SitesBLAST
Comparing SMc01035 SMc01035 dihydrolipoamide dehydrogenase to proteins with known functional sites using BLASTp with E ≤ 0.001.
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Found 20 (the maximum) hits to proteins with known functional sites (download)
3ii4A Structure of mycobacterial lipoamide dehydrogenase bound to a triazaspirodimethoxybenzoyl inhibitor (see paper)
42% identity, 99% coverage: 4:480/481 of query aligns to 2:462/463 of 3ii4A
- active site: W36 (≠ L38), C40 (= C42), C45 (= C47), S48 (≠ T50), A180 (= A198), E184 (= E202), H440 (≠ F458), H442 (= H460), E447 (= E465)
- binding N-[2-(2,4-dichlorophenyl)ethyl]-2-{8-[(2,4-dimethoxyphenyl)carbonyl]-4-oxo-1-phenyl-1,3,8-triazaspiro[4.5]dec-3-yl}acetamide: R146 (= R163), A180 (= A198), I181 (= I199), E184 (= E202), N208 (≠ V226), E209 (= E227), F268 (≠ V287), R287 (= R305), G311 (= G329), Q314 (≠ M332), L315 (= L333), R346 (≠ G364), A347 (≠ C365)
- binding flavin-adenine dinucleotide: L8 (≠ V10), G9 (= G11), G11 (= G13), P12 (= P14), G13 (= G15), V31 (= V33), E32 (= E34), P33 (≠ R35), Y35 (≠ H37), G38 (= G40), V39 (≠ I41), C40 (= C42), G44 (= G46), C45 (= C47), K49 (= K51), Y111 (≠ E114), G112 (≠ A115), A140 (= A157), T141 (= T158), G142 (= G159), Y160 (= Y178), I181 (= I199), Y275 (≠ L294), G307 (= G325), D308 (= D326), Q314 (≠ M332), L315 (= L333), A316 (= A334)
8u0qA Co-crystal structure of optimized analog tdi-13537 provided new insights into the potency determinants of the sulfonamide inhibitor series (see paper)
42% identity, 99% coverage: 4:480/481 of query aligns to 3:463/464 of 8u0qA
- binding flavin-adenine dinucleotide: L9 (≠ V10), G10 (= G11), G12 (= G13), P13 (= P14), G14 (= G15), V32 (= V33), E33 (= E34), P34 (≠ R35), Y36 (≠ H37), G39 (= G40), V40 (≠ I41), C41 (= C42), G45 (= G46), C46 (= C47), K50 (= K51), Y112 (≠ E114), G113 (≠ A115), A141 (= A157), T142 (= T158), G143 (= G159), Y161 (= Y178), I182 (= I199), Y276 (≠ L294), G308 (= G325), D309 (= D326), Q315 (≠ M332), L316 (= L333), A317 (= A334), H318 (= H335)
- binding N-(3-acetamidophenyl)-N~2~-[3-(difluoromethyl)-5-methylbenzene-1-sulfonyl]-N~2~-methylglycinamide: Y16 (= Y17), R93 (≠ L95), G96 (= G98), F99 (= F101), E321 (= E338), A381 (= A398), A383 (≠ G400), H443 (= H460), E448 (= E465), N463 (= N480)
Sites not aligning to the query:
8ct4A Cryo-em structure of mtb lpd bound to inhibitor complex with 2-((2- cyano-n,5-dimethyl-1h-indole)-7-sulfonamido)-n-(4-(oxetan-3-yl)-3,4- dihydro-2h-benzo[b] [1,4]oxazin-7-yl)acetamide
42% identity, 99% coverage: 4:480/481 of query aligns to 3:463/464 of 8ct4A
- binding flavin-adenine dinucleotide: L9 (≠ V10), G10 (= G11), G12 (= G13), P13 (= P14), E33 (= E34), P34 (≠ R35), Y36 (≠ H37), G39 (= G40), V40 (≠ I41), C41 (= C42), G45 (= G46), C46 (= C47), K50 (= K51), Y112 (≠ E114), G113 (≠ A115), T142 (= T158), G143 (= G159), Y161 (= Y178), I182 (= I199), Y276 (≠ L294), D309 (= D326), Q315 (≠ M332), L316 (= L333), A317 (= A334)
- binding N~2~-(2-cyano-5-methyl-1H-indole-7-sulfonyl)-N~2~-methyl-N-[4-(oxetan-3-yl)-3,4-dihydro-2H-1,4-benzoxazin-7-yl]glycinamide: Y16 (= Y17), R93 (≠ L95), F99 (= F101), E321 (= E338), F377 (≠ Y394), A381 (= A398), A383 (≠ G400), H443 (= H460), E448 (= E465), A449 (≠ M466), E452 (= E469), N463 (= N480)
P9WHH9 Dihydrolipoyl dehydrogenase; LPD; Component of peroxynitrite reductase/peroxidase complex; Component of PNR/P; Dihydrolipoamide dehydrogenase; E3 component of alpha-ketoacid dehydrogenase complexes; EC 1.8.1.4 from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (see 2 papers)
42% identity, 99% coverage: 4:480/481 of query aligns to 3:463/464 of P9WHH9
- D5 (= D6) mutation to A: Reduces lipoamide dehydrogenase activity by 95%.
- 33:41 (vs. 34:42, 44% identical) binding
- C41 (= C42) modified: Disulfide link with 46, Redox-active
- N43 (= N44) mutation to A: Reduces lipoamide dehydrogenase activity by 89%.
- C46 (= C47) modified: Disulfide link with 41, Redox-active
- K50 (= K51) binding
- R93 (≠ L95) mutation to A: Reduces lipoamide dehydrogenase activity by 94%.; mutation to E: Reduces lipoamide dehydrogenase activity by 96%.
- K103 (= K105) mutation to E: Reduces lipoamide dehydrogenase activity by 82%.
- D309 (= D326) binding
- A317 (= A334) binding
- H386 (≠ I403) mutation to K: Reduces lipoamide dehydrogenase activity by 91%.
Sites not aligning to the query:
- 464 F→A: Reduces lipoamide dehydrogenase activity by 95%.
7kmyA Structure of mtb lpd bound to 010705 (see paper)
42% identity, 99% coverage: 4:480/481 of query aligns to 4:464/465 of 7kmyA
- active site: W38 (≠ L38), C42 (= C42), C47 (= C47), S50 (≠ T50), A182 (= A198), E186 (= E202), H442 (≠ F458), H444 (= H460), E449 (= E465)
- binding flavin-adenine dinucleotide: L10 (≠ V10), G11 (= G11), G13 (= G13), P14 (= P14), V33 (= V33), E34 (= E34), P35 (≠ R35), Y37 (≠ H37), G40 (= G40), V41 (≠ I41), C42 (= C42), G46 (= G46), C47 (= C47), K51 (= K51), Y113 (≠ E114), G114 (≠ A115), A142 (= A157), T143 (= T158), G144 (= G159), Y162 (= Y178), I183 (= I199), Y277 (≠ L294), G309 (= G325), D310 (= D326), Q316 (≠ M332), L317 (= L333), A318 (= A334)
- binding N~2~-methyl-N~2~-[(5-methyl-1H-indazol-7-yl)sulfonyl]-N-(1-methyl-2-oxo-1,2-dihydropyridin-4-yl)glycinamide: Y17 (= Y17), R94 (≠ L95), G97 (= G98), F100 (= F101), E322 (= E338), A382 (= A398), H444 (= H460), E449 (= E465), N464 (= N480)
4m52A Structure of mtb lpd bound to sl827 (see paper)
42% identity, 99% coverage: 4:480/481 of query aligns to 4:464/465 of 4m52A
- active site: W38 (≠ L38), C42 (= C42), C47 (= C47), S50 (≠ T50), A182 (= A198), E186 (= E202), H442 (≠ F458), H444 (= H460), E449 (= E465)
- binding flavin-adenine dinucleotide: L10 (≠ V10), G11 (= G11), G13 (= G13), P14 (= P14), V33 (= V33), E34 (= E34), P35 (≠ R35), Y37 (≠ H37), V41 (≠ I41), C42 (= C42), G46 (= G46), C47 (= C47), K51 (= K51), Y113 (≠ E114), G114 (≠ A115), A142 (= A157), T143 (= T158), Y162 (= Y178), I183 (= I199), F270 (≠ V287), Y277 (≠ L294), G309 (= G325), D310 (= D326), Q316 (≠ M332), L317 (= L333), A318 (= A334)
- binding N~2~-[(2-amino-5-bromopyridin-3-yl)sulfonyl]-N-(4-methoxyphenyl)-N~2~-methylglycinamide: P14 (= P14), Y17 (= Y17), R94 (≠ L95), F100 (= F101), E322 (= E338), A382 (= A398), H444 (= H460), N464 (= N480)
2eq6A Crystal structure of lipoamide dehydrogenase from thermus thermophilus hb8
41% identity, 97% coverage: 3:470/481 of query aligns to 2:447/460 of 2eq6A
- active site: V37 (≠ L38), C41 (= C42), C46 (= C47), T49 (= T50), A176 (= A198), E180 (= E202), H435 (≠ F458), H437 (= H460), E442 (= E465)
- binding flavin-adenine dinucleotide: I9 (≠ V10), G10 (= G11), G12 (= G13), P13 (= P14), G14 (= G15), E33 (= E34), A34 (≠ R35), G39 (= G40), V40 (≠ I41), C41 (= C42), G45 (= G46), C46 (= C47), K50 (= K51), F111 (≠ E114), A112 (= A115), A135 (= A157), T136 (= T158), G137 (= G159), S155 (≠ Y178), R269 (≠ N290), D306 (= D326), L312 (≠ M332), L313 (= L333), A314 (= A334), H315 (= H335), Y344 (= Y367)
Sites not aligning to the query:
6uziC Crystal structure of dihydrolipoyl dehydrogenase from elizabethkingia anophelis nuhp1
39% identity, 99% coverage: 4:477/481 of query aligns to 6:465/470 of 6uziC
- active site: C45 (= C42), C50 (= C47), S53 (≠ T50), V187 (≠ A198), E191 (= E202), H448 (= H460), E453 (= E465)
- binding flavin-adenine dinucleotide: I12 (≠ V10), G13 (= G11), G15 (= G13), P16 (= P14), G17 (= G15), E36 (= E34), K37 (≠ R35), G43 (= G40), T44 (≠ I41), C45 (= C42), G49 (= G46), C50 (= C47), S53 (≠ T50), K54 (= K51), V117 (≠ E114), G118 (≠ A115), T147 (= T158), G148 (= G159), I188 (= I199), R276 (≠ V287), D316 (= D326), M322 (= M332), L323 (= L333), A324 (= A334)
- binding zinc ion: H448 (= H460), E453 (= E465)
P31023 Dihydrolipoyl dehydrogenase, mitochondrial; Dihydrolipoamide dehydrogenase; Glycine cleavage system L protein; Pyruvate dehydrogenase complex E3 subunit; E3; PDC-E3; EC 1.8.1.4 from Pisum sativum (Garden pea) (Lathyrus oleraceus) (see 2 papers)
39% identity, 99% coverage: 2:477/481 of query aligns to 35:497/501 of P31023
- 67:76 (vs. 34:42, 60% identical) binding
- C76 (= C42) modified: Disulfide link with 81, Redox-active
- C81 (= C47) modified: Disulfide link with 76, Redox-active
- G149 (≠ A115) binding
- D348 (= D326) binding
- MLAH 354:357 (= MLAH 332:335) binding
Sites not aligning to the query:
- 1:31 modified: transit peptide, Mitochondrion
1dxlA Dihydrolipoamide dehydrogenase of glycine decarboxylase from pisum sativum (see paper)
39% identity, 99% coverage: 2:477/481 of query aligns to 1:463/467 of 1dxlA
- active site: L38 (= L38), C42 (= C42), C47 (= C47), S50 (≠ T50), Y184 (≠ A198), E188 (= E202), H444 (≠ F458), H446 (= H460), E451 (= E465)
- binding flavin-adenine dinucleotide: I9 (≠ V10), P13 (= P14), G14 (= G15), E33 (= E34), K34 (vs. gap), R35 (= R35), G40 (= G40), T41 (≠ I41), C42 (= C42), G46 (= G46), C47 (= C47), K51 (= K51), Y114 (≠ E114), G115 (≠ A115), T144 (= T158), G145 (= G159), Y184 (≠ A198), I185 (= I199), R274 (≠ V287), D314 (= D326), M320 (= M332), L321 (= L333), A322 (= A334), H323 (= H335)
1ebdA Dihydrolipoamide dehydrogenase complexed with the binding domain of the dihydrolipoamide acetylase (see paper)
38% identity, 97% coverage: 6:470/481 of query aligns to 5:450/455 of 1ebdA
- active site: P13 (= P14), L37 (= L38), C41 (= C42), C46 (= C47), S49 (≠ T50), N74 (≠ K76), V75 (≠ I77), Y180 (≠ A198), E184 (= E202), S320 (≠ E338), H438 (≠ F458), H440 (= H460), E445 (= E465)
- binding flavin-adenine dinucleotide: G10 (= G11), G12 (= G13), P13 (= P14), V32 (= V33), E33 (= E34), K34 (≠ R35), G39 (= G40), V40 (≠ I41), C41 (= C42), G45 (= G46), C46 (= C47), K50 (= K51), E112 (= E114), A113 (= A115), T141 (= T158), G142 (= G159), Y180 (≠ A198), I181 (= I199), R268 (≠ V287), D308 (= D326), A314 (≠ M332), L315 (= L333), A316 (= A334)
P11959 Dihydrolipoyl dehydrogenase; Dihydrolipoamide dehydrogenase; E3 component of pyruvate complex; EC 1.8.1.4 from Geobacillus stearothermophilus (Bacillus stearothermophilus) (see paper)
38% identity, 98% coverage: 6:476/481 of query aligns to 11:462/470 of P11959
- 39:47 (vs. 34:42, 56% identical) binding
- K56 (= K51) binding
- D314 (= D326) binding
- A322 (= A334) binding
6aonA 1.72 angstrom resolution crystal structure of 2-oxoglutarate dehydrogenase complex subunit dihydrolipoamide dehydrogenase from bordetella pertussis in complex with fad
37% identity, 99% coverage: 3:480/481 of query aligns to 1:472/473 of 6aonA
- active site: P43 (vs. gap), C47 (= C42), C52 (= C47), S55 (≠ T50), V191 (≠ A198), E195 (= E202), H450 (≠ F458), H452 (= H460), E457 (= E465)
- binding calcium ion: A218 (≠ P225), A220 (≠ E227), Q222 (≠ A229)
- binding flavin-adenine dinucleotide: I8 (≠ V10), G11 (= G13), P12 (= P14), G13 (= G15), D32 (≠ E34), A33 (≠ R35), W34 (≠ E36), G45 (= G40), T46 (≠ I41), C47 (= C42), G51 (= G46), C52 (= C47), K56 (= K51), K119 (≠ E114), G120 (≠ A115), T151 (= T158), G152 (= G159), N171 (≠ Y178), I192 (= I199), R280 (≠ V287), Y283 (≠ N290), G319 (= G325), D320 (= D326), M326 (= M332), L327 (= L333), A328 (= A334), H329 (= H335)
3urhB Crystal structure of a dihydrolipoamide dehydrogenase from sinorhizobium meliloti 1021
39% identity, 98% coverage: 5:475/481 of query aligns to 1:460/465 of 3urhB
- active site: Y35 (≠ L38), C39 (= C42), C44 (= C47), S47 (≠ T50), V183 (≠ A198), E187 (= E202), H443 (≠ F458), H445 (= H460), E450 (= E465)
- binding flavin-adenine dinucleotide: I6 (≠ V10), G7 (= G11), G9 (= G13), P10 (= P14), G11 (= G15), E30 (= E34), K31 (vs. gap), G37 (= G40), T38 (≠ I41), C39 (= C42), G43 (= G46), C44 (= C47), K48 (= K51), T111 (≠ E114), G112 (≠ A115), A140 (= A157), T141 (= T158), G142 (= G159), I184 (= I199), R273 (≠ V287), G312 (= G325), D313 (= D326), M319 (= M332), L320 (= L333), A321 (= A334), H322 (= H335)
P18925 Dihydrolipoyl dehydrogenase; Dihydrolipoamide dehydrogenase; E3 component of pyruvate complex; EC 1.8.1.4 from Azotobacter vinelandii (see 2 papers)
38% identity, 100% coverage: 1:480/481 of query aligns to 1:471/477 of P18925
- 34:49 (vs. 34:42, 31% identical) binding
- C49 (= C42) modified: Disulfide link with 54, Redox-active
- C54 (= C47) modified: Disulfide link with 49, Redox-active
- K58 (= K51) binding
- D319 (= D326) binding
- A327 (= A334) binding
6awaA 1.83 angstrom resolution crystal structure of dihydrolipoyl dehydrogenase from pseudomonas putida in complex with fad and adenosine-5'-monophosphate.
38% identity, 99% coverage: 1:476/481 of query aligns to 1:467/475 of 6awaA
- active site: L45 (= L38), C49 (= C42), C54 (= C47), S57 (≠ T50), V191 (≠ A198), E195 (= E202), F449 (= F458), H451 (= H460), E456 (= E465)
- binding adenosine monophosphate: I187 (≠ M194), E211 (= E218), A212 (≠ L219), L213 (= L220), V245 (= V252), V277 (= V285)
- binding flavin-adenine dinucleotide: I10 (≠ V10), G13 (= G13), P14 (= P14), G15 (= G15), E34 (= E34), K35 (≠ R35), T48 (≠ I41), C49 (= C42), G53 (= G46), C54 (= C47), K58 (= K51), H121 (≠ E114), G122 (≠ A115), S151 (≠ T158), G152 (= G159), I192 (= I199), R279 (≠ V287), G318 (= G325), D319 (= D326), M325 (= M332), L326 (= L333), A327 (= A334), Y358 (= Y367)
Sites not aligning to the query:
P14218 Dihydrolipoyl dehydrogenase; Dihydrolipoamide dehydrogenase; E3 component of 2-oxoglutarate dehydrogenase complex; EC 1.8.1.4 from Pseudomonas fluorescens (see 2 papers)
38% identity, 100% coverage: 1:480/481 of query aligns to 1:471/478 of P14218
- M1 (= M1) modified: Initiator methionine, Removed
- 34:49 (vs. 34:42, 31% identical) binding
- C49 (= C42) modified: Disulfide link with 54, Redox-active
- C54 (= C47) modified: Disulfide link with 49, Redox-active
- K58 (= K51) binding
- G122 (≠ A115) binding
- D319 (= D326) binding
- A327 (= A334) binding
5u8uD Dihydrolipoamide dehydrogenase (lpdg) from pseudomonas aeruginosa (see paper)
38% identity, 100% coverage: 1:480/481 of query aligns to 3:473/477 of 5u8uD
- active site: P16 (= P14), L47 (= L38), C51 (= C42), C56 (= C47), S59 (≠ T50), G85 (= G75), V86 (≠ I77), V193 (≠ A198), E197 (= E202), S333 (≠ E338), F451 (= F458), H453 (= H460), E458 (= E465)
- binding flavin-adenine dinucleotide: I12 (≠ V10), G15 (= G13), P16 (= P14), G17 (= G15), E36 (= E34), K37 (≠ R35), G49 (= G40), T50 (≠ I41), C51 (= C42), G55 (= G46), C56 (= C47), K60 (= K51), H123 (≠ E114), G124 (≠ A115), A152 (= A157), S153 (≠ T158), G154 (= G159), I194 (= I199), R281 (≠ V287), G320 (= G325), D321 (= D326), M327 (= M332), L328 (= L333), A329 (= A334), H330 (= H335), H453 (= H460), P454 (= P461)
Sites not aligning to the query:
3ladA Refined crystal structure of lipoamide dehydrogenase from azotobacter vinelandii at 2.2 angstroms resolution. A comparison with the structure of glutathione reductase (see paper)
38% identity, 100% coverage: 2:480/481 of query aligns to 1:470/472 of 3ladA
- active site: L44 (= L38), C48 (= C42), C53 (= C47), S56 (≠ T50), V190 (≠ A198), E194 (= E202), F448 (= F458), H450 (= H460), E455 (= E465)
- binding flavin-adenine dinucleotide: I9 (≠ V10), G10 (= G11), G12 (= G13), P13 (= P14), E33 (= E34), K34 (≠ R35), G46 (= G40), T47 (≠ I41), C48 (= C42), G52 (= G46), C53 (= C47), H120 (≠ E114), G121 (≠ A115), A149 (= A157), S150 (≠ T158), G151 (= G159), I191 (= I199), R278 (≠ V287), D318 (= D326), L325 (= L333), A326 (= A334)
5u8wA Dihydrolipoamide dehydrogenase (lpdg) from pseudomonas aeruginosa bound to nadh (see paper)
38% identity, 100% coverage: 2:480/481 of query aligns to 1:470/473 of 5u8wA
- active site: P13 (= P14), L44 (= L38), C48 (= C42), C53 (= C47), S56 (≠ T50), G82 (= G75), V83 (≠ I77), V190 (≠ A198), E194 (= E202), S330 (≠ E338), F448 (= F458), H450 (= H460), E455 (= E465)
- binding flavin-adenine dinucleotide: I9 (≠ V10), G12 (= G13), P13 (= P14), G14 (= G15), E33 (= E34), K34 (≠ R35), G46 (= G40), T47 (≠ I41), C48 (= C42), G52 (= G46), C53 (= C47), K57 (= K51), H120 (≠ E114), G121 (≠ A115), A149 (= A157), S150 (≠ T158), G151 (= G159), S170 (≠ Y178), G317 (= G325), D318 (= D326), M324 (= M332), L325 (= L333), A326 (= A334), H327 (= H335), Y357 (= Y367), H450 (= H460), P451 (= P461)
- binding 1,4-dihydronicotinamide adenine dinucleotide: I186 (≠ M194), G189 (= G197), V190 (≠ A198), I191 (= I199), E194 (= E202), E210 (= E218), A211 (≠ L219), L212 (= L220), A275 (= A284), V276 (= V285), G277 (= G286), R278 (≠ V287), M324 (= M332), L325 (= L333), V355 (≠ C365), Y357 (= Y367)
Sites not aligning to the query:
Query Sequence
>SMc01035 SMc01035 dihydrolipoamide dehydrogenase
MAENYDVIVVGSGPGGYVTAIRSAQLGLKTAIVEREHLGGICLNWGCIPTKALLRSAEIL
DHANHAKNYGLTLEGKITANVKDVVARSRGVSARLNGGVAFLMKKNKVDVIWGEAKLTKP
GEIVVGAPSKPAVQPQNPVPKGVKGEGTYTAKHIIVATGARPRALPGIEPDGKLIWTYFE
AMKPEEFPKSLLVMGSGAIGIEFASFYRSMGVDVTVVELLPQIMPVEDAEISAFARKQLE
KRGLKIITDAKVTKVEKGANDVTAHVETKDGKVTPIKADRLISAVGVQGNIENLGLEALG
VKTDRGCIVTDGYGKTNVAGIYAIGDVAGPPMLAHKAEHEGVICVEKIAGVPGVHALDKG
KIPGCTYCDPQVASVGLTEAKAKELGRDIRVGRYSFGANGKAIALGEDQGLIKTIFDKKT
GELIGAHMVGAEVTELIQGFVVAMNLETTEEELMHTVFPHPTLSEMMKESVLDAYGRVLN
A
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SitesBLAST's Database
SitesBLAST's database includes
(1) SwissProt
entries with experimentally-supported functional features;
and (2) protein structures with bound ligands, from the
BioLip database.
by Morgan Price,
Arkin group
Lawrence Berkeley National Laboratory