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Dihydrolipoyl dehydrogenase (LPD) (EC 1.8.1.4) (Component of peroxynitrite reductase/peroxidase complex) (Component of PNR/P) (Dihydrolipoamide dehydrogenase) (E3 component of alpha-ketoacid dehydrogenase complexes)

 DLDH_MYCTU              Reviewed;         464 AA.
P9WHH9; L0T3N4; O53747; P66004;
16-APR-2014, integrated into UniProtKB/Swiss-Prot.
16-APR-2014, sequence version 1.
25-OCT-2017, entry version 28.
RecName: Full=Dihydrolipoyl dehydrogenase;
Short=LPD;
EC=1.8.1.4;
AltName: Full=Component of peroxynitrite reductase/peroxidase complex;
Short=Component of PNR/P;
AltName: Full=Dihydrolipoamide dehydrogenase;
AltName: Full=E3 component of alpha-ketoacid dehydrogenase complexes;
Name=lpdC; Synonyms=lpd; OrderedLocusNames=Rv0462; ORFNames=MTV038.06;
Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv).
Bacteria; Actinobacteria; Corynebacteriales; Mycobacteriaceae;
Mycobacterium; Mycobacterium tuberculosis complex.
NCBI_TaxID=83332;
[1]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=ATCC 25618 / H37Rv;
PubMed=9634230; DOI=10.1038/31159;
Cole S.T., Brosch R., Parkhill J., Garnier T., Churcher C.M.,
Harris D.E., Gordon S.V., Eiglmeier K., Gas S., Barry C.E. III,
Tekaia F., Badcock K., Basham D., Brown D., Chillingworth T.,
Connor R., Davies R.M., Devlin K., Feltwell T., Gentles S., Hamlin N.,
Holroyd S., Hornsby T., Jagels K., Krogh A., McLean J., Moule S.,
Murphy L.D., Oliver S., Osborne J., Quail M.A., Rajandream M.A.,
Rogers J., Rutter S., Seeger K., Skelton S., Squares S., Squares R.,
Sulston J.E., Taylor K., Whitehead S., Barrell B.G.;
"Deciphering the biology of Mycobacterium tuberculosis from the
complete genome sequence.";
Nature 393:537-544(1998).
[2]
FUNCTION, CATALYTIC ACTIVITY, SUBSTRATE SPECIFICITY, KINETIC
PARAMETERS, COFACTOR, GENE NAME, SUBUNIT, AND REACTION MECHANISM.
STRAIN=ATCC 25618 / H37Rv;
PubMed=11560483; DOI=10.1021/bi010575o;
Argyrou A., Blanchard J.S.;
"Mycobacterium tuberculosis lipoamide dehydrogenase is encoded by
Rv0462 and not by the lpdA or lpdB genes.";
Biochemistry 40:11353-11363(2001).
[3]
FUNCTION AS AN ANTIOXIDANT, AND SUBUNIT.
STRAIN=ATCC 25618 / H37Rv;
PubMed=11799204; DOI=10.1126/science.1067798;
Bryk R., Lima C.D., Erdjument-Bromage H., Tempst P., Nathan C.;
"Metabolic enzymes of mycobacteria linked to antioxidant defense by a
thioredoxin-like protein.";
Science 295:1073-1077(2002).
[4]
FUNCTION AS A PDH COMPONENT, BIOPHYSICOCHEMICAL PROPERTIES, AND
IDENTIFICATION IN THE PDH COMPLEX.
STRAIN=ATCC 25618 / H37Rv;
PubMed=16045627; DOI=10.1111/j.1365-2958.2005.04741.x;
Tian J., Bryk R., Shi S., Erdjument-Bromage H., Tempst P., Nathan C.;
"Mycobacterium tuberculosis appears to lack alpha-ketoglutarate
dehydrogenase and encodes pyruvate dehydrogenase in widely separated
genes.";
Mol. Microbiol. 57:859-868(2005).
[5]
FUNCTION AS A BCKADH COMPONENT, ROLE IN VIRULENCE, DISRUPTION
PHENOTYPE, AND IDENTIFICATION IN THE BCKADH COMPLEX.
STRAIN=ATCC 25618 / H37Rv;
PubMed=21238944; DOI=10.1016/j.chom.2010.12.004;
Venugopal A., Bryk R., Shi S., Rhee K., Rath P., Schnappinger D.,
Ehrt S., Nathan C.;
"Virulence of Mycobacterium tuberculosis depends on lipoamide
dehydrogenase, a member of three multienzyme complexes.";
Cell Host Microbe 9:21-31(2011).
[6]
IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
STRAIN=ATCC 25618 / H37Rv;
PubMed=21969609; DOI=10.1074/mcp.M111.011627;
Kelkar D.S., Kumar D., Kumar P., Balakrishnan L., Muthusamy B.,
Yadav A.K., Shrivastava P., Marimuthu A., Anand S., Sundaram H.,
Kingsbury R., Harsha H.C., Nair B., Prasad T.S., Chauhan D.S.,
Katoch K., Katoch V.M., Kumar P., Chaerkady R., Ramachandran S.,
Dash D., Pandey A.;
"Proteogenomic analysis of Mycobacterium tuberculosis by high
resolution mass spectrometry.";
Mol. Cell. Proteomics 10:M111.011627-M111.011627(2011).
[7]
X-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS) IN COMPLEX WITH FAD, DISULFIDE
BOND, SUBUNIT, FUNCTION, AND MUTAGENESIS OF ASP-5; ASN-43; ARG-93;
LYS-103; HIS-386 AND PHE-464.
PubMed=16093239; DOI=10.1074/jbc.M507466200;
Rajashankar K.R., Bryk R., Kniewel R., Buglino J.A., Nathan C.F.,
Lima C.D.;
"Crystal structure and functional analysis of lipoamide dehydrogenase
from Mycobacterium tuberculosis.";
J. Biol. Chem. 280:33977-33983(2005).
[8]
X-RAY CRYSTALLOGRAPHY (2.42 ANGSTROMS) IN COMPLEX WITH INHIBITOR AND
FAD, ENZYME REGULATION, AND INHIBITORS.
STRAIN=ATCC 25618 / H37Rv;
PubMed=20078138; DOI=10.1021/bi9016186;
Bryk R., Arango N., Venugopal A., Warren J.D., Park Y.H., Patel M.S.,
Lima C.D., Nathan C.;
"Triazaspirodimethoxybenzoyls as selective inhibitors of mycobacterial
lipoamide dehydrogenase.";
Biochemistry 49:1616-1627(2010).
-!- FUNCTION: Lipoamide dehydrogenase is an essential component of the
alpha-ketoacid dehydrogenase complexes, namely the pyruvate
dehydrogenase (PDH) complex, the branched-chain alpha-ketoacid
dehydrogenase (BCKADH) complex, and likely also the 2-oxoglutarate
dehydrogenase (ODH) complex. Catalyzes the reoxidation of
dihydrolipoyl groups which are covalently attached to the lipoate
acyltransferase components (E2) of the complexes. Is also able to
catalyze the transhydrogenation of NADH and thio-NAD(+) in the
absence of D,L-lipoamide, and the NADH-dependent reduction of
quinones in vitro.
-!- FUNCTION: Together with AhpC, AhpD and DlaT, Lpd constitutes an
NADH-dependent peroxidase active against hydrogen and alkyl
peroxides as well as serving as a peroxynitrite reductase, thus
protecting the bacterium against reactive nitrogen intermediates
and oxidative stress generated by the host immune system.
-!- FUNCTION: Appears to be essential for Mtb pathogenesis.
-!- CATALYTIC ACTIVITY: Protein N(6)-(dihydrolipoyl)lysine + NAD(+) =
protein N(6)-(lipoyl)lysine + NADH. {ECO:0000269|PubMed:11560483}.
-!- COFACTOR:
Name=FAD; Xref=ChEBI:CHEBI:57692;
Evidence={ECO:0000269|PubMed:11560483};
Note=Binds 1 FAD per subunit. {ECO:0000269|PubMed:11560483};
-!- ENZYME REGULATION: Triazaspirodimethoxybenzoyls are high-nanomolar
inhibitors of M.tuberculosis Lpd and are non-competitive versus
NADH, NAD(+), and lipoamide and >100-fold selective compared to
human Lpd. {ECO:0000269|PubMed:20078138}.
-!- BIOPHYSICOCHEMICAL PROPERTIES:
Kinetic parameters:
KM=66 uM for NAD(+) {ECO:0000269|PubMed:11560483,
ECO:0000269|PubMed:16045627};
KM=7.3 uM for NADH {ECO:0000269|PubMed:11560483,
ECO:0000269|PubMed:16045627};
KM=110 uM for thio-NADH {ECO:0000269|PubMed:11560483,
ECO:0000269|PubMed:16045627};
KM=16 mM for D,L-lipoamide {ECO:0000269|PubMed:11560483,
ECO:0000269|PubMed:16045627};
KM=120 mM for D,L-lipoate {ECO:0000269|PubMed:11560483,
ECO:0000269|PubMed:16045627};
pH dependence:
Optimum pH is 8.0 for PDH complex activity. Half-maximal
activity is observed at pH 7.0 and pH 9.0. Activity is abolished
at pH < 5. {ECO:0000269|PubMed:16045627};
-!- SUBUNIT: Homodimer. Identified in a complex with AhpC, AhpD and
DlaT. Also is part of the PDH complex, consisting of multiple
copies of AceE (E1), DlaT (E2) and Lpd (E3), and of the BCKADH
complex, consisting of multiple copies of BkdA/BkdB (E1), BkdC
(E2) and Lpd (E3). {ECO:0000269|PubMed:11560483,
ECO:0000269|PubMed:11799204, ECO:0000269|PubMed:16045627,
ECO:0000269|PubMed:16093239, ECO:0000269|PubMed:20078138,
ECO:0000269|PubMed:21238944}.
-!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000305}.
-!- DISRUPTION PHENOTYPE: Cells lacking this gene grow, albeit poorly,
in standard medium with dextrose, glycerol, and fatty acids as
carbon sources, but fail to grow on carbohydrates. They are less
resistant than wild-type to exposition to mildly acidified
nitrite, but are more resistant to oxidative stress in the form of
H(2)O(2) in vitro. Lpd-deficient strains are severely attenuated
in wild-type and immunodeficient mice. In contrast to wild-type or
DlaT lacking strains, strains lacking Lpd are unable to grow on
leucine or isoleucine. Disruption of this gene also leads to
extraordinary accumulations of pyruvate and branched chain amino
and keto acids. {ECO:0000269|PubMed:21238944}.
-!- MISCELLANEOUS: The active site is a redox-active disulfide bond.
-!- SIMILARITY: Belongs to the class-I pyridine nucleotide-disulfide
oxidoreductase family. {ECO:0000305}.
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EMBL; AL123456; CCP43195.1; -; Genomic_DNA.
PIR; B70828; B70828.
RefSeq; NP_214976.1; NC_000962.3.
RefSeq; WP_003402301.1; NZ_KK339370.1.
PDB; 2A8X; X-ray; 2.40 A; A/B=1-464.
PDB; 3II4; X-ray; 2.42 A; A/B=1-464.
PDB; 4M52; X-ray; 2.40 A; A/B/C/D=1-464.
PDBsum; 2A8X; -.
PDBsum; 3II4; -.
PDBsum; 4M52; -.
ProteinModelPortal; P9WHH9; -.
SMR; P9WHH9; -.
STRING; 83332.Rv0462; -.
BindingDB; P9WHH9; -.
PaxDb; P9WHH9; -.
EnsemblBacteria; CCP43195; CCP43195; Rv0462.
GeneID; 886300; -.
KEGG; mtu:Rv0462; -.
TubercuList; Rv0462; -.
eggNOG; ENOG4107QN2; Bacteria.
eggNOG; COG1249; LUCA.
KO; K00382; -.
OMA; TMSEAVM; -.
PhylomeDB; P9WHH9; -.
Reactome; R-HSA-1222541; Cell redox homeostasis.
Proteomes; UP000001584; Chromosome.
GO; GO:0005829; C:cytosol; IDA:MTBBASE.
GO; GO:0005576; C:extracellular region; IDA:MTBBASE.
GO; GO:0005886; C:plasma membrane; IDA:MTBBASE.
GO; GO:0045254; C:pyruvate dehydrogenase complex; IDA:MTBBASE.
GO; GO:0016209; F:antioxidant activity; IEA:UniProtKB-KW.
GO; GO:0004148; F:dihydrolipoyl dehydrogenase activity; IDA:MTBBASE.
GO; GO:0015036; F:disulfide oxidoreductase activity; IDA:MTBBASE.
GO; GO:0009055; F:electron carrier activity; IEA:InterPro.
GO; GO:0050660; F:flavin adenine dinucleotide binding; IDA:MTBBASE.
GO; GO:0070404; F:NADH binding; IDA:MTBBASE.
GO; GO:0016655; F:oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor; IDA:MTBBASE.
GO; GO:0035375; F:zymogen binding; IPI:CAFA.
GO; GO:0045454; P:cell redox homeostasis; IDA:MTBBASE.
GO; GO:0006096; P:glycolytic process; IEA:UniProtKB-KW.
GO; GO:0040007; P:growth; IMP:MTBBASE.
GO; GO:0055114; P:oxidation-reduction process; IDA:MTBBASE.
GO; GO:0009405; P:pathogenesis; IEA:UniProtKB-KW.
GO; GO:0006099; P:tricarboxylic acid cycle; IEA:UniProtKB-KW.
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; Antioxidant; Complete proteome; Cytoplasm;
Disulfide bond; FAD; Flavoprotein; Glycolysis; NAD; Oxidoreductase;
Redox-active center; Reference proteome; Tricarboxylic acid cycle;
Virulence.
CHAIN 1 464 Dihydrolipoyl dehydrogenase.
/FTId=PRO_0000068034.
NP_BIND 33 41 FAD. {ECO:0000269|PubMed:16093239,
ECO:0000269|PubMed:20078138}.
NP_BIND 178 182 NAD. {ECO:0000250}.
NP_BIND 266 269 NAD. {ECO:0000250}.
ACT_SITE 443 443 Proton acceptor. {ECO:0000250}.
BINDING 50 50 FAD. {ECO:0000269|PubMed:16093239,
ECO:0000269|PubMed:20078138}.
BINDING 113 113 FAD; via amide nitrogen and carbonyl
oxygen. {ECO:0000250}.
BINDING 201 201 NAD. {ECO:0000250}.
BINDING 309 309 FAD. {ECO:0000269|PubMed:16093239,
ECO:0000269|PubMed:20078138}.
BINDING 317 317 FAD; via amide nitrogen.
{ECO:0000269|PubMed:16093239,
ECO:0000269|PubMed:20078138}.
DISULFID 41 46 Redox-active.
{ECO:0000269|PubMed:16093239}.
MUTAGEN 5 5 D->A: Reduces lipoamide dehydrogenase
activity by 95%.
{ECO:0000269|PubMed:16093239}.
MUTAGEN 43 43 N->A: Reduces lipoamide dehydrogenase
activity by 89%.
{ECO:0000269|PubMed:16093239}.
MUTAGEN 93 93 R->A: Reduces lipoamide dehydrogenase
activity by 94%.
{ECO:0000269|PubMed:16093239}.
MUTAGEN 93 93 R->E: Reduces lipoamide dehydrogenase
activity by 96%.
{ECO:0000269|PubMed:16093239}.
MUTAGEN 103 103 K->E: Reduces lipoamide dehydrogenase
activity by 82%.
{ECO:0000269|PubMed:16093239}.
MUTAGEN 386 386 H->K: Reduces lipoamide dehydrogenase
activity by 91%.
{ECO:0000269|PubMed:16093239}.
MUTAGEN 464 464 F->A: Reduces lipoamide dehydrogenase
activity by 95%.
{ECO:0000269|PubMed:16093239}.
STRAND 2 9 {ECO:0000244|PDB:2A8X}.
HELIX 13 24 {ECO:0000244|PDB:2A8X}.
STRAND 29 32 {ECO:0000244|PDB:2A8X}.
HELIX 39 44 {ECO:0000244|PDB:2A8X}.
HELIX 46 65 {ECO:0000244|PDB:2A8X}.
TURN 66 70 {ECO:0000244|PDB:2A8X}.
STRAND 71 73 {ECO:0000244|PDB:2A8X}.
HELIX 79 103 {ECO:0000244|PDB:2A8X}.
STRAND 107 109 {ECO:0000244|PDB:2A8X}.
STRAND 111 125 {ECO:0000244|PDB:2A8X}.
STRAND 131 140 {ECO:0000244|PDB:2A8X}.
STRAND 144 146 {ECO:0000244|PDB:2A8X}.
HELIX 161 165 {ECO:0000244|PDB:2A8X}.
STRAND 172 177 {ECO:0000244|PDB:2A8X}.
HELIX 181 192 {ECO:0000244|PDB:2A8X}.
STRAND 196 200 {ECO:0000244|PDB:2A8X}.
STRAND 202 207 {ECO:0000244|PDB:2A8X}.
HELIX 212 225 {ECO:0000244|PDB:2A8X}.
STRAND 228 230 {ECO:0000244|PDB:2A8X}.
STRAND 234 240 {ECO:0000244|PDB:2A8X}.
STRAND 245 253 {ECO:0000244|PDB:2A8X}.
STRAND 255 265 {ECO:0000244|PDB:2A8X}.
STRAND 269 271 {ECO:0000244|PDB:2A8X}.
STRAND 274 276 {ECO:0000244|PDB:2A8X}.
HELIX 278 281 {ECO:0000244|PDB:2A8X}.
STRAND 289 291 {ECO:0000244|PDB:2A8X}.
STRAND 304 306 {ECO:0000244|PDB:2A8X}.
HELIX 308 311 {ECO:0000244|PDB:2A8X}.
HELIX 317 332 {ECO:0000244|PDB:2A8X}.
HELIX 342 344 {ECO:0000244|PDB:2A8X}.
STRAND 347 349 {ECO:0000244|PDB:2A8X}.
STRAND 351 359 {ECO:0000244|PDB:2A8X}.
HELIX 362 367 {ECO:0000244|PDB:2A8X}.
STRAND 372 378 {ECO:0000244|PDB:2A8X}.
HELIX 379 381 {ECO:0000244|PDB:2A8X}.
HELIX 383 388 {ECO:0000244|PDB:2A8X}.
STRAND 394 400 {ECO:0000244|PDB:2A8X}.
TURN 401 404 {ECO:0000244|PDB:2A8X}.
STRAND 405 413 {ECO:0000244|PDB:2A8X}.
HELIX 416 419 {ECO:0000244|PDB:2A8X}.
HELIX 420 428 {ECO:0000244|PDB:2A8X}.
HELIX 433 436 {ECO:0000244|PDB:2A8X}.
HELIX 448 458 {ECO:0000244|PDB:2A8X}.
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


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San Jose, CA 95123
CA 95123
Tel (408) 780-0908,
Fax (408) 780-0908,
sales@genprice.com

Genprice Inc, Invoices and accounting
6017 Snell Ave, Ste 357
San Jose, CA 95123




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