SitesBLAST
Comparing WP_012407235.1 NCBI__GCF_000020025.1:WP_012407235.1 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)
Q9JZG1 2-isopropylmalate synthase; Alpha-IPM synthase; Alpha-isopropylmalate synthase; EC 2.3.3.13 from Neisseria meningitidis serogroup B (strain MC58) (see 2 papers)
38% identity, 98% coverage: 2:370/377 of query aligns to 5:385/517 of Q9JZG1
- D16 (= D13) binding Mn(2+)
- H204 (= H193) binding Mn(2+)
- H206 (= H195) binding Mn(2+)
- N240 (= N229) binding Mn(2+)
Sites not aligning to the query:
- 366:517 Required for the condensation reaction. Not required to bind substrate
6ktqA Crystal structure of catalytic domain of homocitrate synthase from sulfolobus acidocaldarius (sahcs(dram)) in complex with alpha- ketoglutarate/zn2+/coa (see paper)
37% identity, 91% coverage: 6:348/377 of query aligns to 24:370/399 of 6ktqA
- binding 2-oxoglutaric acid: R30 (= R12), R154 (≠ A132), T156 (≠ G134), E158 (= E136), S184 (≠ R162), T188 (= T166), H216 (= H193), H218 (= H195)
- binding coenzyme a: V67 (≠ M49), R96 (= R74), A97 (= A75), F116 (≠ A94), H128 (≠ F106), E158 (= E136)
- binding zinc ion: E31 (≠ D13), H216 (= H193), H218 (= H195)
6e1jA Crystal structure of methylthioalkylmalate synthase (bjumam1.1) from brassica juncea (see paper)
37% identity, 97% coverage: 2:367/377 of query aligns to 16:407/409 of 6e1jA
- binding coenzyme a: Q30 (= Q16), F60 (≠ I46), S63 (≠ M49), I95 (≠ W72), R97 (= R74), F121 (≠ A94), K132 (= K105), L133 (≠ F106), S322 (= S285), G323 (= G286), I324 (= I287), D327 (≠ H290), K331 (≠ Q294), L359 (≠ H318), R362 (= R321), H363 (= H322)
- binding 4-(methylsulfanyl)-2-oxobutanoic acid: P192 (≠ C164), T194 (= T166), H225 (= H193), H227 (= H195)
- binding manganese (ii) ion: D27 (= D13), V82 (vs. gap), E84 (vs. gap), H225 (= H193), H227 (= H195)
Q9FN52 Methylthioalkylmalate synthase 3, chloroplastic; 2-isopropylmalate synthase 2; Methylthioalkylmalate synthase-like; EC 2.3.3.17 from Arabidopsis thaliana (Mouse-ear cress) (see paper)
35% identity, 97% coverage: 2:367/377 of query aligns to 83:474/503 of Q9FN52
- G263 (= G168) mutation to E: In gsm2-1; loss of activity and lack of C6, C7 and C8 aliphatic glucosinolates.
Q9FG67 Methylthioalkylmalate synthase 1, chloroplastic; 2-isopropylmalate synthase 3; EC 2.3.3.17 from Arabidopsis thaliana (Mouse-ear cress) (see paper)
36% identity, 97% coverage: 2:367/377 of query aligns to 83:474/506 of Q9FG67
- S102 (≠ A21) mutation to F: In gsm1-1; loss of conversion of C3 to C4 glucosinolates.
- A290 (≠ E191) mutation to T: In gsm1-2; loss of conversion of C3 to C4 glucosinolates.
3rmjB Crystal structure of truncated alpha-isopropylmalate synthase from neisseria meningitidis (see paper)
36% identity, 82% coverage: 2:309/377 of query aligns to 2:307/308 of 3rmjB
3ivtB Homocitrate synthase lys4 bound to 2-og (see paper)
31% identity, 98% coverage: 1:369/377 of query aligns to 27:396/400 of 3ivtB
Q9Y823 Homocitrate synthase, mitochondrial; HCS; EC 2.3.3.14 from Schizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast) (see 2 papers)
31% identity, 98% coverage: 1:369/377 of query aligns to 32:401/418 of Q9Y823
- R43 (= R12) binding 2-oxoglutarate; mutation R->A,K,Q: Abolishes the catalytic activity.
- E44 (≠ D13) binding 2-oxoglutarate; binding L-lysine; binding Zn(2+)
- Q47 (= Q16) mutation to A: Abolishes the catalytic activity.
- E74 (= E43) mutation to A: Abolishes the catalytic activity.; mutation to Q: Results in a moderate decrease in the turnover number and a slight increase in the Km value for each substrate.
- H103 (≠ W72) binding 2-oxoglutarate; mutation to A: Substantially impairs catalytic efficiency.
- D123 (≠ H92) binding L-lysine; mutation to N: Does not affect the catalytic activity but impairs L-lysine inhibition.
- R163 (≠ A132) binding 2-oxoglutarate; mutation R->A,Q: Abolishes the catalytic activity.; mutation to K: Severely diminishes affinity for 2-oxoglutarate and substantially impairs catalytic efficiency.
- S165 (≠ G134) binding 2-oxoglutarate; mutation to A: Results in a moderate decrease in catalytic efficiency.
- E167 (= E136) mutation E->A,Q: Abolishes the catalytic activity.
- T197 (= T166) binding 2-oxoglutarate; binding L-lysine; mutation to A: Exhibits a 25-fold decrease in catalytic efficiency.; mutation to S: Results in a modest decrease in catalytic efficiency.; mutation to V: Abolishes the catalytic activity.
- E222 (= E191) mutation to Q: Does not affect the catalytic activity but impairs L-lysine inhibition.
- H224 (= H193) binding 2-oxoglutarate; binding Zn(2+)
- H226 (= H195) binding 2-oxoglutarate; binding Zn(2+)
- R288 (≠ L255) mutation to K: Does not affect the catalytic activity but impairs L-lysine inhibition.
- Y332 (= Y299) mutation to A: Abolishes the catalytic activity.; mutation to F: Results in a decrease in catalytic efficiency.
- Q364 (= Q330) mutation to R: Does not affect the catalytic activity but impairs L-lysine inhibition.
3mi3A Homocitrate synthase lys4 bound to lysine (see paper)
30% identity, 98% coverage: 1:369/377 of query aligns to 9:367/370 of 3mi3A
O87198 Homocitrate synthase; HCS; EC 2.3.3.14 from Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27) (see paper)
31% identity, 98% coverage: 1:369/377 of query aligns to 1:372/376 of O87198
- R12 (= R12) binding 2-oxoglutarate
- E13 (≠ D13) binding Mg(2+)
- H72 (≠ W72) binding 2-oxoglutarate; mutation to L: Significant decrease in sensitivity to lysine inhibition. Large decrease in affinity for 2-oxoglutarate. Almost no effect on affinity for acetyl-CoA and on turnover number.
- D92 (≠ H92) binding L-lysine
- R133 (vs. gap) binding 2-oxoglutarate
- S135 (≠ G134) binding L-lysine
- T166 (= T166) binding 2-oxoglutarate; binding L-lysine
- H195 (= H193) binding Mg(2+)
- H197 (= H195) binding Mg(2+)
3ivsA Homocitrate synthase lys4 (see paper)
31% identity, 90% coverage: 1:339/377 of query aligns to 9:337/364 of 3ivsA
4ov4A Isopropylmalate synthase binding with ketoisovalerate (see paper)
30% identity, 96% coverage: 4:366/377 of query aligns to 4:377/379 of 4ov4A
2ztjA Crystal structure of homocitrate synthase from thermus thermophilus complexed with alpha-ketoglutarate (see paper)
32% identity, 84% coverage: 1:316/377 of query aligns to 1:312/312 of 2ztjA
2zyfA Crystal structure of homocitrate synthase from thermus thermophilus complexed with magnesuim ion and alpha-ketoglutarate (see paper)
32% identity, 84% coverage: 1:316/377 of query aligns to 1:314/314 of 2zyfA
Q8F3Q1 (R)-citramalate synthase CimA; LiCMS; EC 2.3.3.21 from Leptospira interrogans serogroup Icterohaemorrhagiae serovar Lai (strain 56601) (see 2 papers)
31% identity, 96% coverage: 6:367/377 of query aligns to 10:379/516 of Q8F3Q1
- R16 (= R12) mutation R->K,Q: Loss of activity.
- RD 16:17 (= RD 12:13) binding pyruvate
- D17 (= D13) mutation to A: 34-fold increase in Km for pyruvate and 315-fold decrease in kcat.; mutation to N: 4.4-fold increase in Km for pyruvate and 480-fold decrease in kcat.
- L81 (= L70) mutation to A: 4.7-fold increase in Km for pyruvate and 15.7-fold decrease in kcat.; mutation to V: 3.3-fold increase in Km for pyruvate and 10.1-fold decrease in kcat.
- F83 (≠ W72) mutation to A: 5-fold increase in Km for acetyl-CoA and 120-fold decrease in kcat.
- L104 (≠ A94) mutation to V: 1.8-fold increase in Km for pyruvate and 3.4-fold decrease in kcat.
- Y144 (≠ G134) binding pyruvate; mutation to L: 259-fold increase in Km for pyruvate and 76-fold decrease in kcat.; mutation to V: 114-fold increase in Km for pyruvate and 5.3-fold decrease in kcat.
- E146 (= E136) mutation E->D,Q: Minor effects on the binding of acetyl-CoA, but causes a strong decrease in kcat.
- T179 (= T166) binding pyruvate; mutation to A: 16.4-fold increase in Km for pyruvate and 186-fold decrease in kcat.
- H302 (= H288) mutation H->A,N: Loss of activity.
- D304 (≠ H290) mutation to A: 5.2-fold increase in Km for acetyl-CoA and 16.6-fold decrease in kcat.
- N310 (≠ P296) mutation to A: 2.2-fold increase in Km for acetyl-CoA and 1.7-fold decrease in kcat.
- L311 (≠ I297) mutation to A: 8-fold increase in Km for acetyl-CoA and 6-fold decrease in kcat.
- Y312 (≠ T298) mutation to A: Loss of activity.
Sites not aligning to the query:
- 430 Y→L: No change in Km for acetyl-CoA and 2.3-fold decrease in kcat. Severely impairs inhibition by isoleucine.
- 431 D→A: 1.8-fold decrease in Km for acetyl-CoA and 5-fold decrease in kcat.
- 451 L→V: 1.5-fold increase in Km for acetyl-CoA and 4.3 decrease in kcat.
- 454 Y→A: 1.4 decrease in Km for acetyl-CoA and 17-fold decrease in kcat. Still inhibited by isoleucine and weakly inhibited by leucine.
- 458 I→A: 1.3-fold decrease in Km for acetyl-CoA and 14-fold decrease in kcat. Abolishes inhibition by isoleucine.
- 464 T→A: 1.8-fold decrease in Km for acetyl-CoA and 4.3-fold decrease in kcat.
- 468 V→A: No change in Km for acetyl-CoA and 2-fold decrease in kcat. Increases inhibition by isoleucine and leucine becomes an effective inhibitor.
- 493 P→A: 1.5-fold decrease in Km for acetyl-CoA and 2.6-fold decrease in kcat.
- 495 Q→A: 1.6-fold decrease in Km for acetyl-CoA and 2.8-fold decrease in kcat.
4ov9A Structure of isopropylmalate synthase binding with alpha- isopropylmalate (see paper)
30% identity, 96% coverage: 4:366/377 of query aligns to 4:379/380 of 4ov9A
3a9iA Crystal structure of homocitrate synthase from thermus thermophilus complexed with lys (see paper)
31% identity, 97% coverage: 6:369/377 of query aligns to 5:343/347 of 3a9iA
3bliA Crystal structure of the catalytic domain of licms in complexed with pyruvate and acetyl-coa (see paper)
31% identity, 79% coverage: 6:303/377 of query aligns to 4:308/311 of 3bliA
Q53WI0 4-hydroxy-2-oxovalerate aldolase; HOA; 4-hydroxy-2-keto-pentanoic acid aldolase; 4-hydroxy-2-oxohexanoate aldolase; 4-hydroxy-2-oxopentanoate aldolase; EC 4.1.3.39; EC 4.1.3.43 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8) (see paper)
30% identity, 68% coverage: 5:261/377 of query aligns to 12:268/347 of Q53WI0
Sites not aligning to the query:
- 324 A→G: Increases the channeling efficiency of propanaldehyde from 57% to 94%.
P51015 4-hydroxy-2-oxovalerate aldolase 4; HOA 4; 4-hydroxy-2-keto-pentanoic acid aldolase 4; 4-hydroxy-2-oxohexanoate aldolase; 4-hydroxy-2-oxopentanoate aldolase 4; EC 4.1.3.39; EC 4.1.3.43 from Paraburkholderia xenovorans (strain LB400) (see 3 papers)
28% identity, 66% coverage: 2:250/377 of query aligns to 6:255/346 of P51015
- R16 (= R12) mutation to A: Loss of aldol cleavage activity.; mutation to K: 4000-fold decrease in the catalytic efficiency of the aldol cleavage reaction.
- H20 (≠ Q16) mutation H->A,S: 100-fold decrease in the catalytic efficiency of the aldol cleavage reaction. Dramatic reduction in acetaldehyde and propanaldehyde channeling efficiency by more than 70%.
- L87 (= L69) mutation to A: 32-fold reduction in the catalytic efficiency with acetaldehyde as substrate of the aldol addition reaction, but no change in the catalytic efficiency using propanaldehyde; thus, exhibits a 40-fold preference for propanaldehyde over acetaldehyde.; mutation L->N,W: Loss of aldolase activity (with either enantiomer of HOPA), but retains some decarboxylase activity for the smaller oxaloacetate substrate. In the retro-aldol cleavage reaction, is inactive toward 4(S)-HOPA but is active toward 4(R)-HOPA, albeit with a great reduction in catalytic efficiency, and in the aldol addition reaction, produces also exclusively the 4(R)-enantiomer; when associated with F-290.
- L89 (≠ G71) mutation to A: As the wild-type enzyme, exhibits similar catalytic efficiency with acetaldehyde or propanaldehyde as substrate in the aldol addition reaction but displays higher catalytic efficiency with longer aldehydes (50-fold increase using pentaldehyde). Shows a reduction in aldehyde channeling efficiency by 30%.
Sites not aligning to the query:
- 290 Y→F: Loss of stereochemical control as the mutant is able to catalyze the aldol cleavage of substrates with both R and S configurations at C4 with similar kinetic parameters. 3.5-fold decrease in the catalytic efficiency of the aldol cleavage reaction. Reduction in aldehyde channeling efficiency by more than 30%. In the retro-aldol cleavage reaction, is inactive toward 4(S)-HOPA but is active toward 4(R)-HOPA, albeit with a great reduction in catalytic efficiency, and in the aldol addition reaction, produces also exclusively the 4(R)-enantiomer; when associated with N-87 or W-87.; Y→S: Loss of stereochemical control as the mutant is able to catalyze the aldol cleavage of substrates with both R and S configurations at C4 with similar kinetic parameters. 3.5-fold decrease in the catalytic efficiency of the aldol cleavage reaction.
- 322 G→A: Displays a reduction in aldehyde channeling efficiency of about 20%.; mutation G->F,L: Unable to channel either acetaldehyde or propanaldehyde.
- 323 G→A: Able to channel butyraldehyde (with less efficiency than wild-type) but not its isomer isobutyraldehyde.; G→F: Unable to channel either acetaldehyde or propanaldehyde.; G→L: Able to channel acetaldehyde but not the larger propanaldehyde.
Query Sequence
>WP_012407235.1 NCBI__GCF_000020025.1:WP_012407235.1
MNQIIINDTTLRDGEQAAGVAFTLQEKVAIAKFLDSIGIPELEVGIPAMGDEETRAIAAI
SDLGLQAKLLGWNRAVISDIKASIACGLNRVHIAIPVSGIQIAAKFHGQWRVSLQKLKDC
ISFAVDQGLWVAVGGEDSSRADENFLLDVALYAQEWGASRFRFCDTVGVLDPFTTYTKVK
RLVSALMIPLEIHTHNDFGLATANALAGIKAGALSVNTTVNGLGERAGNAALEEVVMAIK
RIYGVDLGIDTPGLLELSQLVAAASGASVPPWKAIVGENTFAHESGIHAHGVLQNPITYE
PFAPEEVGWERRLVLGKHSGRHLVSNLLEQHGIFLNSQETQSVLDAVRHQSVQKKRSLTT
EELLNLVREQRYSHATR
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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