SitesBLAST

Q56268 3-isopropylmalate dehydrogenase; 3-IPM-DH; Beta-IPM dehydrogenase; IMDH; EC 1.1.1.85 from Acidithiobacillus ferrooxidans (Thiobacillus ferrooxidans) (see paper)
58% identity, 99% coverage: 6:357/357 of query aligns to 3:354/358 of Q56268

query
sites
Q56268

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R95 (= R98) binding substrate
R105 (= R108) binding substrate
R133 (= R136) binding substrate
D222 (= D225) binding Mg(2+); binding substrate
D246 (= D249) binding Mg(2+)

P93832 3-isopropylmalate dehydrogenase 2, chloroplastic; 3-IPM-DH 2; AtIMDH2; AtIMDH3; IMDH 2; Beta-IPM dehydrogenase 2; Isopropylmalate dehydrogenase 2; AtIMD2; EC 1.1.1.85 from Arabidopsis thaliana (Mouse-ear cress) (see 2 papers)
58% identity, 100% coverage: 2:357/357 of query aligns to 40:397/405 of P93832

query
sites
P93832

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114:129 (vs. 76:91, 56% identical) binding NAD(+)
L132 (= L94) mutation to A: Reduced activity toward 3-isopropylmalate.
L133 (= L95) Confers substrate specificity; mutation to A: Reduced activity toward 3-isopropylmalate.; mutation to F: Enhanced activity toward 3-(2'-methylthio)-ethylmalate, but reduced catalytic efficiency with 3-isopropylmalate.
R136 (= R98) binding substrate; mutation to A: Loss of activity toward 3-isopropylmalate.; mutation to K: Reduced activity toward 3-isopropylmalate.
R146 (= R108) binding substrate; mutation to A: Reduced activity toward 3-isopropylmalate.; mutation to K: Reduced activity toward 3-isopropylmalate.
R174 (= R136) binding substrate; mutation to A: Loss of activity toward 3-isopropylmalate.; mutation to K: Reduced activity toward 3-isopropylmalate.
Y181 (= Y143) Important for catalysis; mutation Y->A,F,H: Reduced activity toward 3-isopropylmalate.
K232 (= K193) Important for catalysis; mutation to M: Loss of activity toward 3-isopropylmalate.
N234 (= N195) binding NAD(+); mutation N->A,D: Loss of activity toward 3-isopropylmalate.
V235 (= V196) mutation to A: Reduced activity toward 3-isopropylmalate.
D264 (= D225) binding Mg(2+); binding substrate; mutation to N: Loss of activity toward 3-isopropylmalate.
N265 (= N226) binding NAD(+)
D288 (= D249) binding Mg(2+); mutation to N: Loss of activity toward 3-isopropylmalate.
D292 (= D253) binding Mg(2+); mutation to N: Reduced activity toward 3-isopropylmalate.
318:334 (vs. 278:294, 82% identical) binding NAD(+)

5j32A Isopropylmalate dehydrogenase in complex with isopropylmalate (see paper)
58% identity, 100% coverage: 2:357/357 of query aligns to 10:367/369 of 5j32A

query
sites
5j32A

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active site: L18 (= L10), Y151 (= Y143), K202 (= K193), D234 (= D225), D258 (= D249), D262 (= D253)
binding 3-isopropylmalic acid: R106 (= R98), R144 (= R136), Y151 (= Y143), D258 (= D249)
binding magnesium ion: D258 (= D249), D262 (= D253)

4xxvA Crystal structure of 3-isopropylmalate dehydrogenase from burkholderia thailandensis in complex with NAD
56% identity, 99% coverage: 4:357/357 of query aligns to 1:356/356 of 4xxvA

query
sites
4xxvA

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N

G

G

D

D

V

I

Y
|
Y

F

F

G

G

E

Q

P

P

R

R

G

G

R

V

E

R

V

A

R

A

-

P

-

D

-

G

-

P

-

F

N

A

G

G

E

E

R

R

V

E

G

G

Y

F

N

D

T

T

M

M

I

R

Y

Y

Y

S

E

E

H

P

E

E

I

V

K

R

R

R

I

I

A

A

K

H

V

V

A

A

F

F

E

Q

M

A

A

A

R

Q

N

K

R

R

R

A

K

K

V

L

T

L

S

S

V

V

D

D

K
|
K

A

S

N
|
N

V

V

L

L

E

E

V

T

S

S

G

Q

L

F

W

W

R

R

E

D

V

V

V

M

N

I

E

D

V

V

H

S

A

K

D

E

Y

Y

L

A

D

D

V

V

D

E

L

L

E

S

H

H

M

M

Y
|
Y

V

V

D
|
D

N
|
N

C

A

A

A

M

M

Q

Q

L

L

I

A

R

K

R

A

P

P

K

K

D

Q

F

F

D

D

V

V

I

I

V

V

T

T

G

G

N

N

I

M

F

F

G

G

D
|
D

I

I

I

L

S

S

D
|
D

E

E

A

A

G

S

A

M

L

L

T

T

G

G

S

S

L

I

G

G

M

M

L

L

P

P

S

S

A

A

S

S

I

L

G

D

E

K

R

N

Y

N

-

K

A

G

F

L

Y

Y

E

E

P

P

I

S

H

H

G

G

S

S

A

A

P

P

D

D

I

I

A

A

G

G

K

K

G

G

I

I

A

A

N

N

P

P

I

L

A

A

T

T

I

I

L

L

S

S

A

A

M

M

M

L

L

L

E

R

I

Y

T

S

C

L

K

N

L

R

P

A

Q

E

A

Q

A

A

R

D

D

R

I

I

E

E

K

R

A

A

V

V

E

K

K

T

V

V

L

L

E

E

D

Q

D

G

Y

Y

R

R

T

T

A

G

D

D

I

I

W

A

S

T

P

P

G

G

T

C

K

R

K

Q

V

V

N

G

T

T

A

A

E

A

M

M

T

G

E

D

E

A

I

V

K

A

R

A

L

L

active site: Y136 (= Y143), K191 (= K193), D223 (= D225), D247 (= D249), D251 (= D253)
binding nicotinamide-adenine-dinucleotide: N193 (= N195), Y221 (= Y223), N224 (= N226)

4iwhA Crystal structure of a 3-isopropylmalate dehydrogenase from burkholderia pseudomallei
56% identity, 99% coverage: 4:357/357 of query aligns to 3:358/358 of 4iwhA

query
sites
4iwhA

H

H

F

M

K

K

I

I

A

A

V

V

L

L

P

P

G

G

D

D

G

G

I

I

G

G

P

P

E

E

I

I

I

V

E

N

S

E

A

A

L

V

K

K

V

V

L

L

D

N

V

A

I

L

S

D

K

E

K

K

Y

-

G

-

I

-

T

-

F

F

E

E

Y

L

K

E

H

H

G

A

L

P

V

V

G

G

A

A

A

G

I

Y

D

E

E

A

T

S

G

G

D

H

P

P

L

L

P

P

P

D

E

A

T

T

L

L

K

A

I

L

C

A

K

K

E

E

S

A

D

D

A

A

V

I

L

L

F

F

G

G

A

A

V

V

G

G

G

D

E

W

K

K

W

Y

D

D

N

S

L

L

P

E

T

R

D

A

K

L

R

R

P

P

E

E

K

Q

G

A

L

I

L

L

R

G

I

L

R

R

K

K

E

H

L

L

E

E

L

L

F

F

A

A

N

N

I

F

R

R

P

P

A

A

K

I

A

C

Y

Y

A

P

P

Q

L

L

L

V

S

D

S

A

S

S

P

P

L

L

K

K

E

P

E

E

V

L

I

V

K

A

G

G

V

L

D

D

L

I

V

L

V

I

L

V

R

R

E

E

L

L

T

N

G

G

D

D

V

I

Y
|
Y

F

F

G

G

E

Q

P

P

R

R

G

G

R

V

E

R

V

A

R

A

-

P

-

D

-

G

-

P

-

F

N

A

G

G

E

E

R

R

V

E

G

G

Y

F

N

D

T

T

M

M

I

R

Y

Y

Y

S

E

E

H

P

E

E

I

V

K

R

R

R

I

I

A

A

K

H

V

V

A

A

F

F

E

Q

M

A

A

A

R

Q

N

K

R

R

R

A

K

K

V

L

T

L

S

S

V

V

D

D

K
|
K

A

S

N

N

V

V

L

L

E

E

V

T

S

S

G

Q

L

F

W

W

R

R

E

D

V

V

V

M

N

I

E

D

V

V

H

S

A

K

D

E

Y

Y

L

A

D

D

V

V

D

E

L

L

E

S

H

H

M

M

Y

Y

V

V

D
|
D

N

N

C

A

A

A

M

M

Q

Q

L

L

I

A

R

K

R

A

P

P

K

K

D

Q

F

F

D

D

V

V

I

I

V

V

T

T

G

G

N

N

I

M

F

F

G

G

D
|
D

I

I

I

L

S

S

D
|
D

E

E

A

A

G

S

A

M

L

L

T

T

G

G

S

S

L

I

G

G

M

M

L

L

P

P

S

S

A

A

S

S

I

L

G

D

E

K

R

N

Y

N

-

K

A

G

F

L

Y

Y

E

E

P

P

I

S

H

H

G

G

S

S

A

A

P

P

D

D

I

I

A

A

G

G

K

K

G

G

I

I

A

A

N

N

P

P

I

L

A

A

T

T

I

I

L

L

S

S

A

A

M

M

M

L

L

L

E

R

I

Y

T

S

C

L

K

N

L

R

P

A

Q

E

A

Q

A

A

R

D

D

R

I

I

E

E

K

R

A

A

V

V

E

K

K

T

V

V

L

L

E

E

D

Q

D

G

Y

Y

R

R

T

T

A

G

D

D

I

I

W

A

S

T

P

P

G

G

T

C

K

R

K

Q

V

V

N

G

T

T

A

A

E

A

M

M

T

G

E

D

E

A

I

V

K

A

R

A

L

L

active site: Y138 (= Y143), K193 (= K193), D225 (= D225), D249 (= D249), D253 (= D253)
binding magnesium ion: D249 (= D249), D253 (= D253)

5j33A Isopropylmalate dehydrogenase in complex with NAD+ (see paper)
57% identity, 99% coverage: 3:357/357 of query aligns to 1:357/360 of 5j33A

query
sites
5j33A

K

K

H

R

F

Y

K

T

I

I

A

T

V

L

L

L

P

P

G

G

D

D

G

G

I

I

G

G

P

P

E

E

I

V

E

S

S

I

A

A

L

K

K

N

V

V

L

L

D

Q

V

Q

I

A

S

G

K

S

K

L

Y

E

G

G

I

V

T

E

F

F

E

N

Y

F

K

R

H

E

G

M

L

P

V

I

G

G

A

A

I

L

D

D

E

L

T

V

G

G

D

V

P

P

L

L

P

P

P

E

E

E

T

T

L

I

K

S

I

A

C

A

K

K

E

E

S

S

D

D

A

A

V

V

L

L

F

L

G

G

A

A

V
x
I

G

G

E

Y

K

K

W

W

D

D

N

N

L

N

P

E

T

K

D

H

K

L

R

R

P

P

E
|
E

K

K

G

G

L
|
L

L

L

R

Q

I

I

R

R

K

A

E

A

L

L

E

K

L

V

F

F

A

A

N

N

I

L

R

R

P

P

A

A

K

T

A

V

Y

L

A

P

P

Q

L

L

L

V

S

D

S

A

S

S

P

T

L

L

K

K

E

R

E

E

V

V

I

A

K

E

G

G

V

V

D

D

L

L

V

M

V

V

L

V

R

R

E

E

L

L

T

T

G

G

D

G

V

I

Y
|
Y

F

F

G

G

E

E

P

P

R

R

G

G

-

I

R

K

E

T

V

N

R

E

N

N

G

G

E

E

R

E

V

V

G

G

Y

F

N

N

T

T

M

E

I

V

Y

Y

Y

A

E

A

H

H

E

E

I

I

K

D

R

R

I

I

A

A

K

R

V

V

A

A

F

F

E

E

M

T

A

A

R

R

N

K

R

R

K

G

K

K

V

L

T

C

S

S

V

V

D

D

K
|
K

A

A

N

N

V

V

L

L

E

E

V

A

S

S

G

I

L

L

W

W

R

R

E

K

V

R

V

V

N

T

E

A

V

L

H

A

A

S

D

E

Y

Y

L

P

D

D

V

V

D

E

L

L

E

S

H

H

M

M

Y

Y

V

V

D
|
D

N

N

C

A

A

A

M

M

Q

Q

L

L

I

V

R

R

R

D

P

P

K

K

D

Q

F

F

D

D

V

T

I

I

V

V

T

T

G

N

N

N

I

I

F

F

G

G

D
|
D

I

I

I

L

S

S

D
|
D

E

E

A

A

G

S

A

M

L

I

T

T

G

G

S

S

L
x
I

G

G

M

M

L

L

P

P

S

S

A

A

S

S

I

L

G

S

E

D

R

S

Y

G

-

P

A

G

F

L

Y

F

E
|
E

P

P

I

I

H
|
H

G
|
G

S
|
S

A
|
A

P

P

D

D

I
|
I

A

A

G

G

K

Q

G

D

I

K

A

A

N
|
N

P

P

I

L

A

A

T

T

I

I

L

L

S

S

A

A

M

M

M

L

L

L

E

K

I

Y

T

G

C

L

K

G

L

E

P

E

Q

K

A

A

R

K

D

R

I

I

E

E

K

D

A

A

V

V

E

L

K

V

V

A

L

L

E

N

D

N

D

G

Y

F

R

R

T

T

A

G

D
|
D

I

I

W

Y

S

S

P

A

G

G

T

T

K

K

K

L

V

V

N

G

T

C

A

K

E

E

M

M

T

G

E

E

I

V

I

L

K

K

R

S

L

V

active site: Y141 (= Y143), K192 (= K193), D224 (= D225), D248 (= D249), D252 (= D253)
binding magnesium ion: D248 (= D249), D252 (= D253)
binding nicotinamide-adenine-dinucleotide: I74 (≠ V76), E89 (= E91), L92 (= L94), I261 (≠ L262), E278 (= E278), H281 (= H281), G282 (= G282), S283 (= S283), A284 (= A284), I287 (= I287), N294 (= N294), D335 (= D335)

Q9SA14 3-isopropylmalate dehydrogenase 3, chloroplastic; 3-IPM-DH 3; AtIMDH2; AtIMDH3; IMDH 3; Beta-IPM dehydrogenase 3; Isopropylmalate dehydrogenase 3; AtIMD3; EC 1.1.1.85 from Arabidopsis thaliana (Mouse-ear cress) (see paper)
57% identity, 100% coverage: 1:357/357 of query aligns to 40:398/404 of Q9SA14

query
sites
Q9SA14

M

V

K

K

H

R

F

Y

K

N

I

I

A

T

V

L

L

L

P

P

G

G

D

D

G

G

I

I

G

G

P

P

E

E

I

V

I

I

E

S

S

V

A

A

L

K

K

N

V

V

L

L

D

Q

V

K

I

A

S

G

K

F

K

L

Y

Q

G

G

I

L

T

E

F

F

E

D

Y

F

K

Q

H

E

G

M

L

P

V

F

G

G

A

A

I

L

D

D

E

L

T

V

G

G

D

V

P

P

L

L

P

P

P

E

E

E

T

T

L

S

K

T

I

A

C

A

K

K

E

Q

S

S

D

D

A

A

V

I

L

L

F

L

G

G

A

A

V

I

G

G

E

Y

K

K

W

W

D

D

N

K

L

N

P

E

T

K

D

H

K

L

R

R

P

P

E

E

K

M

G

G

L

L

L
|
L

R

N

I

I

R

R

K

R

E

D

L

L

E

N

L

V

F

F

A

A

N

N

I

L

R

R

P

P

A

A

K

T

A

V

Y

L

A

P

P

Q

L

L

L

V

S

D

S

A

S

S

P

T

L

L

K

K

E

K

E

E

V

V

I

A

K

Q

G

G

V

V

D

D

L

M

V

M

V

I

L

V

R

R

E

E

L

L

T

T

G

G

D

G

V

I

Y

Y

F

F

G

G

E

E

P

P

R

R

G

G

R

I

E

T

V

I

R

N

-

E

N

N

G

G

E

E

R

E

V

V

G

G

Y

F

N

N

T

T

M

E

I

I

Y

Y

Y

A

E

A

H

H

E

E

I

I

K

D

R

R

I

I

A

A

K

R

V

V

A

A

F

F

E

E

M

T

A

A

R

R

N

K

R

R

K

G

K

K

V

L

T

C

S

S

V

V

D

D

K

K

A

A

N

N

V

V

L

L

E

D

V

A

S

S

G

I

L

L

W

W

R

R

E

K

V

R

V

V

N

T

E

A

V

L

H

A

A

S

D

E

Y

Y

L

P

D

D

V

V

D

E

L

L

E

S

H

H

M

M

Y

Y

V

V

D

D

N

N

C

A

A

A

M

M

Q

Q

L

L

I

V

R

R

R

D

P

P

K

K

D

Q

F

F

D

D

V

T

I

I

V

V

T

T

G

N

N

N

I

I

F

F

G

G

D

D

I

I

I

L

S

S

D

D

E

E

A

A

G

S

A

M

L

I

T

T

G

G

S

S

L

I

G

G

M

M

L

L

P

P

S

S

A

A

S

S

I

L

G

G

E

E

R

S

Y

G

-

P

A

G

F

L

Y

F

E

E

P

P

I

I

H

H

G

G

S

S

A

A

P

P

D

D

I

I

A

A

G

G

K

Q

G

D

I

K

A

A

N

N

P

P

I

L

A

A

T

T

I

I

L

L

S

S

A

A

M

M

M

L

L

L

E

K

I

Y

T

G

C

L

K

G

L

E

P

E

Q

K

A

A

R

K

D

M

I

I

E

E

K

D

A

A

V

V

E

V

K

D

V

A

L

L

E

N

D

K

D

G

Y

F

R

R

T

T

A

G

D

D

I

I

W

Y

S

S

P

P

G

G

T

N

K

K

K

L

V

V

N

G

T

C

A

K

E

E

M

M

T

G

E

E

I

V

I

L

K

K

R

S

L

V

L134 (= L95) Confers substrate specificity; mutation to F: Enhanced activity toward 3-(2'-methylthio)-ethylmalate, but reduced catalytic efficiency with 3-isopropylmalate.

6xxyA Crystal structure of haemophilus influenzae 3-isopropylmalate dehydrogenase in complex with o-isobutenyl oxalylhydroxamate. (see paper)
56% identity, 99% coverage: 3:357/357 of query aligns to 2:358/358 of 6xxyA

query
sites
6xxyA

K

E

H

S

F

Y

K

N

I

I

A

A

V

V

L

L

P

A

G

G

D

D

G

G

I

I

G

G

P

P

E

E

I

V

I

M

E

A

S

E

A

A

L

I

K

K

V

V

L

L

D

N

V

R

I

V

S

Q

K

E

K

K

Y

F

G

G

I

F

T

K

F

L

E

N

Y

F

K

N

H

E

G

F

L

F

V

V

G

G

A

A

I

I

D

E

E

H

T

C

G

G

D

Y

P

P

L

L

P

P

P

A

E

E

T

T

L

L

K

K

I

G

C

C

K

D

E

Q

S

A

D

D

A

A

V

I

L

L

F

F

G

G

A
x
S

V
|
V

G
|
G

G

G

E

P

K

K

W

W

D

T

N

N

L

L

P

P

T

P

D

D

K

Q

R

Q

P

P

E
|
E

K

R

G

G

-

A

L
|
L

L

L

R

P

I

L

R

R

K

K

E

H

L

F

E

K

L

L

F

F

A

C

N

N

I

L

R
|
R

P

P

A

A

K

T

A

L

Y

Y

A

K

P

G

L

L

L

E

S

K

S

F

S

C

P

P

L

L

K

R

E

A

E

D

V

I

I

A

-

A

K

K

G

G

V

F

D

D

L

M

V

V

L

V

R
|
R

E

E

L

L

T

T

G

G

D

G

V

I

Y
|
Y

F

F

G

G

E

Q

P

P

R

K

G

G

R

R

E

E

V

G

R

D

N

G

G

V

E

Q

R

T

V

K

G

A

Y

F

N

D

T

T

M

E

I

V

Y

Y

E

K

H

Y

E

E

I

I

K

E

R

R

I

I

A

A

K

R

V

A

A

A

F

F

E

E

M

A

A

A

R

M

N

K

R

R

R

N

K

K

V

V

T

T

S

S

V

V

D

D

K
|
K

A

A

N

N

V
|
V

L

L

E

Q

V

S

S

S

G

I

L

L

W

W

R

R

E

E

V

T

V

V

N

T

E

E

V

M

H

A

A

K

D

D

Y

Y

L

P

D

E

V

V

D

T

L

L

E

E

H

H

M

I

Y
|
Y

V

I

D
|
D

N
|
N

C

A

A

T

M
|
M

Q

Q

L

L

I

I

R

K

R

S

P

P

K

E

D

S

F

F

D

D

V

V

I

L

V

L

T

C

G

S

N

N

I

I

F

F

G

G

D
|
D

I

I

S

S

D
|
D

E

E

A

A

G

A

A

M

L

I

T

T

G

G

S

S

L
x
M

G
|
G

M

M

L

L

P

P

S

S

A

A

S

S

I

L

G

N

E

E

R

E

-

G

Y

F

A

G

F

L

Y

Y

E
|
E

P

P

I

A

H
x
G

G
|
G

S
|
S

A
|
A

P
|
P

D
|
D

I
|
I

A

A

G

G

K

K

G

G

I

I

A

A

N
|
N

P

P

I

I

A

A

T

Q

I

I

L

L

S

S

A

A

M

M

L

L

E

R

I

Y

T

S

C

F

K

N

L

L

P

N

Q

E

A

A

R

D

D

A

I

I

E

E

K

S

A

A

V

V

E

Q

K

K

V

V

L

L

E

A

D

S

D

G

Y

H

R

R

T

T

A

A

D
|
D

I

L

W

A

S

D

P

D

G

S

T

T

K

-

K

P

V

V

N

S

T

T

A

A

E

E

M

M

T

G

E

T

E

L

I

I

I

T

K

Q

R

A

L

I

active site: Y144 (= Y143), K194 (= K193), D226 (= D225), D250 (= D249)
binding magnesium ion: D250 (= D249), D254 (= D253)
binding nicotinamide-adenine-dinucleotide: S74 (≠ A75), V75 (= V76), G76 (= G77), E90 (= E91), L94 (= L94), Y224 (= Y223), N227 (= N226), M230 (= M229), M263 (≠ L262), G264 (= G263), E280 (= E278), G283 (≠ H281), G284 (= G282), S285 (= S283), A286 (= A284), P287 (= P285), D288 (= D286), I289 (= I287), N296 (= N294), D337 (= D335)
binding 2-(2-methylprop-2-enoxyamino)-2-oxidanylidene-ethanoic acid: E90 (= E91), R108 (= R108), R137 (= R136), K194 (= K193), V197 (= V196), D226 (= D225), D250 (= D249)

Q9FMT1 3-isopropylmalate dehydrogenase 1, chloroplastic; 3-IPM-DH 1; AtIMDH1; IMDH 1; Beta-IPM dehydrogenase 1; Isopropylmalate dehydrogenase 1; AtIMD1; Methylthioalkylmalate dehydrogenase 1; EC 1.1.1.85 from Arabidopsis thaliana (Mouse-ear cress) (see 2 papers)
57% identity, 100% coverage: 2:357/357 of query aligns to 44:401/409 of Q9FMT1

query
sites
Q9FMT1

K

K

H

R

F

Y

K

N

I

I

A

A

V

L

L

L

P

P

G

G

D

D

G

G

I

I

G

G

P

P

E

E

I

V

I

I

E

S

S

V

A

A

L

K

K

N

V

V

L

L

D

Q

V

K

I

A

S

G

K

S

K

L

Y

E

G

G

I

L

T

E

F

F

E

D

Y

F

K

K

H

E

G

M

L

P

V

V

G

G

A

A

I

L

D

D

E

L

T

V

G

G

D

V

P

P

L

L

P

P

P

E

E

E

T

T

L

F

K

T

I

A

C

A

K

K

E

L

S

S

D

D

A

A

V

I

L

L

F

L

G

G

A

A

V

I

G

G

E

Y

K

K

W

W

D

D

N

K

L

N

P

E

T

K

D

H

K

L

R

R

P

P

E

E

K

M

G

A

L

L

L
x
F

R

Y

I

L

R

R

K

R

E

D

L

L

E

K

L

V

F

F

A

A

N

N

I

L

R

R

P

P

A

A

K

T

A

V

Y

L

A

P

P

Q

L

L

L

V

S

D

S

A

S

S

P

T

L

L

K

K

E

K

E

E

V

V

I

A

K

E

G

G

V

V

D

D

L

M

V

M

V

I

L

V

R

R

E

E

L

L

T

T

G

G

D

G

V

I

Y

Y

F

F

G

G

E

E

P

P

R

R

G

G

R

I

E

T

V

I

R

N

-

E

N

N

G

G

E

E

R

E

V

V

G

G

Y

V

N

S

T

T

M

E

I

I

Y

Y

Y

A

E

A

H

H

E

E

I

I

K

D

R

R

I

I

A

A

K

R

V

V

A

A

F

F

E

E

M

T

A

A

R

R

N

K

R

R

K

G

K

K

V

L

T
x
C

S

S

V

V

D

D

K

K

A

A

N

N

V

V

L

L

E

D

V

A

S

S

G

I

L

L

W

W

R

R

E

K

V

R

V

V

N

T

E

A

V

L

H

A

A

S

D

E

Y

Y

L

P

D

D

V

V

D

E

L

L

E

S

H

H

M

M

Y

Y

V

V

D

D

N

N

C

A

A

A

M

M

Q

Q

L

L

I

I

R

R

R

D

P

P

K

K

D

Q

F

F

D

D

V

T

I

I

V

V

T

T

G

N

N

N

I

I

F

F

G

G

D

D

I

I

I

L

S

S

D

D

E

E

A

A

G

S

A

M

L

I

T

T

G

G

S

S

L

I

G

G

M

M

L

L

P

P

S

S

A

A

S

S

I

L

G

G

E

E

R

S

Y

G

-

P

A

G

F

L

Y

F

E

E

P

P

I

I

H

H

G

G

S

S

A

A

P

P

D

D

I

I

A

A

G

G

K

Q

G

D

I

K

A

A

N

N

P

P

I

L

A

A

T

T

I

I

L

L

S

S

A

A

M

M

M

L

L

L

E

K

I

Y

T

G

C

L

K

G

L

E

P

E

Q

K

A

A

R

K

D

R

I

I

E

E

K

D

A

A

V

V

E

V

K

D

V

A

L

L

E

N

D

K

D

G

Y

F

R

R

T

T

A

G

D

D

I

I

W

Y

S

S

P

P

G

G

T

N

K

K

K

L

V

V

N

G

T
x
C

A

K

E

E

M

M

T

G

E

E

I

V

I

L

K

K

R

S

L

V

F137 (≠ L95) Confers substrate specificity; mutation to L: Reduced activity toward 3-(2'-methylthio)-ethylmalate, but enhanced catalytic efficiency with 3-isopropylmalate.
C232 (≠ T189) Essential for redox regulation; mutation to S: Reduced sensitivity to oxidation on enzyme activity regulation.
C390 (≠ T346) Essential for redox regulation; mutation to S: Reduced sensitivity to oxidation on enzyme activity regulation.

1cnzA 3-isopropylmalate dehydrogenase (ipmdh) from salmonella typhimurium (see paper)
51% identity, 99% coverage: 1:355/357 of query aligns to 1:357/363 of 1cnzA

query
sites
1cnzA

M

M

K

S

K

K

H

N

F

Y

K

H

I

I

A

A

V

V

L

L

P

P

G

G

D

D

G

G

I

I

G

G

P

P

E

E

I

V

I

M

E

A

S

Q

A

A

L

L

K

K

V

V

L

M

D

D

V

A

I

V

S

R

K

S

K

R

Y

F

G

D

I

M

T

R

F

I

E

T

Y

T

K

S

H

H

G

Y

L

D

V

V

G

G

A

I

A

A

I

I

D

D

E

N

T

H

G

G

D

H

P

P

L

L

P

P

P

K

E

A

T

T

L

V

K

E

I

G

C

C

K

E

E

Q

S

A

D

D

A

A

V

I

L

L

F

F

G

G

A

S

V

V

G

G

E

P

K

K

W

W

D

E

N

N

L

L

P

P

T

P

D

E

K

S

R

Q

P

P

E

E

K

R

G

G

-

A

L

L

R

P

I

L

R

R

K

K

E

H

L

F

E

K

L

L

F

F

A

S

N

N

I

L

R

R

P

P

A

A

K

K

A

L

Y

Y

A

Q

P

G

L

L

L

E

S

A

S

F

S

C

P

P

L

L

K

R

E

A

E

D

V

I

I

A

-

A

K

N

G

G

V

F

D

D

L

I

V

L

V

C

L

V

R

R

E

E

L

L

T

T

G

G

D

G

V

I

Y
|
Y

F

F

G

G

E

Q

P

P

R

K

G

G

R

R

E

E

V

G

R

S

N

G

G

Q

E

Y

R

E

V

K

G

A

Y

F

N

D

T

T

M

E

I

V

Y

Y

Y

H

E

R

H

F

E

E

I

I

K

E

R

R

I

I

A

A

K

R

V

I

A

A

F

F

E

E

M

S

A

A

R

R

N

K

R

R

K

R

K

K

V

V

T

T

S

S

V

I

D

D

K
|
K

A

A

N

N

V

V

L

L

E

Q

V

S

S

S

G

I

L

L

W

W

R

R

E

E

V

I

V

V

N

N

E

D

V

V

H

A

A

K

D

T

Y

Y

L

P

D

D

V

V

D

E

L

L

E

A

H

H

M

M

Y

Y

V

I

D
|
D

N

N

C

A

A

T

M

M

Q

Q

L

L

I

I

R

K

R

D

P

P

K

S

D

Q

F

F

D

D

V

V

I

L

V

L

T

C

G

S

N

N

I

L

F

F

G

G

D
|
D

I

I

I

L

S

S

D
|
D

E

E

A

C

G

A

A

M

L

I

T

T

G

G

S

S

L

M

G

G

M

M

L

L

P

P

S

S

A

A

S

S

I

L

G

N

E

E

R

Q

-

G

Y

F

A

G

F

L

Y

Y

E

E

P

P

I

A

H

G

G

G

S

S

A

A

P

P

D

D

I

I

A

A

G

G

K

K

G

N

I

I

A

A

N

N

P

P

I

I

A

A

T

Q

I

I

L

L

S

S

A

L

A

A

M

L

L

L

E

R

I

Y

T

S

C

L

K

D

L

A

P

N

Q

D

A

A

R

T

D

A

I

I

E

E

K

Q

A

A

V

I

E

N

K

R

V

A

L

L

E

E

D

E

D

G

Y

V

R

R

T

T

A

G

D

D

I

L

W

-

S

A

P

R

G

G

T

A

K

A

V

V

N

S

T

T

A

D

E

E

M

M

T

G

E

D

E

I

I

I

I

A

K

R

active site: Y145 (= Y143), K195 (= K193), D227 (= D225), D251 (= D249)
binding manganese (ii) ion: D251 (= D249), D255 (= D253)

P37412 3-isopropylmalate dehydrogenase; 3-IPM-DH; Beta-IPM dehydrogenase; IMDH; EC 1.1.1.85 from Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (see paper)
51% identity, 99% coverage: 1:355/357 of query aligns to 1:357/363 of P37412

query
sites
P37412

M

M

K

S

K

K

H

N

F

Y

K

H

I

I

A

A

V

V

L

L

P

P

G

G

D

D

G

G

I

I

G

G

P

P

E

E

I

V

I

M

E

A

S

Q

A

A

L

L

K

K

V

V

L

M

D

D

V

A

I

V

S

R

K

S

K

R

Y

F

G

D

I

M

T

R

F

I

E

T

Y

T

K

S

H

H

G

Y

L

D

V

V

G

G

A

I

A

A

I

I

D

D

E

N

T

H

G

G

D

H

P

P

L

L

P

P

P

K

E

A

T

T

L

V

K

E

I

G

C

C

K

E

E

Q

S

A

D

D

A

A

V

I

L

L

F

F

G

G

A

S

V

V

G

G

E

P

K

K

W

W

D

E

N

N

L

L

P

P

T

P

D

E

K

S

R

Q

P

P

E

E

K

R

G

G

-

A

L

L

R

P

I

L

R

R

K

K

E

H

L

F

E

K

L

L

F

F

A

S

N

N

I

L

R

R

P

P

A

A

K

K

A

L

Y

Y

A

Q

P

G

L

L

L

E

S

A

S

F

S

C

P

P

L

L

K

R

E

A

E

D

V

I

I

A

-

A

K

N

G

G

V

F

D

D

L

I

V

L

V

C

L

V

R

R

E

E

L

L

T

T

G

G

D

G

V

I

Y

Y

F

F

G

G

E

Q

P

P

R

K

G

G

R

R

E

E

V

G

R

S

N

G

G

Q

E

Y

R

E

V

K

G

A

Y

F

N

D

T

T

M

E

I

V

Y

Y

Y

H

E

R

H

F

E

E

I

I

K

E

R

R

I

I

A

A

K

R

V

I

A

A

F

F

E

E

M

S

A

A

R

R

N

K

R

R

K

R

K

K

V

V

T

T

S

S

V

I

D

D

K

K

A

A

N

N

V

V

L

L

E

Q

V

S

S

S

G

I

L

L

W

W

R

R

E

E

V

I

V

V

N

N

E

D

V

V

H

A

A

K

D

T

Y

Y

L

P

D

D

V

V

D

E

L

L

E

A

H

H

M

M

Y

Y

V

I

D
|
D

N

N

C

A

A

T

M

M

Q

Q

L

L

I

I

R

K

R

D

P

P

K

S

D

Q

F

F

D

D

V

V

I

L

V

L

T

C

G

S

N

N

I

L

F

F

G

G

D
|
D

I

I

I

L

S

S

D
|
D

E

E

A

C

G

A

A

M

L

I

T

T

G

G

S

S

L

M

G

G

M

M

L

L

P

P

S

S

A

A

S

S

I

L

G

N

E

E

R

Q

-

G

Y

F

A

G

F

L

Y

Y

E

E

P

P

I

A

H

G

G

G

S

S

A

A

P

P

D

D

I

I

A

A

G

G

K

K

G

N

I

I

A

A

N

N

P

P

I

I

A

A

T

Q

I

I

L

L

S

S

A

L

A

A

M

L

L

L

E

R

I

Y

T

S

C

L

K

D

L

A

P

N

Q

D

A

A

R

T

D

A

I

I

E

E

K

Q

A

A

V

I

E

N

K

R

V

A

L

L

E

E

D

E

D

G

Y

V

R

R

T

T

A

G

D

D

I

L

W

-

S

A

P

R

G

G

T

A

K

A

V

V

N

S

T

T

A

D

E

E

M

M

T

G

E

D

E

I

I

I

I

A

K

R

D227 (= D225) binding Mn(2+)
D251 (= D249) binding Mn(2+)
D255 (= D253) binding Mn(2+)

3vmkA 3-isopropylmalate dehydrogenase from shewanella benthica db21 mt-2 (see paper)
53% identity, 99% coverage: 5:357/357 of query aligns to 9:366/369 of 3vmkA

query
sites
3vmkA

F

Y

K

Q

I

I

A

A

V

V

L

L

P

A

G

G

D

D

G

G

I

I

G

G

P

P

E

E

I

V

I

M

E

A

S

E

A

A

L

R

K

K

V

V

L

L

D

A

V

A

I

V

S

E

K

K

K

R

Y

F

G

D

I

L

T

S

F

I

E

E

Y

Y

K

S

H

E

G

Y

L

D

V

V

G

G

A

A

I

I

D

D

E

N

T

H

G

G

D

C

P

P

L

L

P

P

P

E

E

A

T

T

L

L

K

K

I

G

C

C

K

E

E

A

S

A

D

D

A

A

V

V

L

L

F

F

G

G

A

S

V

V

G

G

E

P

K

K

W

W

D

E

N

H

L

L

P

P

T

P

D

N

K

D

R

Q

P

P

E

E

K

R

G

G

-

A

L

L

R

P

I

L

R
|
R

K

G

E

H

L

F

E

E

L

L

F

F

A

C

N

N

I

M

R

R

P

P

A

A

K

K

A

L

Y

H

A

P

P

G

L

L

L

E

S

H

S

M

S

S

P

P

L

L

K

R

E

S

E

D

V

I

I

S

-

E

K

K

G

G

V

F

D

D

L

I

V

L

V

C

L

V

R
|
R

E

E

L

L

T

T

G

G

D

G

V

I

Y
|
Y

F

F

G

G

E

K

P

P

R

K

G

G

R

R

E

Q

V

G

R

E

N

G

G

E

E

N

R

E

V

E

G

A

Y

F

N

D

T

T

M

M

I

R

Y

Y

Y

S

E

R

H

K

E

E

I

I

K

R

R

R

I

I

A

A

K

K

V

I

A

A

F

F

E

E

M

S

A

A

R

Q

N

G

R

R

K

K

V

V

T

T

S

S

V

V

D

D

K
|
K

A

A

N
|
N

V

V

L

L

E

A

V

C

S

S

G

V

L

L

W

W

R

R

E

E

V

V

N

E

E

E

V

V

H

A

A

K

D

D

Y

Y

L

P

D

D

V

V

D

E

L

L

E

E

H

H

M

I

Y

Y

V

I

D
|
D

N

N

C

A

A

T

M

M

Q

Q

L

L

I

L

R

R

P

P

K

N

D

E

F

F

D

D

V

V

I

M

V

L

T

C

G

S

N

N

I

L

F

F

G

G

D
|
D

I

I

I

V

S

S

D
|
D

E

E

A

I

G

A

A

M

L

L

T

T

G

G

S

S

L

M

G

G

M

L

L

L

P

A

S

S

A

I

S

S

I

M

G

N

E

S

R

Q

-

G

Y

F

A

G

F

M

Y

Y

E

E

P

P

I

A

H

G

G

G

S

S

A

A

P

P

D

D

I

I

A

A

G

G

K

Q

G

G

I

I

A

A

N

N

P

P

I

V

A

A

T

Q

I

I

L

L

S

S

A

A

M

L

L

L

E

R

I

H

T

S

C

L

K

K

L

L

P

E

Q

D

A

A

R

L

D

A

I

I

E

E

K

A

A

A

V

V

E

S

K

K

V

A

L

L

E

S

D

D

D

G

Y

Y

R

L

T

T

A

C

D

E

I

L

W

L

-

P

-

A

S

S

P

E

G

R

T

S

K

Q

K

A

V

K

N

S

T

T

A

S

E

Q

M

M

T

G

E

D

E

Y

I

I

I

A

K

Q

R

A

L

I

active site: Y149 (= Y143), K199 (= K193), D231 (= D225), D255 (= D249), D259 (= D253)
binding 3-isopropylmalic acid: R103 (= R98), R142 (= R136), Y149 (= Y143), K199 (= K193), N201 (= N195), D255 (= D249)

2ztwA Structure of 3-isopropylmalate dehydrogenase in complex with the inhibitor and NAD+ (see paper)
59% identity, 90% coverage: 5:327/357 of query aligns to 1:319/345 of 2ztwA

query
sites
2ztwA

F

M

K

K

I

V

A

A

V

V

L

L

P

P

G

G

D

D

G

G

I
|
I

G

G

P

P

E

E

I

V

I

T

E

E

S

A

A

A

L

L

K

K

V

V

L

L

D

R

V

A

I

L

S

D

K

E

K

A

Y

E

G

G

I

L

T

G

F

L

E

A

Y

Y

K

E

H

V

G

F

L

P

V

F

G

G

A

A

I

I

D

D

E

A

T

F

G

G

D

E

P

P

L

F

P

P

P

E

E

P

T

T

L

R

K

K

I

G

C

V

K

E

E

E

S

A

D

E

A

A

V

V

L

L

F

L

G

G

A

S

V

V

G

G

E

P

K

K

W

W

D

D

N

G

L

L

P

P

T

R

D

K

K

I

R

R

P

P

E

E

K

T

G

G

L

L

R

S

I

L

R

R

K

K

E

S

L

Q

E

D

L

L

F

F

A

A

N

N

I

L

R

R

P

P

A

A

K

K

A

V

Y

F

A

P

P

G

L

L

L

E

S

R

S

L

S

S

P

P

L

L

K

K

E

E

V

I

I

A

K

R

G

G

V

V

D

D

L

V

V

L

V

I

L

V

R

R

E

E

L

L

T

T

G

G

D

G

V

I

Y
|
Y

F

F

G

G

E

E

P

P

R

R

G

G

R

M

E

S

V

-

R

-

N

-

G

-

E

E

R

A

V

E

G

A

Y

W

N

N

T

T

M

E

I

R

Y

Y

Y

S

E

K

H

P

E

E

I

V

K

E

R

R

I

V

A

A

K

R

V

V

A

A

F

F

E

E

M

A

A

A

R

R

N

K

R

R

K

K

K

H

V

V

T

V

S

S

V

V

D

D

K
|
K

A

A

N

N

V

V

L

L

E

E

V

V

S

G

G

E

L

F

W

W

R

R

E

K

V

T

V

V

N

E

E

E

V

V

H
x
G

A

R

D

G

Y
|
Y

L

P

D

D

V
|
V

D

A

L

L

E

E

H

H

M

Q

Y

Y

V

V

D
|
D

N

A

C

M

A

A

M

M

Q

H

L

L

I

V

R

R

R

S

P

P

K

A

D

R

F

F

D

D

V

V

I

V

V

V

T

T

G

G

N

N

I

I

F

F

G

G

D
|
D

I

I

I

L

S

S

D
|
D

E

L

A

A

G

S

A

V

L

L

T

P

G

G

S

S

L

L

G

G

M

L

L

L

P

P

S

S

A

A

S

S

I

L

G

G

E

R

R

G

Y

T

A

P

F

V

Y

F

E

E

P

P

I

V

H
|
H

G
|
G

S

S

A
|
A

P

P

D
|
D

I
|
I

A

A

G

G

K

K

G

G

I

I

A
|
A

N
|
N

P

P

I

T

A

A

T

A

I

I

L

L

S

S

A

A

M

M

L

L

E

E

I

H

T

A

C

F

K

G

L

L

P

V

Q

E

A

L

A

A

R

R

D

K

I

V

E

E

K

D

A

A

V

V

E

A

K

K

V

A

L

L

active site: Y139 (= Y143), K185 (= K193), D217 (= D225), D241 (= D249), D245 (= D253)
binding magnesium ion: G203 (≠ H211), Y206 (= Y214), V209 (= V217)
binding nicotinamide-adenine-dinucleotide: I11 (= I15), H273 (= H281), G274 (= G282), A276 (= A284), D278 (= D286), I279 (= I287), A285 (= A293), N286 (= N294)

Q5SIY4 3-isopropylmalate dehydrogenase; 3-IPM-DH; Beta-IPM dehydrogenase; IMDH; EC 1.1.1.85 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8) (see 2 papers)
59% identity, 90% coverage: 5:327/357 of query aligns to 1:319/345 of Q5SIY4

query
sites
Q5SIY4

F

M

K

K

I

V

A

A

V

V

L

L

P

P

G

G

D

D

G

G

I

I

G

G

P

P

E

E

I

V

I

T

E

E

S

A

A

A

L

L

K

K

V

V

L

L

D

R

V

A

I

L

S

D

K

E

K

A

Y

E

G

G

I

L

T

G

F

L

E

A

Y

Y

K

E

H

V

G

F

L

P

V

F

G

G

A

A

I

I

D

D

E

A

T

F

G

G

D

E

P

P

L

F

P

P

P

E

E

P

T

T

L

R

K

K

I

G

C

V

K

E

E

E

S

A

D

E

A

A

V

V

L

L

F

L

G

G

A

S

V

V

G

G

G
|
G

E
x
P

K
|
K

W
|
W

D
|
D

N
x
G

L
|
L

P
|
P

T
x
R

D
x
K

K
x
I

R
|
R

P
|
P

E
|
E

K

T

G

G

L

L

R

S

I

L

R

R

K

K

E

S

L

Q

E

D

L

L

F

F

A

A

N

N

I

L

R

R

P

P

A

A

K

K

A

V

Y

F

A

P

P

G

L

L

L

E

S

R

S

L

S

S

P

P

L

L

K

K

E

E

V

I

I

A

K

R

G

G

V

V

D

D

L

V

V

L

V

I

L

V

R

R

E

E

L

L

T

T

G

G

D

G

V

I

Y
|
Y

F

F

G

G

E

E

P

P

R

R

G

G

R

M

E

S

V

-

R

-

N

-

G

-

E

E

R

A

V

E

G

A

Y

W

N

N

T

T

M

E

I

R

Y

Y

Y

S

E

K

H

P

E

E

I

V

K

E

R

R

I

V

A

A

K

R

V

V

A

A

F

F

E

E

M

A

A

A

R

R

N

K

R

R

K

K

K

H

V

V

T

V

S

S

V

V

D

D

K

K

A

A

N

N

V

V

L

L

E

E

V

V

S

G

G

E

L

F

W

W

R

R

E

K

V

T

V

V

N

E

E

E

V

V

H

G

A

R

D

G

Y

Y

L

P

D

D

V

V

D

A

L

L

E

E

H

H

M

Q

Y

Y

V

V

D

D

N

A

C

M

A

A

M

M

Q

H

L

L

I

V

R

R

R

S

P

P

K

A

D

R

F

F

D

D

V

V

I

V

V

V

T

T

G

G

N

N

I

I

F

F

G

G

D

D

I

I

I

L

S

S

D

D

E

L

A

A

G

S

A

V

L

L

T

P

G

G

S

S

L

L

G

G

M

L

L

L

P

P

S

S

A

A

S

S

I

L

G

G

E

R

R

G

Y

T

A

P

F

V

Y

F

E

E

P

P

I

V

H

H

G
|
G

S
|
S

A
|
A

P
|
P

D
|
D

I
|
I

A
|
A

G
|
G

K
|
K

G
|
G

I
|
I

A
|
A

N
|
N

P

P

I

T

A

A

T

A

I

I

L

L

S

S

A

A

M

M

L

L

E

E

I

H

T

A

C

F

K

G

L

L

P

V

Q

E

A

L

A

A

R

R

D

K

I

V

E

E

K

D

A

A

V

V

E

A

K

K

V

A

L

L

74:87 (vs. 78:91, 64% identical) binding NAD(+)
Y139 (= Y143) mutation to F: Large decrease in activity and a small decrease in substrate affinity.
274:286 (vs. 282:294, 100% identical) binding NAD(+)

2y42D Structure of isopropylmalate dehydrogenase from thermus thermophilus - complex with nadh and mn (see paper)
59% identity, 90% coverage: 5:327/357 of query aligns to 2:320/355 of 2y42D

query
sites
2y42D

F

M

K

K

I

V

A

A

V

V

L

L

P

P

G

G

D

D

G

G

I
|
I

G

G

P

P

E

E

I

V

I

T

E

E

S

A

A

A

L

L

K

K

V

V

L

L

D

R

V

A

I

L

S

D

K

E

K

A

Y

E

G

G

I

L

T

G

F

L

E

A

Y

Y

K

E

H

V

G

F

L

P

V

F

G

G

A

A

I

I

D

D

E

A

T

F

G

G

D

E

P

P

L

F

P

P

P

E

E

P

T

T

L

R

K

K

I

G

C

V

K

E

E

E

S

A

D

E

A

A

V

V

L

L

F

L

G

G

A

S

V

V

G

G

E

P

K

K

W

W

D
|
D

N

G

L

L

P

P

T

R

D

K

K

I

R

R

P

P

E

E

K

T

G

G

L

L

R

S

I

L

R

R

K

K

E

S

L

Q

E

D

L

L

F

F

A

A

N

N

I

L

R

R

P

P

A

A

K

K

A

V

Y

F

A

P

P

G

L

L

L

E

S

R

S

L

S

S

P

P

L

L

K

K

E

E

V

I

I

A

K

R

G

G

V

V

D

D

L

V

V

L

V

I

L

V

R

R

E

E

L

L

T

T

G

G

D

G

V

I

Y
|
Y

F

F

G

G

E

E

P

P

R

R

G

G

R

M

E

S

V

-

R

-

N

-

G

-

E

E

R

A

V

E

G

A

Y

W

N

N

T

T

M

E

I

R

Y

Y

Y

S

E

K

H

P

E

E

I

V

K

E

R

R

I

V

A

A

K

R

V

V

A

A

F

F

E

E

M

A

A

A

R

R

N

K

R

R

K

K

K

H

V

V

T

V

S

S

V

V

D

D

K
|
K

A

A

N

N

V

V

L

L

E

E

V

V

S

G

G

E

L

F

W

W

R

R

E

K

V

T

V

V

N

E

E

E

V

V

H

G

A

R

D

G

Y

Y

L

P

D

D

V

V

D

A

L

L

E

E

H

H

M

Q

Y

Y

V

V

D
|
D

N

A

C

M

A

A

M

M

Q

H

L

L

I

V

R

R

R

S

P

P

K

A

D

R

F

F

D

D

V

V

I

V

V

V

T

T

G

G

N

N

I

I

F

F

G

G

D
|
D

I

I

I

L

S

S

D
|
D

E

L

A

A

G

S

A

V

L

L

T

P

G

G

S

S

L

L

G

G

M

L

L

L

P

P

S

S

A

A

S

S

I

L

G

G

E

R

R

G

Y

T

A

P

F

V

Y

F

E

E

P

P

I

V

H
|
H

G
|
G

S

S

A
|
A

P

P

D
|
D

I
|
I

A

A

G

G

K

K

G

G

I

I

A

A

N
|
N

P

P

I

T

A

A

T

A

I

I

L

L

S

S

A

A

M

M

L

L

E

E

I

H

T

A

C

F

K

G

L

L

P

V

Q

E

A

L

A

A

R

R

D

K

I

V

E

E

K

D

A

A

V

V

E

A

K

K

V

A

L

L

active site: Y140 (= Y143), K186 (= K193), D218 (= D225), D242 (= D249), D246 (= D253)
binding manganese (ii) ion: D242 (= D249), D246 (= D253)
binding nicotinamide-adenine-dinucleotide: I12 (= I15), D79 (= D82), H274 (= H281), G275 (= G282), A277 (= A284), D279 (= D286), I280 (= I287), N287 (= N294)

2y41A Structure of isopropylmalate dehydrogenase from thermus thermophilus - complex with ipm and mn (see paper)
59% identity, 90% coverage: 5:327/357 of query aligns to 2:320/346 of 2y41A

query
sites
2y41A

F

M

K

K

I

V

A

A

V

V

L

L

P

P

G

G

D

D

G

G

I

I

G

G

P

P

E

E

I

V

I

T

E

E

S

A

A

A

L

L

K

K

V

V

L

L

D

R

V

A

I

L

S

D

K

E

K

A

Y

E

G

G

I

L

T

G

F

L

E

A

Y

Y

K

E

H

V

G

F

L

P

V

F

G

G

A

A

I

I

D

D

E

A

T

F

G

G

D

E

P

P

L

F

P

P

P

E

E

P

T

T

L

R

K

K

I

G

C

V

K

E

E

E

S

A

D

E

A

A

V

V

L

L

F

L

G

G

A

S

V

V

G

G

E

P

K

K

W

W

D

D

N

G

L

L

P

P

T

R

D

K

K

I

R

R

P

P

E

E

K

T

G

G

L

L

R

S

I

L

R
|
R

K

K

E

S

L

Q

E

D

L

L

F

F

A

A

N

N

I

L

R
|
R

P

P

A

A

K

K

A

V

Y

F

A

P

P

G

L

L

L

E

S

R

S

L

S

S

P

P

L

L

K

K

E

E

V

I

I

A

K

R

G

G

V

V

D

D

L

V

V

L

V

I

L

V

R
|
R

E

E

L

L

T

T

G

G

D

G

V

I

Y
|
Y

F

F

G

G

E

E

P

P

R

R

G

G

R

M

E

S

V

-

R

-

N

-

G

-

E

E

R

A

V

E

G

A

Y

W

N

N

T

T

M

E

I

R

Y

Y

Y

S

E

K

H

P

E

E

I

V

K

E

R

R

I

V

A

A

K

R

V

V

A

A

F

F

E

E

M

A

A

A

R

R

N

K

R

R

K

K

K

H

V

V

T

V

S

S

V

V

D

D

K
|
K

A

A

N

N

V

V

L

L

E

E

V

V

S

G

G

E

L

F

W

W

R

R

E

K

V

T

V

V

N

E

E

E

V

V

H

G

A

R

D

G

Y

Y

L

P

D

D

V

V

D

A

L

L

E

E

H

H

M

Q

Y

Y

V

V

D
|
D

N

A

C

M

A

A

M

M

Q

H

L

L

I

V

R

R

R

S

P

P

K

A

D

R

F

F

D

D

V

V

I

V

V

V

T

T

G

G

N

N

I

I

F

F

G

G

D
|
D

I

I

I

L

S

S

D
|
D

E

L

A

A

G

S

A

V

L

L

T

P

G

G

S

S

L

L

G

G

M

L

L

L

P

P

S

S

A

A

S

S

I

L

G

G

E

R

R

G

Y

T

A

P

F

V

Y

F

E

E

P

P

I

V

H

H

G

G

S

S

A

A

P

P

D

D

I

I

A

A

G

G

K

K

G

G

I

I

A

A

N

N

P

P

I

T

A

A

T

A

I

I

L

L

S

S

A

A

M

M

L

L

E

E

I

H

T

A

C

F

K

G

L

L

P

V

Q

E

A

L

A

A

R

R

D

K

I

V

E

E

K

D

A

A

V

V

E

A

K

K

V

A

L

L

active site: Y140 (= Y143), K186 (= K193), D218 (= D225), D242 (= D249), D246 (= D253)
binding 3-isopropylmalic acid: R95 (= R98), R105 (= R108), R133 (= R136), Y140 (= Y143), D242 (= D249)

3vkzA 3-isopropylmalate dehydrogenase from shewanella oneidensis mr-1 at atmospheric pressure (see paper)
54% identity, 94% coverage: 5:338/357 of query aligns to 3:339/364 of 3vkzA

query
sites
3vkzA

F

Y

K

Q

I

I

A

A

V

V

L

L

P

A

G

G

D

D

G

G

I

I

G

G

P

P

E

E

I

V

I

M

E

A

S

E

A

A

L

R

K

K

V

V

L

L

D

K

V

A

I

V

S

E

K

A

K

R

Y

F

G

G

I

L

T

N

F

I

E

E

Y

Y

K

T

H

E

G

Y

L

D

V

V

G

G

A

I

A

A

I

I

D

D

E

N

T

H

G

G

D

C

P

P

L

L

P

P

P

E

E

A

T

T

L

L

K

K

I

G

C

C

K

E

E

A

S

A

D

D

A

A

V

I

L

L

F

F

G

G

A

S

V

V

G

G

E

P

K

K

W

W

D

E

N

K

L

L

P

P

T

P

D

N

K

E

R

Q

P

P

E

E

K

R

G

G

-

A

L

L

R

P

I

L

R
|
R

K

G

E

H

L

F

E

E

L

L

F

F

A

C

N

N

I

L

R

R

P

P

A

A

K

K

A

L

Y

H

A

D

P

G

L

L

L

E

S

H

S

M

S

S

P

P

L

L

K

R

E

S

E

D

V

I

-

S

I

A

K

R

G

G

V

F

D

D

L

V

V

L

V

C

L

V

R
|
R

E

E

L

L

T

T

G

G

D

G

V

I

Y
|
Y

F

F

G

G

E

K

P

P

R

K

G

G

R

R

E

Q

V

G

R

E

N

G

G

E

E

S

R

E

V

E

G

A

Y

F

N

D

T

T

M

M

I

R

Y

Y

Y

S

E

R

H

R

E

E

I

I

K

S

R

R

I

I

A

A

K

R

V

I

A

A

F

F

E

E

M

A

A

A

R

R

N

G

R

R

K

K

V

V

T

T

S

S

V

V

D

D

K
|
K

A

A

N

N

V

V

L

L

E

A

V

C

S

S

G

V

L

L

W

W

R

R

E

Q

V

V

N

E

E

E

V

V

H

A

A

V

D

D

Y

F

L

P

D

D

V

V

D

E

L

L

E

E

H

H

M

I

Y

Y

V

I

D
|
D

N

N

C

A

A

T

M

M

Q

Q

L

L

I

L

R

R

P

P

K

D

D

E

F

F

D

D

V

V

I

M

V

L

T

C

G

S

N

N

I

L

F

F

G

G

D
|
D

I

I

I

L

S

S

D
|
D

E

E

A

I

G

A

A

M

L

L

T

T

G

G

S

S

L

M

G

G

M

L

L

L

P

S

S

S

A

A

S

S

I

M

G

N

E

S

R

T

-

G

Y

F

A

G

F

L

Y

F

E

E

P

P

I

A

H

G

G

G

S

S

A

A

P

P

D

D

I

I

A

A

G

G

K

K

G

G

I

I

A

A

N

N

P

P

I

I

A

A

T

Q

I

I

L

L

S

S

A

A

M

L

M

M

L

L

E

R

I

H

T

S

C

L

K

K

L

Q

P

E

Q

E

A

A

R

S

D

A

I

I

E

E

K

R

A

A

V

V

E

T

K

K

V

A

L

L

E

N

D

S

D

G

Y

Y

R

L

T

T

A

G

D

E

I

L

W

L

S

S

active site: Y143 (= Y143), K193 (= K193), D225 (= D225), D249 (= D249), D253 (= D253)
binding calcium ion: D249 (= D249), D253 (= D253)
binding 3-isopropylmalic acid: R97 (= R98), R136 (= R136), Y143 (= Y143), D249 (= D249)

P18869 3-isopropylmalate dehydrogenase; 3-IPM-DH; IMDH; Beta-IPM dehydrogenase; EC 1.1.1.85 from Schizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast) (see paper)
48% identity, 91% coverage: 6:329/357 of query aligns to 5:337/371 of P18869

query
sites
P18869

K

K

I

I

A

V

V

V

L

L

P

P

G

G

D

D

G

H

I

I

G

G

P

P

E

E

I

I

I

V

E

A

S

S

A

A

L

L

K

E

V

V

L

L

D

K

V

V

I

V

S

E

K

K

Y

R

G

P

-

E

I

L

T

K

F

L

E

E

Y

F

K

E

H

E

G

H

L

K

V

I

G

G

A

A

A

S

I

I

D

D

E

A

T

Y

G

G

D
x
T

P

P

L

L

P

T

P

D

E

E

T

T

L

V

K

K

I

A

C

C

K

L

E

E

S

A

D

D

A

G

V

V

L

L

F

L

G

G

A

A

V

V

G

G

E

P

K

E

W

W

D

T

N

N

L

-

P

-

T

P

D

N

K

C

R

R

P

P

E

E

K

Q

G

G

L

L

R

K

I

L

R

R

K

K

E

S

L

M

E

G

L

V

F

W

A

A

N

N

I

L

R

R

P

P

A

C

K

N

-

F

A

A

Y

S

A

K

P

S

L

L

L

V

S

K

S

Y

S

S

P

P

L

L

K

K

E

P

E

E

V

I

I

V

K

E

G

G

V

V

D

D

L

F

V

C

V

V

L

V

R

R

E

E

L

L

T

T

G

G

D

G

V

C

Y

Y

F

F

G

G

E

E

P

-

R

-

G

-

R

R

E

T

V

E

R

D

N

N

G

G

E

S

R

G

V

Y

G

A

Y

M

N

D

T

T

M

W

I

P

Y

Y

Y

S

E

L

H

E

E

E

I

V

K

S

R

R

I

I

A

A

K

R

V

L

A

A

F

A

E

W

M

L

A

A

R

E

-

T

-

S

N

N

R

P

K

A

K

P

V

V

T

T

S

L

V

L

D

D

K

K

A

A

N

N

V

V

L

L

E

A

V

T

S

S

G

R

L

L

W

W

R

R

E

K

V

T

V

V

N

A

E

K

V

I

H

F

A

K

D

E

-

E

Y

Y

L

P

D

H

V

L

D

T

L

L

E

K

H

N

M

Q

Y

L

V

I

D

D

N

S

C

A

A

A

M

M

Q

L

L

L

I

V

R

K

R

S

P

P

K

R

D

T

F

L

D

N

-

G

V

V

I

V

V

L

T

T

G

D

N

N

I

L

F

F

G

G

D

D

I

I

S

S

D

D

E

E

A

A

G

S

A

V

L

I

T

P

G

G

S

S

L

L

G

G

M

L

L

L

P

P

S

S

A

A

S

S

I

L

G

S

-

G

-

V

-

G

-

K

-

S

-

E

E

K

R

V

Y

H

A

C

F

L

Y

V

E

E

P

P

I

I

H

H

G

G

S

S

A

A

P

P

D

D

I

I

A

A

G

G

K

K

G

G

I

I

A

V

N

N

P

P

I

V

A

G

T

T

I

I

L

L

S

S

A

A

A

S

M

L

L

L

E

R

I

Y

T

G

C

L

K

N

L

A

P

P

Q

K

A

E

A

A

R

E

D

A

I

I

E

E

K

A

A

A

V

V

E

R

K

K

V

V

L

L

E

D

D

D

T55 (≠ D55) modified: Phosphothreonine

Q72IW9 Isocitrate/homoisocitrate dehydrogenase; Homoisocitrate dehydrogenase; HICDH; EC 1.1.1.286 from Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27) (see 4 papers)
41% identity, 98% coverage: 5:353/357 of query aligns to 3:331/334 of Q72IW9

query
sites
Q72IW9

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E57 (≠ K63) mutation to V: Confers enzyme activity with 3-isopropylmalate; when associated with I-72; M-85; A-86; T-208; Y-217; M-238 and M-310.
A------TS 70:72 (≠ VGGEKWDNL 76:84) binding NADH
S72 (≠ L84) binding in other chain; mutation to I: Confers enzyme activity with 3-isopropylmalate; when associated with V-57; M-85; A-86; T-208; Y-217; M-238 and M-310.
R85 (= R96) binding in other chain; mutation to M: Confers enzyme activity with 3-isopropylmalate; when associated with V-57; I-72; A-86; T-208; Y-217; M-238 and M-310.; mutation to V: Confers low enzyme activity with 3-isopropylmalate. Reduces activity with homoisocitrate. Abolishes activity with isocitrate.
Y86 (vs. gap) mutation to A: Confers enzyme activity with 3-isopropylmalate; when associated with V-57; I-72; M-85; T-208; Y-217; M-238 and M-310.
R88 (= R98) binding in other chain
R98 (= R108) binding in other chain
R118 (= R136) binding in other chain
Y125 (= Y143) binding in other chain; mutation to A: Reduces catalytic efficiency with isocitrate.
V135 (= V158) mutation to M: Formation of homodimers instead of homotetramers. Increased affinity for isocitrate. Reduces enzyme activity with isocitrate.
K171 (= K193) binding (2R,3S)-homoisocitrate
N173 (= N195) binding (2R,3S)-homoisocitrate; binding NADH
D204 (= D225) binding Mg(2+)
M208 (= M229) mutation to T: Confers enzyme activity with 3-isopropylmalate; when associated with V-57; I-72; M-85; A-86; T-208; Y-217; M-238 and M-310.
F217 (= F238) mutation to Y: Confers enzyme activity with 3-isopropylmalate; when associated with V-57; I-72; M-85; A-86; T-208; M-238 and M-310.
D228 (= D249) binding Mg(2+)
D232 (= D253) binding Mg(2+)
V238 (≠ T259) mutation to M: Confers enzyme activity with 3-isopropylmalate; when associated with V-57; I-72; M-85; A-86; T-208; Y-217; and M-310.
GSAPD 261:265 (= GSAPD 282:286) binding NADH
N273 (= N294) binding NADH
R310 (= R332) mutation to M: Confers enzyme activity with 3-isopropylmalate; when associated with V-57; I-72; M-85; A-86; T-208; Y-217; and M-238.

Query Sequence

>WP_012674776.1 NCBI__GCF_000021545.1:WP_012674776.1
MKKHFKIAVLPGDGIGPEIIESALKVLDVISKKYGITFEYKHGLVGGAAIDETGDPLPPE
TLKICKESDAVLFGAVGGEKWDNLPTDKRPEKGLLRIRKELELFANIRPAKAYAPLLSSS
PLKEEVIKGVDLVVLRELTGDVYFGEPRGREVRNGERVGYNTMIYYEHEIKRIAKVAFEM
ARNRRKKVTSVDKANVLEVSGLWREVVNEVHADYLDVDLEHMYVDNCAMQLIRRPKDFDV
IVTGNIFGDIISDEAGALTGSLGMLPSASIGERYAFYEPIHGSAPDIAGKGIANPIATIL
SAAMMLEITCKLPQAARDIEKAVEKVLEDDYRTADIWSPGTKKVNTAEMTEEIIKRL

Or try a new SitesBLAST search

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