICATION IN THE PDH COMPLEX.
RC STRAIN=ATCC 25618 / H37Rv;
RX PubMed=16045627; DOI=10.1111/j.1365-2958.2005.04741.x;
RA Tian J., Bryk R., Shi S., Erdjument-Bromage H., Tempst P., Nathan C.;
RT "Mycobacterium tuberculosis appears to lack alpha-ketoglutarate
RT dehydrogenase and encodes pyruvate dehydrogenase in widely separated
RT genes.";
RL Mol. Microbiol. 57:859-868(2005).
RN [5]
RP FUNCTION AS A BCKADH COMPONENT, ROLE IN VIRULENCE, DISRUPTION PHENOTYPE,
RP AND IDENTIFICATION IN THE BCKADH COMPLEX.
RC STRAIN=ATCC 25618 / H37Rv;
RX PubMed=21238944; DOI=10.1016/j.chom.2010.12.004;
RA Venugopal A., Bryk R., Shi S., Rhee K., Rath P., Schnappinger D., Ehrt S.,
RA Nathan C.;
RT "Virulence of Mycobacterium tuberculosis depends on lipoamide
RT dehydrogenase, a member of three multienzyme complexes.";
RL Cell Host Microbe 9:21-31(2011).
RN [6]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC STRAIN=ATCC 25618 / H37Rv;
RX PubMed=21969609; DOI=10.1074/mcp.m111.011627;
RA Kelkar D.S., Kumar D., Kumar P., Balakrishnan L., Muthusamy B., Yadav A.K.,
RA Shrivastava P., Marimuthu A., Anand S., Sundaram H., Kingsbury R.,
RA Harsha H.C., Nair B., Prasad T.S., Chauhan D.S., Katoch K., Katoch V.M.,
RA Kumar P., Chaerkady R., Ramachandran S., Dash D., Pandey A.;
RT "Proteogenomic analysis of Mycobacterium tuberculosis by high resolution
RT mass spectrometry.";
RL Mol. Cell. Proteomics 10:M111.011627-M111.011627(2011).
RN [7]
RP X-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS) IN COMPLEX WITH FAD, DISULFIDE BOND,
RP SUBUNIT, FUNCTION, AND MUTAGENESIS OF ASP-5; ASN-43; ARG-93; LYS-103;
RP HIS-386 AND PHE-464.
RX PubMed=16093239; DOI=10.1074/jbc.m507466200;
RA Rajashankar K.R., Bryk R., Kniewel R., Buglino J.A., Nathan C.F.,
RA Lima C.D.;
RT "Crystal structure and functional analysis of lipoamide dehydrogenase from
RT Mycobacterium tuberculosis.";
RL J. Biol. Chem. 280:33977-33983(2005).
RN [8]
RP X-RAY CRYSTALLOGRAPHY (2.42 ANGSTROMS) IN COMPLEX WITH INHIBITOR AND FAD,
RP ACTIVITY REGULATION, AND INHIBITORS.
RC STRAIN=ATCC 25618 / H37Rv;
RX PubMed=20078138; DOI=10.1021/bi9016186;
RA Bryk R., Arango N., Venugopal A., Warren J.D., Park Y.H., Patel M.S.,
RA Lima C.D., Nathan C.;
RT "Triazaspirodimethoxybenzoyls as selective inhibitors of mycobacterial
RT lipoamide dehydrogenase.";
RL Biochemistry 49:1616-1627(2010).
CC -!- FUNCTION: Lipoamide dehydrogenase is an essential component of the
CC alpha-ketoacid dehydrogenase complexes, namely the pyruvate
CC dehydrogenase (PDH) complex, the branched-chain alpha-ketoacid
CC dehydrogenase (BCKADH) complex, and likely also the 2-oxoglutarate
CC dehydrogenase (ODH) complex. Catalyzes the reoxidation of dihydrolipoyl
CC groups which are covalently attached to the lipoate acyltransferase
CC components (E2) of the complexes. Is also able to catalyze the
CC transhydrogenation of NADH and thio-NAD(+) in the absence of D,L-
CC lipoamide, and the NADH-dependent reduction of quinones in vitro.
CC -!- FUNCTION: Together with AhpC, AhpD and DlaT, Lpd constitutes an NADH-
CC dependent peroxidase active against hydrogen and alkyl peroxides as
CC well as serving as a peroxynitrite reductase, thus protecting the
CC bacterium against reactive nitrogen intermediates and oxidative stress
CC generated by the host immune system.
CC -!- FUNCTION: Appears to be essential for Mtb pathogenesis.
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 Evidence={ECO:0000269|PubMed:11560483};
CC -!- COFACTOR:
CC Name=FAD; Xref=ChEBI:CHEBI:57692;
CC Evidence={ECO:0000269|PubMed:11560483};
CC Note=Binds 1 FAD per subunit. {ECO:0000269|PubMed:11560483};
CC -!- ACTIVITY REGULATION: Triazaspirodimethoxybenzoyls are high-nanomolar
CC inhibitors of M.tuberculosis Lpd and are non-competitive versus NADH,
CC NAD(+), and lipoamide and >100-fold selective compared to human Lpd.
CC {ECO:0000269|PubMed:20078138}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=66 uM for NAD(+) {ECO:0000269|PubMed:11560483,
CC ECO:0000269|PubMed:16045627};
CC KM=7.3 uM for NADH {ECO:0000269|PubMed:11560483,
CC ECO:0000269|PubMed:16045627};
CC KM=110 uM for thio-NADH {ECO:0000269|PubMed:11560483,
CC ECO:0000269|PubMed:16045627};
CC KM=16 mM for D,L-lipoamide {ECO:0000269|PubMed:11560483,
CC ECO:0000269|PubMed:16045627};
CC KM=120 mM for D,L-lipoate {ECO:0000269|PubMed:11560483,
CC ECO:0000269|PubMed:16045627};
CC pH dependence:
CC Optimum pH is 8.0 for PDH complex activity. Half-maximal activity is
CC observed at pH 7.0 and pH 9.0. Activity is abolished at pH < 5.
CC {ECO:0000269|PubMed:16045627};
CC -!- SUBUNIT: Homodimer. Identified in a complex with AhpC, AhpD and DlaT.
CC Also is part of the PDH complex, consisting of multiple copies of AceE
CC (E1), DlaT (E2) and Lpd (E3), and of the BCKADH complex, consisting of
CC multiple copies of BkdA/BkdB (E1), BkdC (E2) and Lpd (E3).
CC {ECO:0000269|PubMed:11560483, ECO:0000269|PubMed:11799204,
CC ECO:0000269|PubMed:16045627, ECO:0000269|PubMed:16093239,
CC ECO:0000269|PubMed:20078138, ECO:0000269|PubMed:21238944}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000305}.
CC -!- DISRUPTION PHENOTYPE: Cells lacking this gene grow, albeit poorly, in
CC standard medium with dextrose, glycerol, and fatty acids as carbon
CC sources, but fail to grow on carbohydrates. They are less resistant
CC than wild-type to exposition to mildly acidified nitrite, but are more
CC resistant to oxidative stress in the form of H(2)O(2) in vitro. Lpd-
CC deficient strains are severely attenuated in wild-type and
CC immunodeficient mice. In contrast to wild-type or DlaT lacking strains,
CC strains lacking Lpd are unable to grow on leucine or isoleucine.
CC Disruption of this gene also leads to extraordinary accumulations of
CC pyruvate and branched chain amino and keto acids.
CC {ECO:0000269|PubMed:21238944}.
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}.
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DR EMBL; AL123456; CCP43195.1; -; Genomic_DNA.
DR PIR; B70828; B70828.
DR RefSeq; NP_214976.1; NC_000962.3.
DR RefSeq; WP_003402301.1; NZ_NVQJ01000002.1.
DR PDB; 2A8X; X-ray; 2.40 A; A/B=1-464.
DR PDB; 3II4; X-ray; 2.42 A; A/B=1-464.
DR PDB; 4M52; X-ray; 2.40 A; A/B/C/D=1-464.
DR PDB; 7KMY; X-ray; 2.21 A; A/B/C/D/I/J/M/N=1-464.
DR PDBsum; 2A8X; -.
DR PDBsum; 3II4; -.
DR PDBsum; 4M52; -.
DR PDBsum; 7KMY; -.
DR AlphaFoldDB; P9WHH9; -.
DR SMR; P9WHH9; -.
DR STRING; 83332.Rv0462; -.
DR BindingDB; P9WHH9; -.
DR ChEMBL; CHEMBL3988585; -.
DR PaxDb; P9WHH9; -.
DR DNASU; 886300; -.
DR GeneID; 45424424; -.
DR GeneID; 886300; -.
DR KEGG; mtu:Rv0462; -.
DR TubercuList; Rv0462; -.
DR eggNOG; COG1249; Bacteria.
DR OMA; DAKYGEW; -.
DR PhylomeDB; P9WHH9; -.
DR BRENDA; 1.8.1.4; 3445.
DR Reactome; R-HSA-1222541; Cell redox homeostasis.
DR Reactome; R-HSA-9636383; Prevention of phagosomal-lysosomal fusion.
DR SABIO-RK; P9WHH9; -.
DR PHI-base; PHI:7582; -.
DR Proteomes; UP000001584; Chromosome.
DR GO; GO:0005829; C:cytosol; HDA:MTBBASE.
DR GO; GO:0005576; C:extracellular region; IDA:CAFA.
DR GO; GO:0005886; C:plasma membrane; HDA:MTBBASE.
DR GO; GO:0045254; C:pyruvate dehydrogenase complex; IDA:MTBBASE.
DR GO; GO:0016209; F:antioxidant activity; IEA:UniProtKB-KW.
DR GO; GO:0004148; F:dihydrolipoyl dehydrogenase activity; IDA:MTBBASE.
DR GO; GO:0015036; F:disulfide oxidoreductase activity; IDA:MTBBASE.
DR GO; GO:0050660; F:flavin adenine dinucleotide binding; IDA:MTBBASE.
DR GO; GO:0070404; F:NADH binding; IDA:MTBBASE.
DR GO; GO:0016655; F:oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor; IDA:MTBBASE.
DR GO; GO:0035375; F:zymogen binding; IPI:CAFA.
DR GO; GO:0045454; P:cell redox homeostasis; IDA:MTBBASE.
DR GO; GO:0006096; P:glycolytic process; IEA:UniProtKB-KW.
DR GO; GO:0006099; P:tricarboxylic acid cycle; IEA:UniProtKB-KW.
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; Antioxidant; Cytoplasm; Disulfide bond; FAD; Flavoprotein;
KW Glycolysis; NAD; Oxidoreductase; Redox-active center; Reference proteome;
KW Tricarboxylic acid cycle; Virulence.
FT CHAIN 1..464
FT /note="Dihydrolipoyl dehydrogenase"
FT /id="PRO_0000068034"
FT ACT_SITE 443
FT /note="Proton acceptor"
FT /evidence="ECO:0000250"
FT BINDING 33..41
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000269|PubMed:16093239,
FT ECO:0000269|PubMed:20078138"
FT BINDING 50
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000269|PubMed:16093239,
FT ECO:0000269|PubMed:20078138"
FT BINDING 113
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000250"
FT BINDING 178..182
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000250"
FT BINDING 201
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000250"
FT BINDING 266..269
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000250"
FT BINDING 309
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000269|PubMed:16093239,
FT ECO:0000269|PubMed:20078138"
FT BINDING 317
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000269|PubMed:16093239,
FT ECO:0000269|PubMed:20078138"
FT DISULFID 41..46
FT /note="Redox-active"
FT /evidence="ECO:0000269|PubMed:16093239"
FT MUTAGEN 5
FT /note="D->A: Reduces lipoamide dehydrogenase activity by
FT 95%."
FT /evidence="ECO:0000269|PubMed:16093239"
FT MUTAGEN 43
FT /note="N->A: Reduces lipoamide dehydrogenase activity by
FT 89%."
FT /evidence="ECO:0000269|PubMed:16093239"
FT MUTAGEN 93
FT /note="R->A: Reduces lipoamide dehydrogenase activity by
FT 94%."
FT /evidence="ECO:0000269|PubMed:16093239"
FT MUTAGEN 93
FT /note="R->E: Reduces lipoamide dehydrogenase activity by
FT 96%."
FT /evidence="ECO:0000269|PubMed:16093239"
FT MUTAGEN 103
FT /note="K->E: Reduces lipoamide dehydrogenase activity by
FT 82%."
FT /evidence="ECO:0000269|PubMed:16093239"
FT MUTAGEN 386
FT /note="H->K: Reduces lipoamide dehydrogenase activity by
FT 91%."
FT /evidence="ECO:0000269|PubMed:16093239"
FT MUTAGEN 464
FT /note="F->A: Reduces lipoamide dehydrogenase activity by
FT 95%."
FT /evidence="ECO:0000269|PubMed:16093239"
FT STRAND 1..9
FT /evidence="ECO:0007829|PDB:7KMY"
FT HELIX 13..24
FT /evidence="ECO:0007829|PDB:7KMY"
FT STRAND 29..32
FT /evidence="ECO:0007829|PDB:7KMY"
FT HELIX 39..44
FT /evidence="ECO:0007829|PDB:7KMY"
FT HELIX 46..65
FT /evidence="ECO:0007829|PDB:7KMY"
FT TURN 66..70
FT /evidence="ECO:0007829|PDB:7KMY"
FT STRAND 71..73
FT /evidence="ECO:0007829|PDB:2A8X"
FT HELIX 79..103
FT /evidence="ECO:0007829|PDB:7KMY"
FT STRAND 107..109
FT /evidence="ECO:0007829|PDB:7KMY"
FT STRAND 111..117
FT /evidence="ECO:0007829|PDB:7KMY"
FT STRAND 120..125
FT /evidence="ECO:0007829|PDB:7KMY"
FT STRAND 130..140
FT /evidence="ECO:0007829|PDB:7KMY"
FT STRAND 144..146
FT /evidence="ECO:0007829|PDB:7KMY"
FT HELIX 161..165
FT /evidence="ECO:0007829|PDB:7KMY"
FT STRAND 172..177
FT /evidence="ECO:0007829|PDB:7KMY"
FT HELIX 181..192
FT /evidence="ECO:0007829|PDB:7KMY"
FT STRAND 196..200
FT /evidence="ECO:0007829|PDB:7KMY"
FT STRAND 202..207
FT /evidence="ECO:0007829|PDB:7KMY"
FT HELIX 212..225
FT /evidence="ECO:0007829|PDB:7KMY"
FT STRAND 228..230
FT /evidence="ECO:0007829|PDB:7KMY"
FT STRAND 234..240
FT /evidence="ECO:0007829|PDB:7KMY"
FT STRAND 245..251
FT /evidence="ECO:0007829|PDB:7KMY"
FT STRAND 254..265
FT /evidence="ECO:0007829|PDB:7KMY"
FT STRAND 269..271
FT /evidence="ECO:0007829|PDB:7KMY"
FT STRAND 274..276
FT /evidence="ECO:0007829|PDB:7KMY"
FT HELIX 278..281
FT /evidence="ECO:0007829|PDB:7KMY"
FT STRAND 289..291
FT /evidence="ECO:0007829|PDB:7KMY"
FT STRAND 304..306
FT /evidence="ECO:0007829|PDB:7KMY"
FT HELIX 308..311
FT /evidence="ECO:0007829|PDB:7KMY"
FT HELIX 317..331
FT /evidence="ECO:0007829|PDB:7KMY"
FT HELIX 342..344
FT /evidence="ECO:0007829|PDB:7KMY"
FT STRAND 345..349
FT /evidence="ECO:0007829|PDB:7KMY"
FT STRAND 351..359
FT /evidence="ECO:0007829|PDB:7KMY"
FT HELIX 362..367
FT /evidence="ECO:0007829|PDB:7KMY"
FT STRAND 372..378
FT /evidence="ECO:0007829|PDB:7KMY"
FT HELIX 379..381
FT /evidence="ECO:0007829|PDB:7KMY"
FT HELIX 383..388
FT /evidence="ECO:0007829|PDB:7KMY"
FT STRAND 394..400
FT /evidence="ECO:0007829|PDB:7KMY"
FT TURN 401..403
FT /evidence="ECO:0007829|PDB:7KMY"
FT STRAND 406..413
FT /evidence="ECO:0007829|PDB:7KMY"
FT HELIX 416..419
FT /evidence="ECO:0007829|PDB:7KMY"
FT HELIX 421..428
FT /evidence="ECO:0007829|PDB:7KMY"
FT HELIX 433..436
FT /evidence="ECO:0007829|PDB:7KMY"
FT HELIX 448..458
FT /evidence="ECO:0007829|PDB:7KMY"
SQ SEQUENCE 464 AA; 49239 MW; DD93D95DC6F76B22 CRC64;
MTHYDVVVLG AGPGGYVAAI RAAQLGLSTA IVEPKYWGGV CLNVGCIPSK ALLRNAELVH
IFTKDAKAFG ISGEVTFDYG IAYDRSRKVA EGRVAGVHFL MKKNKITEIH GYGTFADANT
LLVDLNDGGT ESVTFDNAII ATGSSTRLVP GTSLSANVVT YEEQILSREL PKSIIIAGAG
AIGMEFGYVL KNYGVDVTIV EFLPRALPNE DADVSKEIEK QFKKLGVTIL TATKVESIAD
GGSQVTVTVT KDGVAQELKA EKVLQAIGFA PNVEGYGLDK AGVALTDRKA IGVDDYMRTN
VGHIYAIGDV NGLLQLAHVA EAQGVVAAET IAGAETLTLG DHRMLPRATF CQPNVASFGL
TEQQARNEGY DVVVAKFPFT ANAKAHGVGD PSGFVKLVAD AKHGELLGGH LVGHDVAELL
PELTLAQRWD LTASELARNV HTHPTMSEAL QECFHGLVGH MINF
