SitesBLAST

SitesBLAST – Find functional sites

SitesBLAST

Comparing WP_041088807.1 NCBI__GCF_000829435.1:WP_041088807.1 to proteins with known functional sites using BLASTp with E ≤ 0.001.

Or try Sites on a Tree, PaperBLAST, Conserved Domains, or compare to all protein structures

Found 20 (the maximum) hits to proteins with known functional sites (download)

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)
53% identity, 96% coverage: 4:355/366 of query aligns to 44:400/405 of P93832

query
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P93832

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114:129 (vs. 74:89, 69% identical) binding NAD(+)
L132 (= L92) mutation to A: Reduced activity toward 3-isopropylmalate.
L133 (= L93) 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 (= R96) binding substrate; mutation to A: Loss of activity toward 3-isopropylmalate.; mutation to K: Reduced activity toward 3-isopropylmalate.
R146 (= R106) binding substrate; mutation to A: Reduced activity toward 3-isopropylmalate.; mutation to K: Reduced activity toward 3-isopropylmalate.
R174 (= R134) binding substrate; mutation to A: Loss of activity toward 3-isopropylmalate.; mutation to K: Reduced activity toward 3-isopropylmalate.
Y181 (= Y141) Important for catalysis; mutation Y->A,F,H: Reduced activity toward 3-isopropylmalate.
K232 (= K187) Important for catalysis; mutation to M: Loss of activity toward 3-isopropylmalate.
N234 (= N189) binding NAD(+); mutation N->A,D: Loss of activity toward 3-isopropylmalate.
V235 (= V190) mutation to A: Reduced activity toward 3-isopropylmalate.
D264 (= D219) binding Mg(2+); binding substrate; mutation to N: Loss of activity toward 3-isopropylmalate.
N265 (≠ A220) binding NAD(+)
D288 (= D243) binding Mg(2+); mutation to N: Loss of activity toward 3-isopropylmalate.
D292 (= D247) binding Mg(2+); mutation to N: Reduced activity toward 3-isopropylmalate.
318:334 (vs. 273:289, 76% identical) binding NAD(+)

5j33A Isopropylmalate dehydrogenase in complex with NAD+ (see paper)
53% identity, 96% coverage: 4:355/366 of query aligns to 4:360/360 of 5j33A

query
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5j33A

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active site: Y141 (= Y141), K192 (= K187), D224 (= D219), D248 (= D243), D252 (= D247)
binding magnesium ion: D248 (= D243), D252 (= D247)
binding nicotinamide-adenine-dinucleotide: I74 (≠ V74), E89 (= E89), L92 (= L92), I261 (≠ L256), E278 (= E273), H281 (= H276), G282 (= G277), S283 (= S278), A284 (= A279), I287 (= I282), N294 (= N289), D335 (= D330)

5j32A Isopropylmalate dehydrogenase in complex with isopropylmalate (see paper)
54% identity, 96% coverage: 4:353/366 of query aligns to 14:368/369 of 5j32A

query
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5j32A

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active site: L18 (= L8), Y151 (= Y141), K202 (= K187), D234 (= D219), D258 (= D243), D262 (= D247)
binding 3-isopropylmalic acid: R106 (= R96), R144 (= R134), Y151 (= Y141), D258 (= D243)
binding magnesium ion: D258 (= D243), D262 (= D247)

1cnzA 3-isopropylmalate dehydrogenase (ipmdh) from salmonella typhimurium (see paper)
55% identity, 93% coverage: 5:344/366 of query aligns to 7:351/363 of 1cnzA

query
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1cnzA

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F

A

S

N

N

L

L

R

R

P

P

V

A

K

K

A

L

I

Y

P

Q

G

G

I

L

I

E

S

A

A

F

S

C

P

P

L

L

K

R

E

A

D

D

V

I

V

A

K

A

S

N

-

G

V

F

D

D

M

I

M

L

I

C

V

V

R

R

E

E

L

L

T

T

G

G

L

I

Y
|
Y

F

F

G

G

E

Q

P

P

K

K

R

G

K

R

T

E

D

G

N

S

G

G

-

Q

-

Y

-

E

-

K

A

A

V

F

D

D

T

T

L

E

V

V

Y

Y

S

H

R

R

E

F

E

E

I

I

E

E

R

R

I

I

V

A

E

R

K

I

A

A

F

F

E

E

L

S

A

A

R

R

L

K

R

R

G

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

S

S

K

I

L

L

W

W

R

R

E

E

V

I

V

V

E

N

Q

D

K

V

K

A

L

K

K

T

Y

Y

P

P

D

D

V

V

E

E

L

L

D

A

H

H

L

M

L

Y

V

I

D
|
D

A

N

A

A

A

T

M

M

K

Q

L

L

I

I

T

K

N

D

P

P

S

S

M

Q

F

F

D

D

V

V

V

L

T

C

E

S

N

N

L

L

F

F

G

G

D
|
D

I

I

L

L

S

S

D
|
D

E

E

A

C

S

A

V

M

I

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

R

N

A

E

D

Q

G

G

F

F

G

G

L

L

Y

Y

E

E

P

P

V

A

H

G

G

G

S

S

A

A

P

P

D

D

I

I

A

A

G

G

K

K

G

N

L

I

A

A

N

N

P

P

A

I

A

A

A

Q

I

I

L

L

S

S

V

L

A

A

M

L

L

L

K

R

Y

Y

S

S

F

L

G

D

M

A

E

N

T

D

E

A

A

A

S

T

S

A

I

I

E

E

E

Q

A

A

V

I

F

N

S

R

V

A

Y

L

E

E

D

E

G

G

Y

V

C

R

T

T

S

G

D

D

M

L

K

A

Q

R

D

-

G

G

Y

A

R

A

V

A

L

V

S

S

T

T

S

D

E

E

F

M

active site: Y145 (= Y141), K195 (= K187), D227 (= D219), D251 (= D243)
binding manganese (ii) ion: D251 (= D243), D255 (= D247)

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)
55% identity, 93% coverage: 5:344/366 of query aligns to 7:351/363 of P37412

query
sites
P37412

I

I

A

A

V

V

L

L

P

P

G

G

D

D

G

G

I

I

G

G

K

P

E

E

V

V

T

M

E

A

S

Q

A

A

L

L

K

K

V

V

L

M

Q

D

A

A

I

V

G

R

R

S

R

R

Y

F

N

D

H

M

R

R

Y

I

H

T

V

T

N

S

T

H

G

Y

L

D

I

V

G

G

D

I

A

A

I

I

D

D

Q

N

K

H

G

G

H

H

P

P

L

L

P

P

Q

K

D

A

T

T

I

V

D

E

L

G

C

C

E

E

N

Q

S

A

D

D

A

A

I

I

L

L

L

F

G

G

A

S

V

V

G

G

L

P

K

K

W

W

D

E

Q

N

N

L

P

P

S

P

H

E

L

S

R

Q

P

P

E

E

K

R

G

G

-

A

L

L

A

P

I

L

R

R

K

K

H

H

F

F

D

K

L

L

F

F

A

S

N

N

L

L

R

R

P

P

V

A

K

K

A

L

I

Y

P

Q

G

G

I

L

I

E

S

A

A

F

S

C

P

P

L

L

K

R

E

A

D

D

V

I

V

A

K

A

S

N

-

G

V

F

D

D

M

I

M

L

I

C

V

V

R

R

E

E

L

L

T

T

G

G

L

I

Y

Y

F

F

G

G

E

Q

P

P

K

K

R

G

K

R

T

E

D

G

N

S

G

G

-

Q

-

Y

-

E

-

K

A

A

V

F

D

D

T

T

L

E

V

V

Y

Y

S

H

R

R

E

F

E

E

I

I

E

E

R

R

I

I

V

A

E

R

K

I

A

A

F

F

E

E

L

S

A

A

R

R

L

K

R

R

G

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

S

S

K

I

L

L

W

W

R

R

E

E

V

I

V

V

E

N

Q

D

K

V

K

A

L

K

K

T

Y

Y

P

P

D

D

V

V

E

E

L

L

D

A

H

H

L

M

L

Y

V

I

D
|
D

A

N

A

A

A

T

M

M

K

Q

L

L

I

I

T

K

N

D

P

P

S

S

M

Q

F

F

D

D

V

V

V

L

T

C

E

S

N

N

L

L

F

F

G

G

D
|
D

I

I

L

L

S

S

D
|
D

E

E

A

C

S

A

V

M

I

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

R

N

A

E

D

Q

G

G

F

F

G

G

L

L

Y

Y

E

E

P

P

V

A

H

G

G

G

S

S

A

A

P

P

D

D

I

I

A

A

G

G

K

K

G

N

L

I

A

A

N

N

P

P

A

I

A

A

A

Q

I

I

L

L

S

S

V

L

A

A

M

L

L

L

K

R

Y

Y

S

S

F

L

G

D

M

A

E

N

T

D

E

A

A

A

S

T

S

A

I

I

E

E

E

Q

A

A

V

I

F

N

S

R

V

A

Y

L

E

E

D

E

G

G

Y

V

C

R

T

T

S

G

D

D

M

L

K

A

Q

R

D

-

G

G

Y

A

R

A

V

A

L

V

S

S

T

T

S

D

E

E

F

M

D227 (= D219) binding Mn(2+)
D251 (= D243) binding Mn(2+)
D255 (= D247) binding Mn(2+)

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)
53% identity, 96% coverage: 4:353/366 of query aligns to 48:402/409 of Q9FMT1

query
sites
Q9FMT1

T

N

I

I

A

A

V

L

L

L

P

P

G

G

D

D

G

G

I

I

G

G

K

P

E

E

V

V

T

I

E

S

S

V

A

A

L

K

K

N

V

V

L

L

Q

Q

A

K

I

A

G

G

R

S

R

L

Y

E

N

G

H

L

R

E

Y

F

H

D

V

F

N

K

T

E

G

M

L

P

I

V

G

G

D

A

A

A

I

L

D

D

Q

L

K

V

G

G

H

V

P

P

L

L

P

P

Q

E

D

E

T

T

I

F

D

T

L

A

C

A

E

K

N

L

S

S

D

D

A

A

I

I

L

L

G

G

A

A

V

I

G

G

L

Y

K

K

W

W

D

D

Q

K

N

N

P

E

S

K

H

H

L

L

R

R

P

P

E

E

K

M

G

A

L

L

L
x
F

A

Y

I

L

R

R

K

R

H

D

F

L

D

K

L

V

F

F

A

A

N

N

L

L

R

R

P

P

V

A

K

T

A

V

I

L

P

P

G

Q

I

L

I

V

S

D

A

A

S

S

P

T

L

L

K

K

E

K

D

E

V

V

V

A

K

E

S

G

V

V

D

D

M

M

I

I

V

V

R

R

E

E

L

L

T

T

G

G

L

I

Y

Y

F

F

G

G

E

E

P

P

K

R

R

G

K

I

T

T

-

I

-

N

D

E

N

N

G

G

-

E

-

V

A

G

V

V

D

S

T

T

L

E

V

I

Y

Y

S

A

R

A

E

H

E

E

I

I

E

D

R

R

I

I

V

A

E

R

K

V

A

A

F

F

E

E

L

T

A

A

R

R

L

K

R

R

G

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

S

A

S

S

K

I

L

L

W

W

R

R

E

K

V

R

V

V

E

T

Q

A

K

L

K

A

L

S

K

E

Y

Y

P

P

D

D

V

V

E

E

L

L

D

S

H

H

L

M

L

Y

V

V

D

D

A

N

A

A

M

M

K

Q

L

L

I

I

T

R

N

D

P

P

S

K

M

Q

F

F

D

D

V

T

V

I

V

V

T

T

E

N

N

N

L

I

F

F

G

G

D

D

I

I

L

L

S

S

D

D

E

E

A

A

S

S

V

M

I

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

R

G

A

E

D

S

G

G

F

P

G

G

L

L

Y

F

E

E

P

P

V

I

H

H

G

G

S

S

A

A

P

P

D

D

I

I

A

A

G

G

K

Q

G

D

L

K

A

A

N

N

P

P

A

L

A

A

A

T

I

I

L

L

S

S

V

A

A

A

M

M

M

L

L

L

K

K

Y

Y

S

G

F

L

G

G

M

E

E

E

T

K

E

A

A

A

S

K

S

R

I

I

E

E

E

D

A

A

V

V

F

V

S

D

V

A

Y

L

E

N

D

K

G

G

Y

F

C

R

T

T

S

G

D

D

M

I

K

Y

Q

S

D

P

G

G

Y

N

R

K

V

L

L

V

S

G

T
x
C

S

K

E

E

F

M

T

G

E

E

K

E

V

V

I

L

E

K

E

S

L

V

E

E

F137 (≠ L93) Confers substrate specificity; mutation to L: Reduced activity toward 3-(2'-methylthio)-ethylmalate, but enhanced catalytic efficiency with 3-isopropylmalate.
C232 (≠ T183) Essential for redox regulation; mutation to S: Reduced sensitivity to oxidation on enzyme activity regulation.
C390 (≠ T341) Essential for redox regulation; mutation to S: Reduced sensitivity to oxidation on enzyme activity regulation.

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)
53% identity, 96% coverage: 4:353/366 of query aligns to 45:399/404 of Q9SA14

query
sites
Q9SA14

T

N

I

I

A

T

V

L

L

L

P

P

G

G

D

D

G

G

I

I

G

G

K

P

E

E

V

V

T

I

E

S

S

V

A

A

L

K

K

N

V

V

L

L

Q

Q

A

K

I

A

G

G

R

F

R

L

Y

Q

N

G

H

L

R

E

Y

F

H

D

V

F

N

Q

T

E

G

M

L

P

I

F

G

G

D

A

A

A

I

L

D

D

Q

L

K

V

G

G

H

V

P

P

L

L

P

P

Q

E

D

E

T

T

I

S

D

T

L

A

C

A

E

K

N

Q

S

S

D

D

A

A

I

I

L

L

G

G

A

A

V

I

G

G

L

Y

K

K

W

W

D

D

Q

K

N

N

P

E

S

K

H

H

L

L

R

R

P

P

E

E

K

M

G

G

L

L

L
|
L

A

N

I

I

R

R

K

R

H

D

F

L

D

N

L

V

F

F

A

A

N

N

L

L

R

R

P

P

V

A

K

T

A

V

I

L

P

P

G

Q

I

L

I

V

S

D

A

A

S

S

P

T

L

L

K

K

E

K

D

E

V

V

V

A

K

Q

S

G

V

V

D

D

M

M

I

I

V

V

R

R

E

E

L

L

T

T

G

G

L

I

Y

Y

F

F

G

G

E

E

P

P

K

R

R

G

K

I

T

T

-

I

-

N

D

E

N

N

G

G

-

E

-

V

A

G

V

F

D

N

T

T

L

E

V

I

Y

Y

S

A

R

A

E

H

E

E

I

I

E

D

R

R

I

I

V

A

E

R

K

V

A

A

F

F

E

E

L

T

A

A

R

R

L

K

R

R

G

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

S

A

S

S

K

I

L

L

W

W

R

R

E

K

V

R

V

V

E

T

Q

A

K

L

K

A

L

S

K

E

Y

Y

P

P

D

D

V

V

E

E

L

L

D

S

H

H

L

M

L

Y

V

V

D

D

A

N

A

A

M

M

K

Q

L

L

I

V

T

R

N

D

P

P

S

K

M

Q

F

F

D

D

V

T

V

I

V

V

T

T

E

N

N

N

L

I

F

F

G

G

D

D

I

I

L

L

S

S

D

D

E

E

A

A

S

S

V

M

I

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

R

G

A

E

D

S

G

G

F

P

G

G

L

L

Y

F

E

E

P

P

V

I

H

H

G

G

S

S

A

A

P

P

D

D

I

I

A

A

G

G

K

Q

G

D

L

K

A

A

N

N

P

P

A

L

A

A

A

T

I

I

L

L

S

S

V

A

A

A

M

M

M

L

L

L

K

K

Y

Y

S

G

F

L

G

G

M

E

E

E

T

K

E

A

A

A

S

K

S

M

I

I

E

E

E

D

A

A

V

V

F

V

S

D

V

A

Y

L

E

N

D

K

G

G

Y

F

C

R

T

T

S

G

D

D

M

I

K

Y

Q

S

D

P

G

G

Y

N

R

K

V

L

L

V

S

G

T

C

S

K

E

E

F

M

T

G

E

E

K

E

V

V

I

L

E

K

E

S

L

V

E

D

L134 (= L93) 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)
53% identity, 93% coverage: 4:343/366 of query aligns to 5:349/358 of 6xxyA

query
sites
6xxyA

T

N

I

I

A

A

V

V

L

L

P

A

G

G

D

D

G

G

I

I

G

G

K

P

E

E

V

V

T

M

E

A

S

E

A

A

L

I

K

K

V

V

L

L

Q

N

A

R

I

V

G

Q

R

E

R

K

Y

F

N

G

H

F

R

K

Y

L

H

N

V

F

N

N

T

E

G

F

L

F

I

V

G

G

D

A

A

A

I

I

D

E

Q

H

K

C

G

G

H

Y

P

P

L

L

P

P

Q

A

D

E

T

T

I

L

D

K

L

G

C

C

E

D

N

Q

S

A

D

D

A

A

I

I

L

L

L

F

G

G

A
x
S

V
|
V

G
|
G

G

G

L

P

K

K

W

W

D

T

Q

N

N

L

P

P

S

P

H

D

L

Q

R

Q

P

P

E
|
E

K

R

G

G

-

A

L
|
L

L

L

A

P

I

L

R

R

K

K

H

H

F

F

D

K

L

L

F

F

A

C

N

N

L

L

R
|
R

P

P

V

A

K

T

A

L

I

Y

P

K

G

G

I

L

I

E

S

K

A

F

S

C

P

P

L

L

K

R

E

A

D

D

V

I

V

A

-

A

K

K

S

G

V

F

D

D

M

M

M

V

I

V

V

V

R
|
R

E

E

L

L

T

T

G

G

L

I

Y
|
Y

F

F

G

G

E

Q

P

P

K

K

R

G

K

R

T

E

D

G

N

D

G

G

-

V

-

Q

-

T

-

K

A

A

V

F

D

D

T

T

L

E

V

V

Y

Y

S

Y

R

K

E

Y

E

E

I

I

E

E

R

R

I

I

V

A

E

R

K

A

A

A

F

F

E

E

L

A

A

A

R

M

L

K

R

R

R

N

G

K

K

K

V

V

T

T

S

S

V

V

D

D

K
|
K

A

A

N

N

V
|
V

L

L

E

Q

S

S

K

I

L

L

W

W

R

R

E

E

V

T

V

V

E

T

Q

E

K

M

K

A

L

K

K

D

Y

Y

P

P

D

E

V

V

E

T

L

L

D

E

H

H

L

I

L
x
Y

V

I

D
|
D

A
x
N

A

A

A

T

M
|
M

K

Q

L

L

I

I

T

K

N

S

P

P

S

E

M

S

F

F

D

D

V

V

V

L

T

C

E

S

N

N

L

I

F

F

G

G

D
|
D

I

I

L

I

S

S

D
|
D

E

E

A

A

S

A

V

M

I

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

R

N

A

E

D

E

G

G

F

F

G

G

L

L

Y

Y

E
|
E

P

P

V

A

H
x
G

G
|
G

S
|
S

A
|
A

P
|
P

D
|
D

I
|
I

A

A

G

G

K

K

G

G

L

I

A

A

N
|
N

P

P

A

I

A

A

A

Q

I

I

L

L

S

S

V

A

A

A

M

M

L

L

K

R

Y

Y

S

S

F

F

G

N

M

L

E

N

T

E

E

A

A

A

S

D

S

A

I

I

E

E

E

S

A

A

V

V

F

Q

S

K

V

V

Y

L

E

A

D

S

G

G

Y

H

C

R

T

T

S

A

D
|
D

M

L

K

A

Q

D

D

D

G

S

Y

T

R

P

V

V

L

-

S

S

T

T

S

A

E

E

active site: Y144 (= Y141), K194 (= K187), D226 (= D219), D250 (= D243)
binding magnesium ion: D250 (= D243), D254 (= D247)
binding nicotinamide-adenine-dinucleotide: S74 (≠ A73), V75 (= V74), G76 (= G75), E90 (= E89), L94 (= L92), Y224 (≠ L217), N227 (≠ A220), M230 (= M223), M263 (≠ L256), G264 (= G257), E280 (= E273), G283 (≠ H276), G284 (= G277), S285 (= S278), A286 (= A279), P287 (= P280), D288 (= D281), I289 (= I282), N296 (= N289), D337 (= D330)
binding 2-(2-methylprop-2-enoxyamino)-2-oxidanylidene-ethanoic acid: E90 (= E89), R108 (= R106), R137 (= R134), K194 (= K187), V197 (= V190), D226 (= D219), D250 (= D243)

2y42D Structure of isopropylmalate dehydrogenase from thermus thermophilus - complex with nadh and mn (see paper)
57% identity, 86% coverage: 5:318/366 of query aligns to 4:316/355 of 2y42D

query
sites
2y42D

I

V

A

A

V

V

L

L

P

P

G

G

D

D

G

G

I
|
I

G

G

K

P

E

E

V

V

T

T

E

E

S

A

A

A

L

L

K

K

V

V

L

L

Q

R

A

A

I

L

G

D

R

E

R

A

Y

E

N

G

H

L

R

G

Y

L

H

A

V

Y

N

E

T

V

G

F

L

P

I

F

G

G

D

A

A

A

I

I

D

D

Q

A

K

F

G

G

H

E

P

P

L

F

P

P

Q

E

D

P

T

T

I

R

D

K

L

G

C

V

E

E

N

E

S

A

D

E

A

A

I

V

L

L

G

G

A

S

V

V

G

G

L

P

K

K

W

W

D
|
D

Q

G

N

L

P

P

S

R

H

K

L

I

R

R

P

P

E

E

K

T

G

G

L

L

A

S

I

L

R

R

K

K

H

S

F

Q

D

D

L

L

F

F

A

A

N

N

L

L

R

R

P

P

V

A

K

K

A

V

I

F

P

P

G

G

I

L

I

E

S

R

A

L

S

S

P

P

L

L

K

K

E

E

D

E

V

I

V

A

K

R

S

G

V

V

D

D

M

V

M

L

I

I

V

V

R

R

E

E

L

L

T

T

G

G

L

I

Y
|
Y

F

F

G

G

E

E

P

P

K

R

R

G

K

M

T

S

D

E

N

A

G

E

A

A

V

W

D

N

T

T

L

E

V

R

Y

Y

S

S

R

K

E

P

E

E

I

V

E

E

R

R

I

V

V

A

E

R

K

V

A

A

F

F

E

E

L

A

A

A

R

R

L

K

R

R

G

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

S

V

S

G

K

E

L

F

W

W

R

R

E

K

V

T

V

V

E

E

Q

E

K

V

K

G

L

R

K

G

Y

Y

P

P

D

D

V

V

E

A

L

L

D

E

H

H

L

Q

L

Y

V

V

D
|
D

A

A

A

M

A

A

M

M

K

H

L

L

I

V

T

R

N

S

P

P

S

A

M

R

F

F

D

D

V

V

T

T

E

G

N

N

L

I

F

F

G

G

D
|
D

I

I

L

L

S

S

D
|
D

E

L

A

A

S

S

V

V

I

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

R

-

A

G

D

R

G

G

F

T

G

P

L

V

Y

F

E

E

P

P

V

V

H
|
H

G
|
G

S

S

A
|
A

P

P

D
|
D

I
|
I

A

A

G

G

K

K

G

G

L

I

A

A

N
|
N

P

P

A

T

A

A

I

I

L

L

S

S

V

A

A

A

M

M

L

L

K

E

Y

H

S

A

F

F

G

G

M

L

E

V

T

E

E

L

A

A

S

R

S

K

I

V

E

E

E

D

A

A

V

V

active site: Y140 (= Y141), K186 (= K187), D218 (= D219), D242 (= D243), D246 (= D247)
binding manganese (ii) ion: D242 (= D243), D246 (= D247)
binding nicotinamide-adenine-dinucleotide: I12 (= I13), D79 (= D80), H274 (= H276), G275 (= G277), A277 (= A279), D279 (= D281), I280 (= I282), N287 (= N289)

2y41A Structure of isopropylmalate dehydrogenase from thermus thermophilus - complex with ipm and mn (see paper)
57% identity, 86% coverage: 5:318/366 of query aligns to 4:316/346 of 2y41A

query
sites
2y41A

I

V

A

A

V

V

L

L

P

P

G

G

D

D

G

G

I

I

G

G

K

P

E

E

V

V

T

T

E

E

S

A

A

A

L

L

K

K

V

V

L

L

Q

R

A

A

I

L

G

D

R

E

R

A

Y

E

N

G

H

L

R

G

Y

L

H

A

V

Y

N

E

T

V

G

F

L

P

I

F

G

G

D

A

A

A

I

I

D

D

Q

A

K

F

G

G

H

E

P

P

L

F

P

P

Q

E

D

P

T

T

I

R

D

K

L

G

C

V

E

E

N

E

S

A

D

E

A

A

I

V

L

L

G

G

A

S

V

V

G

G

L

P

K

K

W

W

D

D

Q

G

N

L

P

P

S

R

H

K

L

I

R

R

P

P

E

E

K

T

G

G

L

L

A

S

I

L

R
|
R

K

K

H

S

F

Q

D

D

L

L

F

F

A

A

N

N

L

L

R
|
R

P

P

V

A

K

K

A

V

I

F

P

P

G

G

I

L

I

E

S

R

A

L

S

S

P

P

L

L

K

K

E

E

D

E

V

I

V

A

K

R

S

G

V

V

D

D

M

V

M

L

I

I

V

V

R
|
R

E

E

L

L

T

T

G

G

L

I

Y
|
Y

F

F

G

G

E

E

P

P

K

R

R

G

K

M

T

S

D

E

N

A

G

E

A

A

V

W

D

N

T

T

L

E

V

R

Y

Y

S

S

R

K

E

P

E

E

I

V

E

E

R

R

I

V

V

A

E

R

K

V

A

A

F

F

E

E

L

A

A

A

R

R

L

K

R

R

G

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

S

V

S

G

K

E

L

F

W

W

R

R

E

K

V

T

V

V

E

E

Q

E

K

V

K

G

L

R

K

G

Y

Y

P

P

D

D

V

V

E

A

L

L

D

E

H

H

L

Q

L

Y

V

V

D
|
D

A

A

A

M

A

A

M

M

K

H

L

L

I

V

T

R

N

S

P

P

S

A

M

R

F

F

D

D

V

V

T

T

E

G

N

N

L

I

F

F

G

G

D
|
D

I

I

L

L

S

S

D
|
D

E

L

A

A

S

S

V

V

I

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

R

-

A

G

D

R

G

G

F

T

G

P

L

V

Y

F

E

E

P

P

V

V

H

H

G

G

S

S

A

A

P

P

D

D

I

I

A

A

G

G

K

K

G

G

L

I

A

A

N

N

P

P

A

T

A

A

I

I

L

L

S

S

V

A

A

A

M

M

L

L

K

E

Y

H

S

A

F

F

G

G

M

L

E

V

T

E

E

L

A

A

S

R

S

K

I

V

E

E

E

D

A

A

V

V

active site: Y140 (= Y141), K186 (= K187), D218 (= D219), D242 (= D243), D246 (= D247)
binding 3-isopropylmalic acid: R95 (= R96), R105 (= R106), R133 (= R134), Y140 (= Y141), D242 (= D243)

2ztwA Structure of 3-isopropylmalate dehydrogenase in complex with the inhibitor and NAD+ (see paper)
57% identity, 86% coverage: 5:318/366 of query aligns to 3:315/345 of 2ztwA

query
sites
2ztwA

I

V

A

A

V

V

L

L

P

P

G

G

D

D

G

G

I
|
I

G

G

K

P

E

E

V

V

T

T

E

E

S

A

A

A

L

L

K

K

V

V

L

L

Q

R

A

A

I

L

G

D

R

E

R

A

Y

E

N

G

H

L

R

G

Y

L

H

A

V

Y

N

E

T

V

G

F

L

P

I

F

G

G

D

A

A

A

I

I

D

D

Q

A

K

F

G

G

H

E

P

P

L

F

P

P

Q

E

D

P

T

T

I

R

D

K

L

G

C

V

E

E

N

E

S

A

D

E

A

A

I

V

L

L

G

G

A

S

V

V

G

G

L

P

K

K

W

W

D

D

Q

G

N

L

P

P

S

R

H

K

L

I

R

R

P

P

E

E

K

T

G

G

L

L

A

S

I

L

R

R

K

K

H

S

F

Q

D

D

L

L

F

F

A

A

N

N

L

L

R

R

P

P

V

A

K

K

A

V

I

F

P

P

G

G

I

L

I

E

S

R

A

L

S

S

P

P

L

L

K

K

E

E

D

E

V

I

V

A

K

R

S

G

V

V

D

D

M

V

M

L

I

I

V

V

R

R

E

E

L

L

T

T

G

G

L

I

Y
|
Y

F

F

G

G

E

E

P

P

K

R

R

G

K

M

T

S

D

E

N

A

G

E

A

A

V

W

D

N

T

T

L

E

V

R

Y

Y

S

S

R

K

E

P

E

E

I

V

E

E

R

R

I

V

V

A

E

R

K

V

A

A

F

F

E

E

L

A

A

A

R

R

L

K

R

R

G

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

S

V

S

G

K

E

L

F

W

W

R

R

E

K

V

T

V

V

E

E

Q

E

K

V

K
x
G

L

R

K

G

Y
|
Y

P

P

D

D

V
|
V

E

A

L

L

D

E

H

H

L

Q

L

Y

V

V

D
|
D

A

A

A

M

A

A

M

M

K

H

L

L

I

V

T

R

N

S

P

P

S

A

M

R

F

F

D

D

V

V

T

T

E

G

N

N

L

I

F

F

G

G

D
|
D

I

I

L

L

S

S

D
|
D

E

L

A

A

S

S

V

V

I

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

R

-

A

G

D

R

G

G

F

T

G

P

L

V

Y

F

E

E

P

P

V

V

H
|
H

G
|
G

S

S

A
|
A

P

P

D
|
D

I
|
I

A

A

G

G

K

K

G

G

L

I

A
|
A

N
|
N

P

P

A

T

A

A

I

I

L

L

S

S

V

A

A

A

M

M

L

L

K

E

Y

H

S

A

F

F

G

G

M

L

E

V

T

E

E

L

A

A

S

R

S

K

I

V

E

E

E

D

A

A

V

V

active site: Y139 (= Y141), K185 (= K187), D217 (= D219), D241 (= D243), D245 (= D247)
binding magnesium ion: G203 (≠ K205), Y206 (= Y208), V209 (= V211)
binding nicotinamide-adenine-dinucleotide: I11 (= I13), H273 (= H276), G274 (= G277), A276 (= A279), D278 (= D281), I279 (= I282), A285 (= A288), N286 (= N289)

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)
57% identity, 86% coverage: 5:318/366 of query aligns to 3:315/345 of Q5SIY4

query
sites
Q5SIY4

I

V

A

A

V

V

L

L

P

P

G

G

D

D

G

G

I

I

G

G

K

P

E

E

V

V

T

T

E

E

S

A

A

A

L

L

K

K

V

V

L

L

Q

R

A

A

I

L

G

D

R

E

R

A

Y

E

N

G

H

L

R

G

Y

L

H

A

V

Y

N

E

T

V

G

F

L

P

I

F

G

G

D

A

A

A

I

I

D

D

Q

A

K

F

G

G

H

E

P

P

L

F

P

P

Q

E

D

P

T

T

I

R

D

K

L

G

C

V

E

E

N

E

S

A

D

E

A

A

I

V

L

L

G

G

A

S

V

V

G

G

G
|
G

L
x
P

K
|
K

W
|
W

D
|
D

Q
x
G

N
x
L

P
|
P

S
x
R

H
x
K

L
x
I

R
|
R

P
|
P

E
|
E

K

T

G

G

L

L

A

S

I

L

R

R

K

K

H

S

F

Q

D

D

L

L

F

F

A

A

N

N

L

L

R

R

P

P

V

A

K

K

A

V

I

F

P

P

G

G

I

L

I

E

S

R

A

L

S

S

P

P

L

L

K

K

E

E

D

E

V

I

V

A

K

R

S

G

V

V

D

D

M

V

M

L

I

I

V

V

R

R

E

E

L

L

T

T

G

G

L

I

Y
|
Y

F

F

G

G

E

E

P

P

K

R

R

G

K

M

T

S

D

E

N

A

G

E

A

A

V

W

D

N

T

T

L

E

V

R

Y

Y

S

S

R

K

E

P

E

E

I

V

E

E

R

R

I

V

V

A

E

R

K

V

A

A

F

F

E

E

L

A

A

A

R

R

L

K

R

R

G

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

S

V

S

G

K

E

L

F

W

W

R

R

E

K

V

T

V

V

E

E

Q

E

K

V

K

G

L

R

K

G

Y

Y

P

P

D

D

V

V

E

A

L

L

D

E

H

H

L

Q

L

Y

V

V

D

D

A

A

A

M

A

A

M

M

K

H

L

L

I

V

T

R

N

S

P

P

S

A

M

R

F

F

D

D

V

V

T

T

E

G

N

N

L

I

F

F

G

G

D

D

I

I

L

L

S

S

D

D

E

L

A

A

S

S

V

V

I

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

R

-

A

G

D

R

G

G

F

T

G

P

L

V

Y

F

E

E

P

P

V

V

H

H

G
|
G

S
|
S

A
|
A

P
|
P

D
|
D

I
|
I

A
|
A

G
|
G

K
|
K

G
|
G

L
x
I

A
|
A

N
|
N

P

P

A

T

A

A

I

I

L

L

S

S

V

A

A

A

M

M

L

L

K

E

Y

H

S

A

F

F

G

G

M

L

E

V

T

E

E

L

A

A

S

R

S

K

I

V

E

E

E

D

A

A

V

V

74:87 (vs. 76:89, 57% identical) binding NAD(+)
Y139 (= Y141) mutation to F: Large decrease in activity and a small decrease in substrate affinity.
274:286 (vs. 277:289, 92% identical) binding NAD(+)

3vkzA 3-isopropylmalate dehydrogenase from shewanella oneidensis mr-1 at atmospheric pressure (see paper)
53% identity, 89% coverage: 5:331/366 of query aligns to 5:337/364 of 3vkzA

query
sites
3vkzA

I

I

A

A

V

V

L

L

P

A

G

G

D

D

G

G

I

I

G

G

K

P

E

E

V

V

T

M

E

A

S

E

A

A

L

R

K

K

V

V

L

L

Q

K

A

A

I

V

G

E

R

A

R

R

Y

F

N

G

H

L

R

N

Y

I

H

E

V

Y

N

T

T

E

G

Y

L

D

I

V

G

G

D

I

A

A

I

I

D

D

Q

N

K

H

G

G

H

C

P

P

L

L

P

P

Q

E

D

A

T

T

I

L

D

K

L

G

C

C

E

E

N

A

S

A

D

D

A

A

I

I

L

L

L

F

G

G

A

S

V

V

G

G

L

P

K

K

W

W

D

E

Q

K

N

L

P

P

S

P

H

N

L

E

R

Q

P

P

E

E

K

R

G

G

-

A

L

L

A

P

I

L

R
|
R

K

G

H

H

F

F

D

E

L

L

F

F

A

C

N

N

L

L

R

R

P

P

V

A

K

K

A

L

I

H

P

D

G

G

I

L

I

E

S

H

A

M

S

S

P

P

L

L

K

R

E

S

D

D

V

I

-

S

V

A

K

R

S

G

V

F

D

D

M

V

M

L

I

C

V

V

R
|
R

E

E

L

L

T

T

G

G

L

I

Y
|
Y

F

F

G

G

E

K

P

P

K

K

R

G

K

R

T

Q

D

G

N

E

G

G

-

E

-

S

-

E

A

A

V

F

D

D

T

T

L

M

V

R

Y

Y

S

S

R

R

E

R

E

E

I

I

E

S

R

R

I

I

V

A

E

R

K

I

A

A

F

F

E

E

L

A

A

A

R

R

L

G

R

R

G

K

K

K

V

V

T

T

S

S

V

V

D

D

K
|
K

A

A

N

N

V

V

L

L

E

A

S

C

S

S

K

V

L

L

W

W

R

R

E

Q

V

V

E

E

Q

E

K

V

K

A

L

V

K

D

Y

F

P

P

D

D

V

V

E

E

L

L

D

E

H

H

L

I

L

Y

V

I

D
|
D

A

N

A

A

A

T

M

M

K

Q

L

L

I

L

T

R

N

R

P

P

S

D

M

E

F

F

D

D

V

V

V

M

V

L

T

C

E

S

N

N

L

L

F

F

G

G

D
|
D

I

I

L

L

S

S

D
|
D

E

E

A

I

S

A

V

M

I

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

R

N

A

S

D

T

G

G

F

F

G

G

L

L

Y

F

E

E

P

P

V

A

H

G

G

G

S

S

A

A

P

P

D

D

I

I

A

A

G

G

K

K

G

G

L

I

A

A

N

N

P

P

A

I

A

A

A

Q

I

I

L

L

S

S

V

A

A

A

M

L

M

M

L

L

K

R

Y

H

S

S

F

L

G

K

M

Q

E

E

T

E

E

A

A

A

S

S

S

A

I

I

E

E

E

R

A

A

V

V

F

T

S

K

V

A

Y

L

E

N

D
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