SitesBLAST

Q56268 3-isopropylmalate dehydrogenase; 3-IPM-DH; Beta-IPM dehydrogenase; IMDH; EC 1.1.1.85 from Acidithiobacillus ferrooxidans (Thiobacillus ferrooxidans) (see paper)
62% identity, 100% coverage: 2:355/355 of query aligns to 3:354/358 of Q56268

query
sites
Q56268

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R95 (= R94) binding substrate
R105 (= R104) binding substrate
R133 (= R133) binding substrate
D222 (= D222) binding Mg(2+); binding substrate
D246 (= D246) 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)
62% identity, 99% coverage: 3:355/355 of query aligns to 45:397/405 of P93832

query
sites
P93832

I

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114:129 (vs. 72:87, 50% identical) binding NAD(+)
L132 (= L90) mutation to A: Reduced activity toward 3-isopropylmalate.
L133 (= L91) 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 (= R94) binding substrate; mutation to A: Loss of activity toward 3-isopropylmalate.; mutation to K: Reduced activity toward 3-isopropylmalate.
R146 (= R104) binding substrate; mutation to A: Reduced activity toward 3-isopropylmalate.; mutation to K: Reduced activity toward 3-isopropylmalate.
R174 (= R133) binding substrate; mutation to A: Loss of activity toward 3-isopropylmalate.; mutation to K: Reduced activity toward 3-isopropylmalate.
Y181 (= Y140) Important for catalysis; mutation Y->A,F,H: Reduced activity toward 3-isopropylmalate.
K232 (= K190) Important for catalysis; mutation to M: Loss of activity toward 3-isopropylmalate.
N234 (= N192) binding NAD(+); mutation N->A,D: Loss of activity toward 3-isopropylmalate.
V235 (= V193) mutation to A: Reduced activity toward 3-isopropylmalate.
D264 (= D222) binding Mg(2+); binding substrate; mutation to N: Loss of activity toward 3-isopropylmalate.
N265 (= N223) binding NAD(+)
D288 (= D246) binding Mg(2+); mutation to N: Loss of activity toward 3-isopropylmalate.
D292 (= D250) binding Mg(2+); mutation to N: Reduced activity toward 3-isopropylmalate.
318:334 (vs. 276:292, 100% identical) binding NAD(+)

4xxvA Crystal structure of 3-isopropylmalate dehydrogenase from burkholderia thailandensis in complex with NAD
61% identity, 100% coverage: 1:355/355 of query aligns to 2:356/356 of 4xxvA

query
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4xxvA

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active site: Y136 (= Y140), K191 (= K190), D223 (= D222), D247 (= D246), D251 (= D250)
binding nicotinamide-adenine-dinucleotide: N193 (= N192), Y221 (= Y220), N224 (= N223)

4iwhA Crystal structure of a 3-isopropylmalate dehydrogenase from burkholderia pseudomallei
61% identity, 100% coverage: 1:355/355 of query aligns to 4:358/358 of 4iwhA

query
sites
4iwhA

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E

L

L

T

N

G

G

G

D

I

I

Y
|
Y

F

F

G

G

E

Q

P

P

R

R

-

G

-

V

-

R

-

A

L

P

E

D

G

G

E

P

I

F

E

A

G

G

E

E

R

R

Y

E

G

G

Y

F

N

D

T

T

M

M

V

R

Y

Y

R

S

E

E

H

P

E

E

I

V

R

R

I

I

A

A

R

H

V

V

A

A

F

F

E

Q

A

A

R

Q

K

K

R

R

G

A

G

K

R

K

V

L

C

L

S

S

V

V

D

D

K
|
K

A

S

N

N

V

V

L

L

D

E

V

T

S

S

R

Q

V

F

W

W

R

R

D

D

V

V

V

M

V

I

D

D

E

V

H

S

A

K

E

E

Y

Y

A

A

D

D

V

V

E

E

L

L

S

S

H

H

M

M

Y

Y

V

V

D
|
D

N

N

A

A

M

M

Q

Q

L

L

V

A

R

K

D

A

P

P

G

K

Q

Q

F

F

D

D

V

V

I

I

V

V

T

T

G

G

N

N

L

M

F

F

G

G

D
|
D

I

I

L

L

S

S

D
|
D

E

E

A

A

A

S

A

M

I

L

T

T

G

G

S

S

I

I

G

G

M

M

L

L

P

P

S

S

A

A

S

S

L

L

G

D

A

K

D

N

G

N

P

K

G

G

L

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

Q

K

D

G

K

I

A

A

N

N

P

P

L

L

A

A

T

T

I

I

L

L

S

S

I

A

A

A

M

M

M

L

L

L

R

R

H

Y

S

S

M

L

D

N

M

R

A

A

E

E

E

Q

A

A

D

D

C

R

I

I

E

E

Q

R

A

A

V

V

Q

K

K

T

T

V

L

L

E

E

Q

Q

G

G

Y

Y

R

R

T

T

G

G

D

D

I

I

M

A

E

T

Q

P

G

G

A

C

K

R

A

Q

V

V

G

G

T

T

K

A

A

A

M

M

G

G

A

D

A

A

V

V

L

V

E

A

N

A

L

L

active site: Y138 (= Y140), K193 (= K190), D225 (= D222), D249 (= D246), D253 (= D250)
binding magnesium ion: D249 (= D246), D253 (= D250)

5j32A Isopropylmalate dehydrogenase in complex with isopropylmalate (see paper)
62% identity, 99% coverage: 3:355/355 of query aligns to 15:367/369 of 5j32A

query
sites
5j32A

I

I

C

T

I

L

L
|
L

A

P

G

G

D

D

G

G

I

I

G

G

P

P

E

E

I

V

V

V

A

S

Q

I

G

A

V

K

K

N

V

V

L

L

D

Q

K

Q

V

A

G

G

E

S

K

L

F

E

G

G

C

V

T

E

F

F

E

N

Y

F

S

R

E

E

A

M

L

P

I

I

G

G

V

A

A

A

I

L

D

D

A

L

T

V

G

G

G

V

P

P

L

L

P

P

D

E

S

E

T

T

V

I

E

S

R

A

C

A

K

K

E

E

A

S

D

D

A

A

V

V

L

L

G

G

A

A

V

I

G

G

P

Y

K

K

W

W

D

D

T

N

I

N

D

E

P

K

S

H

I

L

R

R

P

P

E

E

K

K

G

G

L

L

G

Q

I

I

R
|
R

K

A

A

A

M

L

G

K

L

V

F

F

A

A

N

N

L

L

R

R

P

P

A

A

V

T

L

V

F

L

P

P

Q

Q

L

L

K

V

H

D

A

A

C

S

Y

T

L

L

R

K

P

R

D

E

I

V

V

A

E

E

N

-

G

G

L

V

D

D

V

L

M

M

V

V

R
|
R

E

E

L

L

T

T

G

G

I

I

Y
|
Y

F

F

G

G

E

E

P

P

R

R

-

G

L

I

E

K

G

T

E

N

I

E

E

N

G

G

E

E

R

E

Y

V

G

G

Y

F

N

N

T

T

M

E

V

V

Y

Y

R

A

E

A

H

H

E

E

I

I

R

D

R

R

I

I

A

A

R

R

V

V

A

A

F

F

E

E

A

T

A

A

R

R

K

K

R

R

G

R

G

G

R

K

V

L

C

C

S

S

V

V

D

D

K
|
K

A

A

N

N

V

V

L

L

D

E

V

A

S

S

R

I

V

L

W

W

R

R

D

K

V

R

V

V

V

T

D

A

E

L

H

A

A

S

E

E

Y

Y

A

P

D

D

V

V

E

E

L

L

S

S

H

H

M

M

Y

Y

V

V

D
|
D

N

N

A

A

M

M

Q

Q

L

L

V

V

R

R

D

D

P

P

G

K

Q

Q

F

F

D

D

V

T

I

I

V

V

T

T

G

N

N

N

L

I

F

F

G

G

D
|
D

I

I

L

L

S

S

D
|
D

E

E

A

A

A

S

A

M

I

I

T

T

G

G

S

S

I

I

G

G

M

M

L

L

P

P

S

S

A

A

S

S

L

L

G

S

A

D

D

S

G

G

P

P

G

G

L

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

Q

Q

D

D

K

K

A

A

N

N

P

P

L

L

A

A

T

T

I

I

L

L

S

S

I

A

A

A

M

M

M

L

L

L

R

K

H

Y

S

G

M

L

D

G

M

E

A

E

E

K

E

A

A

A

D

K

C

R

I

I

E

E

Q

D

A

A

V

V

Q

L

K

V

T

A

L

L

E

N

Q

N

G

G

Y

F

R

R

T

T

G

G

D

D

I

I

M

Y

E

S

Q

A

G

G

A

T

K

K

A

L

V

V

G

G

T

C

K

K

A

E

M

M

G

G

A

E

V

V

L

L

E

K

N

S

L

V

active site: L18 (= L6), Y151 (= Y140), K202 (= K190), D234 (= D222), D258 (= D246), D262 (= D250)
binding 3-isopropylmalic acid: R106 (= R94), R144 (= R133), Y151 (= Y140), D258 (= D246)
binding magnesium ion: D258 (= D246), D262 (= D250)

5j33A Isopropylmalate dehydrogenase in complex with NAD+ (see paper)
62% identity, 99% coverage: 3:355/355 of query aligns to 5:357/360 of 5j33A

query
sites
5j33A

I

I

C

T

I

L

L

L

A

P

G

G

D

D

G

G

I

I

G

G

P

P

E

E

I

V

V

V

A

S

Q

I

G

A

V

K

K

N

V

V

L

L

D

Q

K

Q

V

A

G

G

E

S

K

L

F

E

G

G

C

V

T

E

F

F

E

N

Y

F

S

R

E

E

A

M

L

P

I

I

G

G

V

A

A

A

I

L

D

D

A

L

T

V

G

G

G

V

P

P

L

L

P

P

D

E

S

E

T

T

V

I

E

S

R

A

C

A

K

K

E

E

A

S

D

D

A

A

V

V

L

L

G

G

A

A

V
x
I

G

G

P

Y

K

K

W

W

D

D

T

N

I

N

D

E

P

K

S

H

I

L

R

R

P

P

E
|
E

K

K

G

G

L
|
L

L

L

G

Q

I

I

R

R

K

A

A

A

M

L

G

K

L

V

F

F

A

A

N

N

L

L

R

R

P

P

A

A

V

T

L

V

F

L

P

P

Q

Q

L

L

K

V

H

D

A

A

C

S

Y

T

L

L

R

K

P

R

D

E

I

V

V

A

E

E

N

-

G

G

L

V

D

D

V

L

M

M

V

V

R

R

E

E

L

L

T

T

G

G

I

I

Y
|
Y

F

F

G

G

E

E

P

P

R

R

-

G

L

I

E

K

G

T

E

N

I

E

E

N

G

G

E

E

R

E

Y

V

G

G

Y

F

N

N

T

T

M

E

V

V

Y

Y

R

A

E

A

H

H

E

E

I

I

R

D

R

R

I

I

A

A

R

R

V

V

A

A

F

F

E

E

A

T

A

A

R

R

K

K

R

R

G

R

G

G

R

K

V

L

C

C

S

S

V

V

D

D

K
|
K

A

A

N

N

V

V

L

L

D

E

V

A

S

S

R

I

V

L

W

W

R

R

D

K

V

R

V

V

V

T

D

A

E

L

H

A

A

S

E

E

Y

Y

A

P

D

D

V

V

E

E

L

L

S

S

H

H

M

M

Y

Y

V

V

D
|
D

N

N

A

A

M

M

Q

Q

L

L

V

V

R

R

D

D

P

P

G

K

Q

Q

F

F

D

D

V

T

I

I

V

V

T

T

G

N

N

N

L

I

F

F

G

G

D
|
D

I

I

L

L

S

S

D
|
D

E

E

A

A

A

S

A

M

I

I

T

T

G

G

S

S

I
|
I

G

G

M

M

L

L

P

P

S

S

A

A

S

S

L

L

G

S

A

D

D

S

G

G

P

P

G

G

L

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

Q

Q

D

D

K

K

A

A

N
|
N

P

P

L

L

A

A

T

T

I

I

L

L

S

S

I

A

A

A

M

M

M

L

L

L

R

K

H

Y

S

G

M

L

D

G

M

E

A

E

E

K

E

A

A

A

D

K

C

R

I

I

E

E

Q

D

A

A

V

V

Q

L

K

V

T

A

L

L

E

N

Q

N

G

G

Y

F

R

R

T

T

G

G

D
|
D

I

I

M

Y

E

S

Q

A

G

G

A

T

K

K

A

L

V

V

G

G

T

C

K

K

A

E

M

M

G

G

A

E

V

V

L

L

E

K

N

S

L

V

active site: Y141 (= Y140), K192 (= K190), D224 (= D222), D248 (= D246), D252 (= D250)
binding magnesium ion: D248 (= D246), D252 (= D250)
binding nicotinamide-adenine-dinucleotide: I74 (≠ V72), E89 (= E87), L92 (= L90), I261 (= I259), E278 (= E276), H281 (= H279), G282 (= G280), S283 (= S281), A284 (= A282), I287 (= I285), N294 (= N292), D335 (= D333)

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)
60% identity, 100% coverage: 2:355/355 of query aligns to 45:398/404 of Q9SA14

query
sites
Q9SA14

K

N

I

I

C

T

I

L

L

L

A

P

G

G

D

D

G

G

I

I

G

G

P

P

E

E

I

V

V

I

A

S

Q

V

G

A

V

K

K

N

V

V

L

L

D

Q

K

K

V

A

G

G

E

F

K

L

F

Q

G

G

C

L

T

E

F

F

E

D

Y

F

S

Q

E

E

A

M

L

P

I

F

G

G

V

A

A

A

I

L

D

D

A

L

T

V

G

G

G

V

P

P

L

L

P

P

D

E

S

E

T

T

V

S

E

T

R

A

C

A

K

K

E

Q

A

S

D

D

A

A

V

I

L

L

G

G

A

A

V

I

G

G

P

Y

K

K

W

W

D

D

T

K

I

N

D

E

P

K

S

H

I

L

R

R

P

P

E

E

K

M

G

G

L

L

L
|
L

G

N

I

I

R

R

K

R

A

D

M

L

G

N

L

V

F

F

A

A

N

N

L

L

R

R

P

P

A

A

V

T

L

V

F

L

P

P

Q

Q

L

L

K

V

H

D

A

A

C

S

Y

T

L

L

R

K

P

K

D

E

I

V

V

A

E

Q

N

-

G

G

L

V

D

D

V

M

M

M

V

I

V

V

R

R

E

E

L

L

T

T

G

G

I

I

Y

Y

F

F

G

G

E

E

P

P

R

R

-

G

L

I

E

T

G

I

E

N

I

E

E

N

G

G

E

E

R

E

Y

V

G

G

Y

F

N

N

T

T

M

E

V

I

Y

Y

R

A

E

A

H

H

E

E

I

I

R

D

R

R

I

I

A

A

R

R

V

V

A

A

F

F

E

E

A

T

A

A

R

R

K

K

R

R

G

R

G

G

R

K

V

L

C

C

S

S

V

V

D

D

K

K

A

A

N

N

V

V

L

L

D

D

V

A

S

S

R

I

V

L

W

W

R

R

D

K

V

R

V

V

V

T

D

A

E

L

H

A

A

S

E

E

Y

Y

A

P

D

D

V

V

E

E

L

L

S

S

H

H

M

M

Y

Y

V

V

D

D

N

N

A

A

M

M

Q

Q

L

L

V

V

R

R

D

D

P

P

G

K

Q

Q

F

F

D

D

V

T

I

I

V

V

T

T

G

N

N

N

L

I

F

F

G

G

D

D

I

I

L

L

S

S

D

D

E

E

A

A

A

S

A

M

I

I

T

T

G

G

S

S

I

I

G

G

M

M

L

L

P

P

S

S

A

A

S

S

L

L

G

G

A

E

D

S

G

G

P

P

G

G

L

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

Q

Q

D

D

K

K

A

A

N

N

P

P

L

L

A

A

T

T

I

I

L

L

S

S

I

A

A

A

M

M

M

L

L

L

R

K

H

Y

S

G

M

L

D

G

M

E

A

E

E

K

E

A

A

A

D

K

C

M

I

I

E

E

Q

D

A

A

V

V

Q

V

K

D

T

A

L

L

E

N

Q

K

G

G

Y

F

R

R

T

T

G

G

D

D

I

I

M

Y

E

S

Q

P

G

G

A

N

K

K

A

L

V

V

G

G

T

C

K

K

A

E

M

M

G

G

A

E

V

V

L

L

E

K

N

S

L

V

L134 (= L91) Confers substrate specificity; mutation to F: Enhanced activity toward 3-(2'-methylthio)-ethylmalate, but reduced catalytic efficiency with 3-isopropylmalate.

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)
59% identity, 100% coverage: 2:355/355 of query aligns to 48:401/409 of Q9FMT1

query
sites
Q9FMT1

K

N

I

I

C

A

I

L

L

L

A

P

G

G

D

D

G

G

I

I

G

G

P

P

E

E

I

V

V

I

A

S

Q

V

G

A

V

K

K

N

V

V

L

L

D

Q

K

K

V

A

G

G

E

S

K

L

F

E

G

G

C

L

T

E

F

F

E

D

Y

F

S

K

E

E

A

M

L

P

I

V

G

G

V

A

A

A

I

L

D

D

A

L

T

V

G

G

G

V

P

P

L

L

P

P

D

E

S

E

T

T

V

F

E

T

R

A

C

A

K

K

E

L

A

S

D

D

A

A

V

I

L

L

G

G

A

A

V

I

G

G

P

Y

K

K

W

W

D

D

T

K

I

N

D

E

P

K

S

H

I

L

R

R

P

P

E

E

K

M

G

A

L

L

L
x
F

G

Y

I

L

R

R

K

R

A

D

M

L

G

K

L

V

F

F

A

A

N

N

L

L

R

R

P

P

A

A

V

T

L

V

F

L

P

P

Q

Q

L

L

K

V

H

D

A

A

C

S

Y

T

L

L

R

K

P

K

D

E

I

V

V

A

E

E

N

-

G

G

L

V

D

D

V

M

M

M

V

I

V

V

R

R

E

E

L

L

T

T

G

G

I

I

Y

Y

F

F

G

G

E

E

P

P

R

R

-

G

L

I

E

T

G

I

E

N

I

E

E

N

G

G

E

E

R

E

Y

V

G

G

Y

V

N

S

T

T

M

E

V

I

Y

Y

R

A

E

A

H

H

E

E

I

I

R

D

R

R

I

I

A

A

R

R

V

V

A

A

F

F

E

E

A

T

A

A

R

R

K

K

R

R

G

R

G

G

R

K

V

L

C
|
C

S

S

V

V

D

D

K

K

A

A

N

N

V

V

L

L

D

D

V

A

S

S

R

I

V

L

W

W

R

R

D

K

V

R

V

V

V

T

D

A

E

L

H

A

A

S

E

E

Y

Y

A

P

D

D

V

V

E

E

L

L

S

S

H

H

M

M

Y

Y

V

V

D

D

N

N

A

A

M

M

Q

Q

L

L

V

I

R

R

D

D

P

P

G

K

Q

Q

F

F

D

D

V

T

I

I

V

V

T

T

G

N

N

N

L

I

F

F

G

G

D

D

I

I

L

L

S

S

D

D

E

E

A

A

A

S

A

M

I

I

T

T

G

G

S

S

I

I

G

G

M

M

L

L

P

P

S

S

A

A

S

S

L

L

G

G

A

E

D

S

G

G

P

P

G

G

L

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

Q

Q

D

D

K

K

A

A

N

N

P

P

L

L

A

A

T

T

I

I

L

L

S

S

I

A

A

A

M

M

M

L

L

L

R

K

H

Y

S

G

M

L

D

G

M

E

A

E

E

K

E

A

A

A

D

K

C

R

I

I

E

E

Q

D

A

A

V

V

Q

V

K

D

T

A

L

L

E

N

Q

K

G

G

Y

F

R

R

T

T

G

G

D

D

I

I

M

Y

E

S

Q

P

G

G

A

N

K

K

A

L

V

V

G

G

T
x
C

K

K

A

E

M

M

G

G

A

E

V

V

L

L

E

K

N

S

L

V

F137 (≠ L91) Confers substrate specificity; mutation to L: Reduced activity toward 3-(2'-methylthio)-ethylmalate, but enhanced catalytic efficiency with 3-isopropylmalate.
C232 (= C186) Essential for redox regulation; mutation to S: Reduced sensitivity to oxidation on enzyme activity regulation.
C390 (≠ T344) 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)
57% identity, 97% coverage: 3:348/355 of query aligns to 7:352/363 of 1cnzA

query
sites
1cnzA

I

I

C

A

I

V

L

L

A

P

G

G

D

D

G

G

I

I

G

G

P

P

E

E

I

V

V

M

A

A

Q

Q

G

A

V

L

K

K

V

V

L

M

D

D

K

A

V

V

G

R

E

S

K

R

F

F

G

D

C

M

T

R

F

I

E

T

Y

T

S

S

E

H

A

Y

L

D

I

V

G

G

V

I

A

A

I

I

D

D

A

N

T

H

G

G

G

H

P

P

L

L

P

P

D

K

S

A

T

T

V

V

E

E

R

G

C

C

K

E

E

Q

A

A

D

D

A

A

V

I

L

L

L

F

G

G

A

S

V

V

G

G

P

P

K

K

W

W

D

E

T

N

I

L

D

P

P

P

S

E

I

S

R

Q

P

P

E

E

K

R

G

G

-

A

L

L

G

P

I

L

R

R

K

K

A

H

M

F

G

K

L

L

F

F

A

S

N

N

L

L

R

R

P

P

A

A

V

K

L

L

F

Y

P

Q

Q

G

L

L

K

E

H

A

A

F

C

C

Y

P

L

L

R

R

P

A

D

D

I

I

V

A

E

A

N

N

G

G

L

F

D

D

V

I

M

L

V

C

V

V

R

R

E

E

L

L

T

T

G

G

I

I

Y
|
Y

F

F

G

G

E

Q

P

P

R

K

-

G

L

R

E

E

G

G

E

S

I

G

E

Q

G

Y

E

E

R

K

Y

-

G

A

Y

F

N

D

T

T

M

E

V

V

Y

Y

R

H

E

R

H

F

E

E

I

I

R

E

R

R

I

I

A

A

R

R

V

I

A

A

F

F

E

E

A

S

A

A

R

R

K

K

R

R

G

R

R

K

V

V

C

T

S

S

V

I

D

D

K
|
K

A

A

N

N

V

V

L

L

D

Q

V

S

S

S

R

I

V

L

W

W

R

R

D

E

V

I

V

V

V

N

D

D

E

V

H

A

A

K

E

T

Y

Y

A

P

D

D

V

V

E

E

L

L

S

A

H

H

M

M

Y

Y

V

I

D
|
D

N

N

A

A

A

T

M

M

Q

Q

L

L

V

I

R

K

D

D

P

P

G

S

Q

Q

F

F

D

D

V

V

I

L

V

L

T

C

G

S

N

N

L

L

F

F

G

G

D
|
D

I

I

L

L

S

S

D
|
D

E

E

A

C

A

A

A

M

I

I

T

T

G

G

S

S

I

M

G

G

M

M

L

L

P

P

S

S

A

A

S

S

L

L

G

N

A

E

D

Q

G

G

P

F

G

G

L

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

Q

K

D

N

K

I

A

A

N

N

P

P

L

I

A

A

T

Q

I

I

L

L

S

S

I

L

A

A

M

L

L

L

R

R

H

Y

S

S

M

L

D

D

M

A

A

N

E

D

E

A

A

A

D

T

C

A

I

I

E

E

Q

Q

A

A

V

I

Q

N

K

R

T

A

L

L

E

E

Q

E

G

G

Y

V

R

R

T

T

G

G

D

D

I

-

M

L

E

A

Q

R

G

G

A

A

K

A

A

A

V

V

G

S

T

T

K

D

A

E

M

M

G

G

active site: Y145 (= Y140), K195 (= K190), D227 (= D222), D251 (= D246)
binding manganese (ii) ion: D251 (= D246), D255 (= D250)

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)
57% identity, 97% coverage: 3:348/355 of query aligns to 7:352/363 of P37412

query
sites
P37412

I

I

C

A

I

V

L

L

A

P

G

G

D

D

G

G

I

I

G

G

P

P

E

E

I

V

V

M

A

A

Q

Q

G

A

V

L

K

K

V

V

L

M

D

D

K

A

V

V

G

R

E

S

K

R

F

F

G

D

C

M

T

R

F

I

E

T

Y

T

S

S

E

H

A

Y

L

D

I

V

G

G

V

I

A

A

I

I

D

D

A

N

T

H

G

G

G

H

P

P

L

L

P

P

D

K

S

A

T

T

V

V

E

E

R

G

C

C

K

E

E

Q

A

A

D

D

A

A

V

I

L

L

L

F

G

G

A

S

V

V

G

G

P

P

K

K

W

W

D

E

T

N

I

L

D

P

P

P

S

E

I

S

R

Q

P

P

E

E

K

R

G

G

-

A

L

L

G

P

I

L

R

R

K

K

A

H

M

F

G

K

L

L

F

F

A

S

N

N

L

L

R

R

P

P

A

A

V

K

L

L

F

Y

P

Q

Q

G

L

L

K

E

H

A

A

F

C

C

Y

P

L

L

R

R

P

A

D

D

I

I

V

A

E

A

N

N

G

G

L

F

D

D

V

I

M

L

V

C

V

V

R

R

E

E

L

L

T

T

G

G

I

I

Y

Y

F

F

G

G

E

Q

P

P

R

K

-

G

L

R

E

E

G

G

E

S

I

G

E

Q

G

Y

E

E

R

K

Y

-

G

A

Y

F

N

D

T

T

M

E

V

V

Y

Y

R

H

E

R

H

F

E

E

I

I

R

E

R

R

I

I

A

A

R

R

V

I

A

A

F

F

E

E

A

S

A

A

R

R

K

K

R

R

G

R

R

K

V

V

C

T

S

S

V

I

D

D

K

K

A

A

N

N

V

V

L

L

D

Q

V

S

S

S

R

I

V

L

W

W

R

R

D

E

V

I

V

V

V

N

D

D

E

V

H

A

A

K

E

T

Y

Y

A

P

D

D

V

V

E

E

L

L

S

A

H

H

M

M

Y

Y

V

I

D
|
D

N

N

A

A

A

T

M

M

Q

Q

L

L

V

I

R

K

D

D

P

P

G

S

Q

Q

F

F

D

D

V

V

I

L

V

L

T

C

G

S

N

N

L

L

F

F

G

G

D
|
D

I

I

L

L

S

S

D
|
D

E

E

A

C

A

A

A

M

I

I

T

T

G

G

S

S

I

M

G

G

M

M

L

L

P

P

S

S

A

A

S

S

L

L

G

N

A

E

D

Q

G

G

P

F

G

G

L

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

Q

K

D

N

K

I

A

A

N

N

P

P

L

I

A

A

T

Q

I

I

L

L

S

S

I

L

A

A

M

L

L

L

R

R

H

Y

S

S

M

L

D

D

M

A

A

N

E

D

E

A

A

A

D

T

C

A

I

I

E

E

Q

Q

A

A

V

I

Q

N

K

R

T

A

L

L

E

E

Q

E

G

G

Y

V

R

R

T

T

G

G

D

D

I

-

M

L

E

A

Q

R

G

G

A

A

K

A

A

A

V

V

G

S

T

T

K

D

A

E

M

M

G

G

D227 (= D222) binding Mn(2+)
D251 (= D246) binding Mn(2+)
D255 (= D250) binding Mn(2+)

6xxyA Crystal structure of haemophilus influenzae 3-isopropylmalate dehydrogenase in complex with o-isobutenyl oxalylhydroxamate. (see paper)
54% identity, 99% coverage: 2:353/355 of query aligns to 5:356/358 of 6xxyA

query
sites
6xxyA

K

N

I

I

C

A

I

V

L

L

A

A

G

G

D

D

G

G

I

I

G

G

P

P

E

E

I

V

V

M

A

A

Q

E

G

A

V

I

K

K

V

V

L

L

D

N

K

R

V

V

G

Q

E

E

K

K

F

F

G

G

C

F

T

K

F

L

E

N

Y

F

S

N

E

E

A

F

L

F

I

V

G

G

V

A

A

A

I

I

D

E

A

H

T

C

G

G

G

Y

P

P

L

L

P

P

D

A

S

E

T

T

V

L

E

K

R

G

C

C

K

D

E

Q

A

A

D

D

A

A

V

I

L

L

L

F

G

G

A
x
S

V
|
V

G
|
G

G

G

P

P

K

K

W

W

D

T

T

N

I

L

D

P

P

P

S

D

I

Q

R

Q

P

P

E
|
E

K

R

G

G

-

A

L
|
L

L

L

G

P

I

L

R

R

K

K

A

H

M

F

G

K

L

L

F

F

A

C

N

N

L

L

R
|
R

P

P

A

A

V

T

L

L

F

Y

P

K

Q

G

L

L

K

E

H

K

A

F

C

C

Y

P

L

L

R

R

P

A

D

D

I

I

V

A

E

A

N

K

G

G

L

F

D

D

V

M

M

V

V

V

R
|
R

E

E

L

L

T

T

G

G

I

I

Y
|
Y

F

F

G

G

E

Q

P

P

R

K

L

G

E

R

G

E

E

G

I

D

E

G

G

V

E

Q

R

T

Y

K

G

A

Y

F

N

D

T

T

M

E

V

V

Y

Y

R

Y

E

K

H

Y

E

E

I

I

R

E

R

R

I

I

A

A

R

R

V

A

A

A

F

F

E

E

A

A

R

M

K

K

R

R

G

N

G

K

R

K

V

V

C

T

S

S

V

V

D

D

K
|
K

A

A

N

N

V
|
V

L

L

D

Q

V

S

S

S

R

I

V

L

W

W

R

R

D

E

V

T

V

V

V

T

D

E

E

M

H

A

A

K

E

D

Y

Y

A

P

D

E

V

V

E

T

L

L

S

E

H

H

M

I

Y
|
Y

V

I

D
|
D

N
|
N

A

A

A

T

M
|
M

Q

Q

L

L

V

I

R

K

D

S

P

P

G

E

Q

S

F

F

D

D

V

V

I

L

V

L

T

C

G

S

N

N

L

I

F

F

G

G

D
|
D

I

I

L

I

S

S

D
|
D

E

E

A

A

A

M

I

I

T

T

G

G

S

S

I
x
M

G
|
G

M

M

L

L

P

P

S

S

A

A

S

S

L

L

G

N

A

E

D

E

G

G

P

F

G

G

L

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

Q

K

D

G

K

I

A

A

N
|
N

P

P

L

I

A

A

T

Q

I

I

L

L

S

S

I

A

A

A

M

M

L

L

R

R

H

Y

S

S

M

F

D

N

M

L

A

N

E

E

E

A

A

A

D

D

C

A

I

I

E

E

Q

S

A

A

V

V

Q

Q

K

K

T

V

L

L

E

A

Q

S

G

G

Y

H

R

R

T

T

G

A

D
|
D

I

L

M

A

E

D

Q

D

G

-

A

S

K

T

A

P

V

V

G

S

T

T

K

A

A

E

M

M

G

G

A

T

A

L

V

I

L

T

E

Q

active site: Y144 (= Y140), K194 (= K190), D226 (= D222), D250 (= D246)
binding magnesium ion: D250 (= D246), D254 (= D250)
binding nicotinamide-adenine-dinucleotide: S74 (≠ A71), V75 (= V72), G76 (= G73), E90 (= E87), L94 (= L90), Y224 (= Y220), N227 (= N223), M230 (= M226), M263 (≠ I259), G264 (= G260), E280 (= E276), G283 (≠ H279), G284 (= G280), S285 (= S281), A286 (= A282), P287 (= P283), D288 (= D284), I289 (= I285), N296 (= N292), D337 (= D333)
binding 2-(2-methylprop-2-enoxyamino)-2-oxidanylidene-ethanoic acid: E90 (= E87), R108 (= R104), R137 (= R133), K194 (= K190), V197 (= V193), D226 (= D222), D250 (= D246)

3vkzA 3-isopropylmalate dehydrogenase from shewanella oneidensis mr-1 at atmospheric pressure (see paper)
55% identity, 98% coverage: 2:348/355 of query aligns to 4:353/364 of 3vkzA

query
sites
3vkzA

K

Q

I

I

C

A

I

V

L

L

A

A

G

G

D

D

G

G

I

I

G

G

P

P

E

E

I

V

V

M

A

A

Q

E

G

A

V

R

K

K

V

V

L

L

D

K

K

A

V

V

G

E

E

A

K

R

F

F

G

G

C

L

T

N

F

I

E

E

Y

Y

S

T

E

E

A

Y

L

D

I

V

G

G

V

I

A

A

I

I

D

D

A

N

T

H

G

G

G

C

P

P

L

L

P

P

D

E

S

A

T

T

V

L

E

K

R

G

C

C

K

E

E

A

A

A

D

D

A

A

V

I

L

L

L

F

G

G

A

S

V

V

G

G

P

P

K

K

W

W

D

E

T

K

I

L

D

P

P

P

S

N

I

E

R

Q

P

P

E

E

K

R

G

G

-

A

L

L

G

P

I

L

R
|
R

K

G

A

H

M

F

G

E

L

L

F

F

A

C

N

N

L

L

R

R

P

P

A

A

V

K

L

L

F

H

P

D

Q

G

L

L

K

E

H

H

A

M

C

S

Y

P

L

L

R

R

P

S

D

D

I

I

V

S

E

A

N

R

G

G

L

F

D

D

V

V

M

L

V

C

V

V

R
|
R

E

E

L

L

T

T

G

G

I

I

Y
|
Y

F

F

G

G

E

K

P

P

R

K

-

G

L

R

E

Q

G

G

E

E

I

G

E

E

G

S

E

E

R

E

Y

-

G

A

Y

F

N

D

T

T

M

M

V

R

Y

Y

R

S

E

R

H

R

E

E

I

I

R

S

R

R

I

I

A

A

R

R

V

I

A

A

F

F

E

E

A

A

R

R

K

G

R

R

G

R

G

K

R

K

V

V

C

T

S

S

V

V

D

D

K
|
K

A

A

N

N

V

V

L

L

D

A

V

C

S

S

R

V

V

L

W

W

R

R

D

Q

V

V

V

E

D

E

E

V

H

A

A

V

E

D

Y

F

A

P

D

D

V

V

E

E

L

L

S

E

H

H

M

I

Y

Y

V

I

D
|
D

N

N

A

A

A

T

M

M

Q

Q

L

L

V

L

R

R

D

R

P

P

G

D

Q

E

F

F

D

D

V

V

I

M

V

L

T

C

G

S

N

N

L

L

F

F

G

G

D
|
D

I

I

L

L

S

S

D
|
D

E

E

A

I

A

A

A

M

I

L

T

T

G

G

S

S

I

M

G

G

M

L

L

L

P

S

S

S

A

A

S

S

L

M

G

N

A

S

D

T

G

G

P

F

G

G

L

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

Q

K

D

G

K

I

A

A

N

N

P

P

L

I

A

A

T

Q

I

I

L

L

S

S

I

A

A

A

M

L

M

M

L

L

R

R

H

H

S

S

M

L

D

K

M

Q

A

E

E

E

E

A

A

A

D

S

C

A

I

I

E

E

Q

R

A

A

V

V

Q

T

K

K

T

A

L

L

E

N

Q

S

G

G

Y

Y

R

L

T

T

G

G

D

E

I

L

M

L

-

S

E

D

Q

Q

G

R

A

H

K

K

A

A

V

K

G

T

T

T

K

V

A

Q

M

M

G

G

active site: Y143 (= Y140), K193 (= K190), D225 (= D222), D249 (= D246), D253 (= D250)
binding calcium ion: D249 (= D246), D253 (= D250)
binding 3-isopropylmalic acid: R97 (= R94), R136 (= R133), Y143 (= Y140), D249 (= D246)

3vmkA 3-isopropylmalate dehydrogenase from shewanella benthica db21 mt-2 (see paper)
53% identity, 98% coverage: 2:348/355 of query aligns to 10:359/369 of 3vmkA

query
sites
3vmkA

K

Q

I

I

C

A

I

V

L

L

A

A

G

G

D

D

G

G

I

I

G

G

P

P

E

E

I

V

V

M

A

A

Q

E

G

A

V

R

K

K

V

V

L

L

D

A

K

A

V

V

G

E

E

K

K

R

F

F

G

D

C

L

T

S

F

I

E

E

Y

Y

S

S

E

E

A

Y

L

D

I

V

G

G

V

A

A

A

I

I

D

D

A

N

T

H

G

G

G

C

P

P

L

L

P

P

D

E

S

A

T

T

V

L

E

K

R

G

C

C

K

E

E

A

A

A

D

D

A

A

V

V

L

L

L

F

G

G

A

S

V

V

G

G

P

P

K

K

W

W

D

E

T

H

I

L

D

P

P

P

S

N

I

D

R

Q

P

P

E

E

K

R

G

G

-

A

L

L

G

P

I

L

R
|
R

K

G

A

H

M

F

G

E

L

L

F

F

A

C

N

N

L

M

R

R

P

P

A

A

V

K

L

L

F

H

P

P

Q

G

L

L

K

E

H

H

A

M

C

S

Y

P

L

L

R

R

P

S

D

D

I

I

V

S

E

E

N

K

G

G

L

F

D

D

V

I

M

L

V

C

V

V

R
|
R

E

E

L

L

T

T

G

G

I

I

Y
|
Y

F

F

G

G

E

K

P

P

R

K

-

G

L

R

E

Q

G

G

E

E

I

G

E

E

G

N

E

E

R

E

Y

-

G

A

Y

F

N

D

T

T

M

M

V

R

Y

Y

R

S

E

R

H

K

E

E

I

I

R

R

I

I

A

A

R

K

V

I

A

A

F

F

E

E

A

S

A

A

R

Q

K

G

R

R

G

R

G

K

R

K

V

V

C

T

S

S

V

V

D

D

K
|
K

A

A

N
|
N

V

V

L

L

D

A

V

C

S

S

R

V

V

L

W

W

R

R

D

E

V

V

V

E

D

E

E

V

H

A

A

K

E

D

Y

Y

A

P

D

D

V

V

E

E

L

L

S

E

H

H

M

I

Y

Y

V

I

D
|
D

N

N

A

A

A

T

M

M

Q

Q

L

L

V

L

R

R

D

R

P

P

G

N

Q

E

F

F

D

D

V

V

I

M

V

L

T

C

G

S

N

N

L

L

F

F

G

G

D
|
D

I

I

L

V

S

S

D
|
D

E

E

A

I

A

A

A

M

I

L

T

T

G

G

S

S

I

M

G

G

M

L

L

L

P

A

S

S

A

I

S

S

L

M

G

N

A

S

D

Q

G

G

P

F

G

G

L

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

Q

Q

D

G

K

I

A

A

N

N

P

P

L

V

A

A

T

Q

I

I

L

L

S

S

I

A

A

A

M

L

L

L

R

R

H

H

S

S

M

L

D

K

M

L

A

E

E

D

E

A

A

A

D

L

C

A

I

I

E

E

Q

A

A

A

V

V

Q

S

K

K

T

A

L

L

E

S

Q

D

G

G

Y

Y

R

L

T

T

G

C

D

E

I

L

M

L

-

P

-

A

E

S

Q

E

G

R

A

S

K

Q

A

A

V

K

G

S

T

T

K

S

A

Q

M

M

G

G

active site: Y149 (= Y140), K199 (= K190), D231 (= D222), D255 (= D246), D259 (= D250)
binding 3-isopropylmalic acid: R103 (= R94), R142 (= R133), Y149 (= Y140), K199 (= K190), N201 (= N192), D255 (= D246)

2ztwA Structure of 3-isopropylmalate dehydrogenase in complex with the inhibitor and NAD+ (see paper)
53% identity, 100% coverage: 1:355/355 of query aligns to 1:344/345 of 2ztwA

query
sites
2ztwA

M

M

K

K

I

V

C

A

I

V

L

L

A

P

G

G

D

D

G

G

I
|
I

G

G

P

P

E

E

I

V

V

T

A

E

Q

A

G

A

V

L

K

K

V

V

L

L

D

R

K

A

V

L

G

D

E

E

K

A

F

E

G

G

C

L

T

G

F

L

E

A

Y

Y

S

E

E

V

A

F

L

P

I

F

G

G

V

A

A

A

I

I

D

D

A

A

T

F

G

G

G

E

P

P

L

F

P

P

D

E

S

P

T

T

V

R

E

K

R

G

C

V

K

E

E

E

A

A

D

E

A

A

V

V

L

L

G

G

A

S

V

V

G

G

P

P

K

K

W

W

D

D

T

G

I

L

D

P

P

R

S

K

I

I

R

R

P

P

E

E

K

T

G

G

L

L

G

S

I

L

R

R

K

K

A

S

M

Q

G

D

L

L

F

F

A

A

N

N

L

L

R

R

P

P

A

A

V

K

L

V

F

F

P

P

Q

G

L

L

K

E

H

R

A

L

C

S

Y

P

L

L

R

K

P

E

D

E

I

I

V

A

E

-

N

R

G

G

L

V

D

D

V

V

M

L

V

I

V

V

R

R

E

E

L

L

T

T

G

G

I

I

Y
|
Y

F

F

G

G

E

E

P

P

R

R

L

G

E

M

G

S

E

E

I

A

E

E

G

A

E

-

R

-

Y

-

G

-

Y

W

N

N

T

T

M

E

V

R

Y

Y

R

S

E

K

H

P

E

E

I

V

R

E

R

R

I

V

A

A

R

R

V

V

A

A

F

F

E

E

A

A

R

R

K

K

R

R

G

R

G

K

R

H

V

V

C

V

S

S

V

V

D

D

K
|
K

A

A

N

N

V

V

L

L

D

E

V

V

S

G

R

E

V

F

W

W

R

R

D

K

V

T

V

V

V

E

D

E

E

V

H
x
G

A

R

E

G

Y
|
Y

A

P

D

D

V
|
V

E

A

L

L

S

E

H

H

M

Q

Y

Y

V

V

D
|
D

N

A

A

M

A

A

M

M

Q

H

L

L

V

V

R

R

D

S

P

P

G

A

Q

R

F

F

D

D

V

V

I

V

V

V

T

T

G

G

N

N

L

I

F

F

G

G

D
|
D

I

I

L

L

S

S

D
|
D

E

L

A

A

A

S

A

V

I

L

T

P

G

G

S

S

I

L

G

G

M

L

L

L

P

P

S

S

A

A

S

S

L

L

G

G

A

R

D

G

G

T

P

P

G

-

L

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

Q

K

D

G

K

I

A
|
A

N
|
N

P

P

L

T

A

A

T

A

I

I

L

L

S

S

I

A

A

A

M

M

L

L

R

E

H

H

S

A

M

F

D

G

M

L

A

V

E

E

E

L

A

A

D

R

C

K

I

V

E

E

Q

D

A

A

V

V

Q

A

K

K

T

A

L

L

E

L

Q

E

G

T

Y

P

R

P

T

P

G

-

D

-

I

-

M

-

E

D

Q

L

G

G

A

G

K

S

A

A

V

-

G

G

T

T

K

E

A

A

M

F

G

T

A

A

A

T

V

V

L

L

E

R

N

H

L

L

active site: Y139 (= Y140), K185 (= K190), D217 (= D222), D241 (= D246), D245 (= D250)
binding magnesium ion: G203 (≠ H208), Y206 (= Y211), V209 (= V214)
binding nicotinamide-adenine-dinucleotide: I11 (= I11), H273 (= H279), G274 (= G280), A276 (= A282), D278 (= D284), I279 (= I285), A285 (= A291), N286 (= N292)

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)
53% identity, 100% coverage: 1:355/355 of query aligns to 1:344/345 of Q5SIY4

query
sites
Q5SIY4

M

M

K

K

I

V

C

A

I

V

L

L

A

P

G

G

D

D

G

G

I

I

G

G

P

P

E

E

I

V

V

T

A

E

Q

A

G

A

V

L

K

K

V

V

L

L

D

R

K

A

V

L

G

D

E

E

K

A

F

E

G

G

C

L

T

G

F

L

E

A

Y

Y

S

E

E

V

A

F

L

P

I

F

G

G

V

A

A

A

I

I

D

D

A

A

T

F

G

G

G

E

P

P

L

F

P

P

D

E

S

P

T

T

V

R

E

K

R

G

C

V

K

E

E

E

A

A

D

E

A

A

V

V

L

L

G

G

A

S

V

V

G

G

G
|
G

P
|
P

K
|
K

W
|
W

D
|
D

T
x
G

I
x
L

D
x
P

P
x
R

S
x
K

I
|
I

R
|
R

P
|
P

E
|
E

K

T

G

G

L

L

G

S

I

L

R

R

K

K

A

S

M

Q

G

D

L

L

F

F

A

A

N

N

L

L

R

R

P

P

A

A

V

K

L

V

F

F

P

P

Q

G

L

L

K

E

H

R

A

L

C

S

Y

P

L

L

R

K

P

E

D

E

I

I

V

A

E

-

N

R

G

G

L

V

D

D

V

V

M

L

V

I

V

V

R

R

E

E

L

L

T

T

G

G

I

I

Y
|
Y

F

F

G

G

E

E

P

P

R

R

L

G

E

M

G

S

E

E

I

A

E

E

G

A

E

-

R

-

Y

-

G

-

Y

W

N

N

T

T

M

E

V

R

Y

Y

R

S

E

K

H

P

E

E

I

V

R

E

R

R

I

V

A

A

R

R

V

V

A

A

F

F

E

E

A

A

R

R

K

K

R

R

G

R

G

K

R

H

V

V

C

V

S

S

V

V

D

D

K

K

A

A

N

N

V

V

L

L

D

E

V

V

S

G

R

E

V

F

W

W

R

R

D

K

V

T

V

V

V

E

D

E

E

V

H

G

A

R

E

G

Y

Y

A

P

D

D

V

V

E

A

L

L

S

E

H

H

M

Q

Y

Y

V

V

D

D

N

A

A

M

A

A

M

M

Q

H

L

L

V

V

R

R

D

S

P

P

G

A

Q

R

F

F

D

D

V

V

I

V

V

V

T

T

G

G

N

N

L

I

F

F

G

G

D

D

I

I

L

L

S

S

D

D

E

L

A

A

A

S

A

V

I

L

T

P

G

G

S

S

I

L

G

G

M

L

L

L

P

P

S

S

A

A

S

S

L

L

G

G

A

R

D

G

G

T

P

P

G

-

L

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

Q
x
K

D
x
G

K
x
I

A
|
A

N
|
N

P

P

L

T

A

A

T

A

I

I

L

L

S

S

I

A

A

A

M

M

L

L

R

E

H

H

S

A

M

F

D

G

M

L

A

V

E

E

E

L

A

A

D

R

C

K

I

V

E

E

Q

D

A

A

V

V

Q

A

K

K

T

A

L

L

E

L

Q

E

G

T

Y

P

R

P

T

P

G

-

D

-

I

-

M

-

E

D

Q

L

G

G

A

G

K

S

A

A

V

-

G

G

T

T

K

E

A

A

M

F

G

T

A

A

A

T

V

V

L

L

E

R

N

H

L

L

74:87 (vs. 74:87, 64% identical) binding NAD(+)
Y139 (= Y140) mutation to F: Large decrease in activity and a small decrease in substrate affinity.
274:286 (vs. 280:292, 77% identical) binding NAD(+)

2y41A Structure of isopropylmalate dehydrogenase from thermus thermophilus - complex with ipm and mn (see paper)
53% identity, 100% coverage: 1:355/355 of query aligns to 2:345/346 of 2y41A

query
sites
2y41A

M

M

K

K

I

V

C

A

I

V

L

L

A

P

G

G

D

D

G

G

I

I

G

G

P

P

E

E

I

V

V

T

A

E

Q

A

G

A

V

L

K

K

V

V

L

L

D

R

K

A

V

L

G

D

E

E

K

A

F

E

G

G

C

L

T

G

F

L

E

A

Y

Y

S

E

E

V

A

F

L

P

I

F

G

G

V

A

A

A

I

I

D

D

A

A

T

F

G

G

G

E

P

P

L

F

P

P

D

E

S

P

T

T

V

R

E

K

R

G

C

V

K

E

E

E

A

A

D

E

A

A

V

V

L

L

G

G

A

S

V

V

G

G

P

P

K

K

W

W

D

D

T

G

I

L

D

P

P

R

S

K

I

I

R

R

P

P

E

E

K

T

G

G

L

L

G

S

I

L

R
|
R

K

K

A

S

M

Q

G

D

L

L

F

F

A

A

N

N

L

L

R
|
R

P

P

A

A

V

K

L

V

F

F

P

P

Q

G

L

L

K

E

H

R

A

L

C

S

Y

P

L

L

R

K

P

E

D

E

I

I

V

A

E

-

N

R

G

G

L

V

D

D

V

V

M

L

V

I

V

V

R
|
R

E

E

L

L

T

T

G

G

I

I

Y
|
Y

F

F

G

G

E

E

P

P

R

R

L

G

E

M

G

S

E

E

I

A

E

E

G

A

E

-

R

-

Y

-

G

-

Y

W

N

N

T

T

M

E

V

R

Y

Y

R

S

E

K

H

P

E

E

I

V

R

E

R

R

I

V

A

A

R

R

V

V

A

A

F

F

E

E

A

A

R

R

K

K

R

R

G

R

G

K

R

H

V

V

C

V

S

S

V

V

D

D

K
|
K

A

A

N

N

V

V

L

L

D

E

V

V

S

G

R

E

V

F

W

W

R

R

D

K

V

T

V

V

V

E

D

E

E

V

H

G

A

R

E

G

Y

Y

A

P

D

D

V

V

E

A

L

L

S

E

H

H

M

Q

Y

Y

V

V

D
|
D

N

A

A

M

A

A

M

M

Q

H

L

L

V

V

R

R

D

S

P

P

G

A

Q

R

F

F

D

D

V

V

I

V

V

V

T

T

G

G

N

N

L

I

F

F

G

G

D
|
D

I

I

L

L

S

S

D
|
D

E

L

A

A

A

S

A

V

I

L

T

P

G

G

S

S

I

L

G

G

M

L

L

L

P

P

S

S

A

A

S

S

L

L

G

G

A

R

D

G

G

T

P

P

G

-

L

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

Q

K

D

G

K

I

A

A

N

N

P

P

L

T

A

A

T

A

I

I

L

L

S

S

I

A

A

A

M

M

L

L

R

E

H

H

S

A

M

F

D

G

M

L

A

V

E

E

E

L

A

A

D

R

C

K

I

V

E

E

Q

D

A

A

V

V

Q

A

K

K

T

A

L

L

E

L

Q

E

G

T

Y

P

R

P

T

P

G

-

D

-

I

-

M

-

E

D

Q

L

G

G

A

G

K

S

A

A

V

-

G

G

T

T

K

E

A

A

M

F

G

T

A

A

A

T

V

V

L

L

E

R

N

H

L

L

active site: Y140 (= Y140), K186 (= K190), D218 (= D222), D242 (= D246), D246 (= D250)
binding 3-isopropylmalic acid: R95 (= R94), R105 (= R104), R133 (= R133), Y140 (= Y140), D242 (= D246)

2y42D Structure of isopropylmalate dehydrogenase from thermus thermophilus - complex with nadh and mn (see paper)
55% identity, 92% coverage: 1:325/355 of query aligns to 2:320/355 of 2y42D

query
sites
2y42D

M

M

K

K

I

V

C

A

I

V

L

L

A

P

G

G

D

D

G

G

I
|
I

G

G

P

P

E

E

I

V

V

T

A

E

Q

A

G

A

V

L

K

K

V

V

L

L

D

R

K

A

V

L

G

D

E

E

K

A

F

E

G

G

C

L

T

G

F

L

E

A

Y

Y

S

E

E

V

A

F

L

P

I

F

G

G

V

A

A

A

I

I

D

D

A

A

T

F

G

G

G

E

P

P

L

F

P

P

D

E

S

P

T

T

V

R

E

K

R

G

C

V

K

E

E

E

A

A

D

E

A

A

V

V

L

L

G

G

A

S

V

V

G

G

P

P

K

K

W

W

D
|
D

T

G

I

L

D

P

P

R

S

K

I

I

R

R

P

P

E

E

K

T

G

G

L

L

G

S

I

L

R

R

K

K

A

S

M

Q

G

D

L

L

F

F

A

A

N

N

L

L

R

R

P

P

A

A

V

K

L

V

F

F

P

P

Q

G

L

L

K

E

H

R

A

L

C

S

Y

P

L

L

R

K

P

E

D

E

I

I

V

A

E

-

N

R

G

G

L

V

D

D

V

V

M

L

V

I

V

V

R

R

E

E

L

L

T

T

G

G

I

I

Y
|
Y

F

F

G

G

E

E

P

P

R

R

L

G

E

M

G

S

E

E

I

A

E

E

G

A

E

-

R

-

Y

-

G

-

Y

W

N

N

T

T

M

E

V

R

Y

Y

R

S

E

K

H

P

E

E

I

V

R

E

R

R

I

V

A

A

R

R

V

V

A

A

F

F

E

E

A

A

R

R

K

K

R

R

G

R

G

K

R

H

V

V

C

V

S

S

V

V

D

D

K
|
K

A

A

N

N

V

V

L

L

D

E

V

V

S

G

R

E

V

F

W

W

R

R

D

K

V

T

V

V

V

E

D

E

E

V

H

G

A

R

E

G

Y

Y

A

P

D

D

V

V

E

A

L

L

S

E

H

H

M

Q

Y

Y

V

V

D
|
D

N

A

A

M

A

A

M

M

Q

H

L

L

V

V

R

R

D

S

P

P

G

A

Q

R

F

F

D

D

V

V

I

V

V

V

T

T

G

G

N

N

L

I

F

F

G

G

D
|
D

I

I

L

L

S

S

D
|
D

E

L

A

A

A

S

A

V

I

L

T

P

G

G

S

S

I

L

G

G

M

L

L

L

P

P

S

S

A

A

S

S

L

L

G

G

A

R

D

G

G

T

P

P

G

-

L

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

Q

K

D

G

K

I

A

A

N
|
N

P

P

L

T

A

A

T

A

I

I

L

L

S

S

I

A

A

A

M

M

L

L

R

E

H

H

S

A

M

F

D

G

M

L

A

V

E

E

E

L

A

A

D

R

C

K

I

V

E

E

Q

D

A

A

V

V

Q

A

K

K

T

A

L

L

active site: Y140 (= Y140), K186 (= K190), D218 (= D222), D242 (= D246), D246 (= D250)
binding manganese (ii) ion: D242 (= D246), D246 (= D250)
binding nicotinamide-adenine-dinucleotide: I12 (= I11), D79 (= D78), H274 (= H279), G275 (= G280), A277 (= A282), D279 (= D284), I280 (= I285), N287 (= N292)

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, 97% coverage: 2:347/355 of query aligns to 5:363/371 of P18869

query
sites
P18869

K

K

I

I

C

V

I

V

L

L

A

P

G

G

D

D

G

H

I

I

G

G

P

P

E

E

I

I

V

V

A

A

Q

S

G

A

V

L

K

E

V

V

L

L

D

K

K

V

V

V

G

E

E

K

K

K

F

R

G

P

-

E

C

L

T

K

F

L

E

E

Y

F

S

E

E

E

A

H

L

K

I

I

G

G

V

A

A

S

I

I

D

D

A

A

T

Y

G

G

G
x
T

P

P

L

L

P

T

D

D

S

E

T

T

V

V

E

K

R

A

C

C

K

L

E

E

A

A

D

D

A

G

V

V

L

L

G

G

A

A

V

V

G

G

P

P

K

E

W

W

D

-

T

-

I

T

D

N

P

P

S

N

I

C

R

R

P

P

E

E

K

Q

G

G

L

L

G

K

I

L

R

R

K

K

A

S

M

M

G

G

L

V

F

W

A

A

N

N

L

L

R

R

P

P

A

C

V

N

L

F

F

A

P

S

Q

K

-

S

L

L

K

V

H

K

A

Y

C

S

Y

P

L

L

R

K

P

P

D

E

I

I

V

V

E

E

N

-

G

G

L

V

D

D

V

F

M

C

V

V

R

R

E

E

L

L

T

T

G

G

I

C

Y

Y

F

F

G

G

E

E

P

-

R

-

L

-

E

R

G

T

E

E

I

D

E

N

G

G

E

S

R

G

Y

Y

G

A

Y

M

N

D

T

T

M

W

V

P

Y

Y

R

S

E

L

H

E

E

E

I

V

R

S

R

R

I

I

A

A

R

R

V

L

A

A

F

A

E

W

A

L

A

A

R

E

K

T

R

S

G

N

-

P

G

A

R

P

V

V

C

T

S

L

V

L

D

D

K

K

A

A

N

N

V

V

L

L

D

A

V

T

S

S

R

R

V

L

W

W

R

R

D

K

V

T

V

V

V

A

D

K

-

I

E

F

H

K

A

E

E

E

Y

Y

A

P

D

H

V

L

E

T

L

L

S

K

H

N

M

Q

Y

L

V

I

D

D

N

S

A

A

M

M

Q

L

L

L

V

V

R

K

D

S

P

P

G

R

Q

T

F

L

D

N

-

G

V

V

I

V

V

L

T

T

G

D

N

N

L

L

F

F

G

G

D

D

I

I

L

I

S

S

D

D

E

E

A

A

A

S

A

V

I

I

T

P

G

G

S

S

I

L

G

G

M

L

L

L

P

P

S

S

A

A

S

S

L

L

-

S

G

G

A

V

D

V

G

G

P

K

G

S

-

E

-

K

-

V

-

H

-

C

L

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

Q

K

D

G

K

I

A

V

N

N

P

P

L

V

A

G

T

T

I

I

L

L

S

S

I

A

A

S

M

L

L

L

R

R

H

Y

S

G

M

L

D

N

M

A

A

P

E

K

E

E

A

A

D

E

C

A

I

I

E

E

Q

A

A

A

V

V

Q

R

K

K

T

V

L

L

E

D

-

D

-

T

-

S

-

I

-

G

Q

R

G

G

Y

L

R

Y

T

T

G

R

D

D

I

L

M

G

E

G

Q

E

G

A

A

S

K

T

A

A

V

D

G

I

T

T

K

K

A

A

M

V

T55 (≠ G51) modified: Phosphothreonine

2g4oA Anomalous substructure of 3-isopropylmalate dehydrogenase (see paper)
39% identity, 96% coverage: 2:342/355 of query aligns to 3:337/337 of 2g4oA

query
sites
2g4oA

K

K

I

L

C

A

I

I

L

I

A

A

G

G

D

D

G

G

I

I

G

G

P

P

E

E

I

V

V

T

A

A

Q

E

G

A

V

V

K

K

V

V

L

L

D

D

K

A

V

V

G

V

E

P

K

G

F

V

G

Q

C

K

T

T

F

-

E

S

Y

Y

S

D

E

-

A

-

L

-

I

L

G

G

G

A

V

R

A

R

I

F

D

H

A

A

T

T

G

G

G
x
E

P

V

L
|
L

P
|
P

D

D

S

S

T

V

V

V

E

A

R

E

C

L

K

R

E

N

A

H

D

D

A

A

V

I

L

L

G

G

A

A

V

I

G

G

G

D

P

P

K

-

W

-

D

-

T

S

I

V

D

P

P

S

S

G

I

V

R

L

P

E

E

R

K

G

G

L

L

L

G

R

I

L

R

R

K

F

A

E

M

L

G

D

L

H

F

H

A

I

N

N

L

L

R

R

P

P

A

A

V

R

L

L

F

Y

P

P

Q

G

L

V

K

A

H

S

A

P

C

L

Y

S

L

G

R

N

P

P

D

-

I

-

V

-

E

-

N

-

G

G

L

I

D

D

V

F

M

V

V

V

R

R

E

E

L

G

T

T

G

E

G

G

I

P

Y
|
Y

F

T

G

G

E

N

P

G

R

G

L

A

E

I

G

R

E

V

I

G

E

T

G

P

E

N

R

E

Y

V

G

A

Y

T

N

E

T

V

M

S

V

V

Y

N

R

T

E

A

H

F

E

G

I

V

R

R

I

V

A

V

R

A

V

D

A

A

F

F

E

E

A

R

A

A

R

R

K

R

R

R

G

R

G

K

R

H

V

L

C

T

S

L

V

V

D

H

K
|
K

A

T

N

N

V

V

L

L

D

T

V

F

S

A

R

G

V

G

W

L

R

W

D

L

V

R

V

T

V

V

D

D

E

E

H

V

A

G

E

E

-

C

Y

Y

A

P

D

D

V

V

E

E

L

V

S

A

H

Y

M

Q

Y

H

V

V

D
|
D

N

A

A

A

A

T

M

I

Q

H

L

M

V

I

R

T

D

D

P

P

G

G

Q

R

F

F

D

D

V

V

I

I

V

V

T

T

G

D

N

N

L

L

F

F

G

G

D
|
D

I

I

L

I

S

T

D
|
D

E

L

A

A

I

V

T

C

G

G

S

G

I

I

G

G

M

L

L

A

P

A

S

S

A

G

S

N

L

I

G

D

A

A

D

T

-

R

-

A

G

N

P

P

G

S

L

M

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

Q

Q

D

G

K

I

A

A

N

D

P

P

L

T

A

A

T

A

I

I

L

M

S

S

I

V

A

A

M

L

L

L

R

S

H

H

-

L

-

G

S

E

M

H

D

D

M

A

A

A

E

A

E

R

A

V

D

D

-

R

C

A

I

V

E

E

Q

A

A

H

V

L

Q

A

K

T

T

R

L

G

E

S

Q

E

G

R

Y

L

R

A

T

T

G

S

D

D

I

V

M

G

E

E

Q

R

G

I

A

A

K

A

A

A

V

L

active site: Y129 (= Y140), K179 (= K190), D212 (= D222), D236 (= D246), D240 (= D250)
binding sulfate ion: E48 (≠ G51), L50 (= L53), P51 (= P54)

Query Sequence

>WP_018123431.1 NCBI__GCF_000375485.1:WP_018123431.1
MKICILAGDGIGPEIVAQGVKVLDKVGEKFGCTFEYSEALIGGVAIDATGGPLPDSTVER
CKEADAVLLGAVGGPKWDTIDPSIRPEKGLLGIRKAMGLFANLRPAVLFPQLKHACYLRP
DIVENGLDVMVVRELTGGIYFGEPRLEGEIEGERYGYNTMVYREHEIRRIARVAFEAARK
RGGRVCSVDKANVLDVSRVWRDVVVDEHAEYADVELSHMYVDNAAMQLVRDPGQFDVIVT
GNLFGDILSDEAAAITGSIGMLPSASLGADGPGLYEPIHGSAPDIAGQDKANPLATILSI
AMMLRHSMDMAEEADCIEQAVQKTLEQGYRTGDIMEQGAKAVGTKAMGAAVLENL

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