SitesBLAST

SitesBLAST – Find functional sites

SitesBLAST

Comparing WP_013537107.1 NCBI__GCF_000185805.1:WP_013537107.1 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)
58% identity, 97% coverage: 2:350/359 of query aligns to 41:391/405 of P93832

query
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P93832

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114:129 (vs. 75:90, 56% identical) binding NAD(+)
L132 (= L93) mutation to A: Reduced activity toward 3-isopropylmalate.
L133 (= L94) 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 (= R97) binding substrate; mutation to A: Loss of activity toward 3-isopropylmalate.; mutation to K: Reduced activity toward 3-isopropylmalate.
R146 (= R107) binding substrate; mutation to A: Reduced activity toward 3-isopropylmalate.; mutation to K: Reduced activity toward 3-isopropylmalate.
R174 (= R135) binding substrate; mutation to A: Loss of activity toward 3-isopropylmalate.; mutation to K: Reduced activity toward 3-isopropylmalate.
Y181 (= Y142) Important for catalysis; mutation Y->A,F,H: Reduced activity toward 3-isopropylmalate.
K232 (= K192) Important for catalysis; mutation to M: Loss of activity toward 3-isopropylmalate.
N234 (= N194) binding NAD(+); mutation N->A,D: Loss of activity toward 3-isopropylmalate.
V235 (= V195) mutation to A: Reduced activity toward 3-isopropylmalate.
D264 (= D224) binding Mg(2+); binding substrate; mutation to N: Loss of activity toward 3-isopropylmalate.
N265 (= N225) binding NAD(+)
D288 (= D248) binding Mg(2+); mutation to N: Loss of activity toward 3-isopropylmalate.
D292 (= D252) binding Mg(2+); mutation to N: Reduced activity toward 3-isopropylmalate.
318:334 (vs. 277:293, 88% identical) binding NAD(+)

5j33A Isopropylmalate dehydrogenase in complex with NAD+ (see paper)
58% identity, 97% coverage: 2:350/359 of query aligns to 1:351/360 of 5j33A

query
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5j33A

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active site: Y141 (= Y142), K192 (= K192), D224 (= D224), D248 (= D248), D252 (= D252)
binding magnesium ion: D248 (= D248), D252 (= D252)
binding nicotinamide-adenine-dinucleotide: I74 (≠ V75), E89 (= E90), L92 (= L93), I261 (≠ L261), E278 (= E277), H281 (= H280), G282 (= G281), S283 (= S282), A284 (= A283), I287 (= I286), N294 (= N293), D335 (= D334)

5j32A Isopropylmalate dehydrogenase in complex with isopropylmalate (see paper)
58% identity, 97% coverage: 2:350/359 of query aligns to 11:361/369 of 5j32A

query
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active site: L18 (= L9), Y151 (= Y142), K202 (= K192), D234 (= D224), D258 (= D248), D262 (= D252)
binding 3-isopropylmalic acid: R106 (= R97), R144 (= R135), Y151 (= Y142), D258 (= D248)
binding magnesium ion: D258 (= D248), D262 (= D252)

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)
58% identity, 97% coverage: 2:350/359 of query aligns to 42:392/404 of Q9SA14

query
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Q9SA14

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F

A

A

N

N

L

L

R

R

P

P

A

A

R

T

L

V

Y

L

D

P

E

Q

L

L

I

V

D

D

A

A

S

S

T

T

L

L

K

K

P

K

E

E

V

V

V

A

R

Q

G

G

V

V

D

D

I

M

M

M

V

I

I

V

R

R

E

E

L

L

T

T

S

G

G

G

I

I

Y

Y

F

F

G

G

I

E

P

P

K

R

G

G

I

I

F

T

V

I

D

N

G

E

D

N

-

G

E

E

R

E

V

V

G

G

I

F

N

N

T

T

L

E

R

I

Y

Y

Y

A

E

A

H

H

E

E

V

I

E

D

R

R

I

I

A

A

K

R

V

V

A

A

F

F

E

E

V

T

A

A

R

R

K

K

R

R

N

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

A

A

T

S

V

I

L

L

W

W

R

R

E

K

V

R

V

V

E

T

R

A

V

L

H

A

E

S

N

E

Y

Y

P

P

D

D

V

V

E

E

L

L

Q

S

H

H

M

M

Y

Y

V

V

D

D

N

N

A

A

M

M

Q

Q

I

L

I

V

R

R

W

D

P

P

K

K

Q

Q

F

F

D

D

V

T

I

I

V

V

T

T

T

N

N

N

M

I

F

F

G

G

D

D

I

I

L

L

S

S

D

D

A

E

C

A

A

S

M

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

G

S

K

G

I

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

N

D

I

K

A

A

N

N

P

P

I

L

A

A

T

T

I

I

N

L

S

S

A

A

G

A

M

M

M

L

F

L

T

K

Y

Y

S

G

F

L

D

G

M

E

P

E

E

K

V

A

E

A

E

K

A

M

I

I

D

E

K

D

A

A

V

V

R

V

A

D

V

A

L

L

A

N

K

K

G

G

Y

F

R

R

T

T

R

G

D

D

I

I

Y

Y

S

S

E

P

G

G

T

N

K

K

L

L

V

V

S

G

T

C

E

K

E

E

M

M

G

G

D

E

L134 (= L94) 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)
56% identity, 99% coverage: 2:358/359 of query aligns to 45:403/409 of Q9FMT1

query
sites
Q9FMT1

R

K

K

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

V

I

K

S

Q

V

A

A

V

K

K

N

V

V

M

L

E

Q

A

K

A

A

A

G

E

S

K

L

F

E

G

G

F

L

G

E

L

F

E

D

L

F

N

K

Y

E

G

M

L

P

I

V

G

G

A

A

I

L

D

D

E

L

T

V

G

G

V

V

P

P

F

L

P

P

E

E

T

T

K

F

E

T

L

A

I

A

L

K

S

L

S

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

N

K

L

N

P

E

F

K

E

H

I

L

R

R

P

P

E

E

R

M

A

A

L

L

L
x
F

G

Y

M

L

R

R

K

R

L

D

L

L

N

K

A

V

F

F

A

A

N

N

L

L

R

R

P

P

A

A

R

T

L

V

Y

L

D

P

E

Q

L

L

I

V

D

D

A

A

S

S

T

T

L

L

K

K

P

K

E

E

V

V

V

A

R

E

G

G

V

V

D

D

I

M

M

M

V

I

I

V

R

R

E

E

L

L

T

T

S

G

G

G

I

I

Y

Y

F

F

G

G

I

E

P

P

K

R

G

G

I

I

F

T

V

I

D

N

G

E

D

N

-

G

E

E

R

E

V

V

G

G

I

V

N

S

T

T

L

E

R

I

Y

Y

Y

A

E

A

H

H

E

E

V

I

E

D

R

R

I

I

A

A

K

R

V

V

A

A

F

F

E

E

V

T

A

A

R

R

K

K

R

R

N

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

A

A

T

S

V

I

L

L

W

W

R

R

E

K

V

R

V

V

E

T

R

A

V

L

H

A

E

S

N

E

Y

Y

P

P

D

D

V

V

E

E

L

L

Q

S

H

H

M

M

Y

Y

V

V

D

D

N

N

A

A

M

M

Q

Q

I

L

I

I

R

R

W

D

P

P

K

K

Q

Q

F

F

D

D

V

T

I

I

V

V

T

T

T

N

N

N

M

I

F

F

G

G

D

D

I

I

L

L

S

S

D

D

A

E

C

A

A

S

M

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

G

S

K

G

I

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

N

D

I

K

A

A

N

N

P

P

I

L

A

A

T

T

I

I

N

L

S

S

A

A

G

A

M

M

M

L

F

L

T

K

Y

Y

S

G

F

L

D

G

M

E

P

E

E

K

V

A

E

A

E

K

A

R

I

I

D

E

K

D

A

A

V

V

R

V

A

D

V

A

L

L

A

N

K

K

G

G

Y

F

R

R

T

T

R

G

D

D

I

I

Y

Y

S

S

E

P

G

G

T

N

K

K

L

L

V

V

S

G

T
x
C

E

K

E

E

M

M

G

G

D

E

L

E

I

V

A

L

E

K

E

S

L

V

K

E

N

S

F137 (≠ L94) Confers substrate specificity; mutation to L: Reduced activity toward 3-(2'-methylthio)-ethylmalate, but enhanced catalytic efficiency with 3-isopropylmalate.
C232 (≠ T188) Essential for redox regulation; mutation to S: Reduced sensitivity to oxidation on enzyme activity regulation.
C390 (≠ T345) Essential for redox regulation; mutation to S: Reduced sensitivity to oxidation on enzyme activity regulation.

1a05A Crystal structure of the complex of 3-isopropylmalate dehydrogenase from thiobacillus ferrooxidans with 3-isopropylmalate (see paper)
55% identity, 98% coverage: 5:357/359 of query aligns to 3:355/357 of 1a05A

query
sites
1a05A

K

K

I

I

A

A

V

I

L

F

P

A

G

G

D

D

G

G

I

I

G

G

P

P

E

E

I

I

V

V

K

A

Q

A

A

A

V

R

K

Q

V

V

M

L

E

D

A

A

A

V

A

D

E

Q

K

A

F

A

G

H

F

L

G

G

L

L

E

R

L

C

N

T

Y

E

G

G

L

L

I

V

G

G

A

A

I

L

D

D

E

A

T

S

G

D

V

D

P

P

F

L

P

P

E

A

T

S

K

L

E

Q

L

L

I

A

L

M

S

A

D

D

A

A

V

V

L

I

L

L

G

G

A

A

V

V

G

G

P

P

K

R

W

W

D

D

N

A

L

Y

P

P

F

P

E

A

I

K

R

R

P

P

E

E

R

Q

A

G

L

L

G

R

M

L

R
|
R

K

K

L

G

L

L

N

D

A

L

F

Y

A

A

N

N

L

L

R
|
R

P

P

A

A

R

Q

L

I

Y

F

D

P

E

Q

L

L

I

L

D

D

A

A

S

S

T

P

L

L

K

R

P

P

E

E

V

L

V

V

R

R

G

D

V

V

D

D

I

I

M

L

V

V

I

V

R
|
R

E

E

L

L

T

T

S

G

G

D

I

I

Y
|
Y

F

F

G

G

I

Q

P

P

K

R

G

G

I

L

F

E

V

V

D

I

G

D

D

G

E

K

R

R

V

R

G

G

I

F

N

N

T

T

L

M

R

V

Y

Y

Y

D

E

E

H

D

E

E

V

I

E

R

R

R

I

I

A

A

K

H

V

V

A

A

F

F

E

R

V

A

A

A

R

Q

K

G

R

R

N

R

K

K

K

Q

V

L

T

C

S

S

V

V

D

D

K
|
K

A

A

N

N

V

V

L

L

E

E

A

T

T

T

V

R

L

L

W

W

R

R

E

E

V

V

E

T

R

E

V

V

H

A

E

R

N

D

Y

Y

P

P

D

D

V

V

E

R

L

L

Q

S

H

H

M

M

Y

Y

V

V

D
|
D

N

N

A

A

M

M

Q

Q

I

L

I

I

R

R

W

A

P

P

K

A

Q

Q

F

F

D

D

V

V

I

L

V

L

T

T

T

G

N

N

M

M

F

F

G

G

D
|
D

I

I

L

L

S

S

D
|
D

A

E

C

A

A

S

M

Q

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

G

G

E

K

G

I

R

G

A

L

M

Y

Y

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

N

D

I

K

A

A

N

N

P

P

I

L

A

A

T

T

I

I

N

L

S

S

A

V

G

A

M

M

F

L

T

R

Y

H

S

S

F

L

D

N

M

A

P

E

E

P

V

W

E

A

E

Q

A

R

I

V

D

E

K

A

A

A

V

V

R

Q

A

R

V

V

L

L

A

D

K

Q

G

G

Y

L

R

R

T

T

R

A

D

D

I

I

Y

A

S

A

E

P

G

G

T

T

K

P

L

V

V

I

S

G

T

T

E

K

E

A

M

M

G

G

D

A

L

A

I

V

A

V

E

N

E

A

L

L

K

N

active site: Y140 (= Y142), K190 (= K192), D222 (= D224), D246 (= D248), D250 (= D252)
binding 3-isopropylmalic acid: R95 (= R97), R105 (= R107), R133 (= R135), Y140 (= Y142), D246 (= D248)

Q56268 3-isopropylmalate dehydrogenase; 3-IPM-DH; Beta-IPM dehydrogenase; IMDH; EC 1.1.1.85 from Acidithiobacillus ferrooxidans (Thiobacillus ferrooxidans) (see paper)
55% identity, 98% coverage: 5:357/359 of query aligns to 3:355/358 of Q56268

query
sites
Q56268

K

K

I

I

A

A

V

I

L

F

P

A

G

G

D

D

G

G

I

I

G

G

P

P

E

E

I

I

V

V

K

A

Q

A

A

A

V

R

K

Q

V

V

M

L

E

D

A

A

A

V

A

D

E

Q

K

A

F

A

G

H

F

L

G

G

L

L

E

R

L

C

N

T

Y

E

G

G

L

L

I

V

G

G

A

A

I

L

D

D

E

A

T

S

G

D

V

D

P

P

F

L

P

P

E

A

T

S

K

L

E

Q

L

L

I

A

L

M

S

A

D

D

A

A

V

V

L

I

L

L

G

G

A

A

V

V

G

G

P

P

K

R

W

W

D

D

N

A

L

Y

P

P

F

P

E

A

I

K

R

R

P

P

E

E

R

Q

A

G

L

L

G

R

M

L

R
|
R

K

K

L

G

L

L

N

D

A

L

F

Y

A

A

N

N

L

L

R
|
R

P

P

A

A

R

Q

L

I

Y

F

D

P

E

Q

L

L

I

L

D

D

A

A

S

S

T

P

L

L

K

R

P

P

E

E

V

L

V

V

R

R

G

D

V

V

D

D

I

I

M

L

V

V

I

V

R
|
R

E

E

L

L

T

T

S

G

G

D

I

I

Y

Y

F

F

G

G

I

Q

P

P

K

R

G

G

I

L

F

E

V

V

D

I

G

D

D

G

E

K

R

R

V

R

G

G

I

F

N

N

T

T

L

M

R

V

Y

Y

Y

D

E

E

H

D

E

E

V

I

E

R

R

R

I

I

A

A

K

H

V

V

A

A

F

F

E

R

V

A

A

A

R

Q

K

G

R

R

N

R

K

K

K

Q

V

L

T

C

S

S

V

V

D

D

K

K

A

A

N

N

V

V

L

L

E

E

A

T

T

T

V

R

L

L

W

W

R

R

E

E

V

V

E

T

R

E

V

V

H

A

E

R

N

D

Y

Y

P

P

D

D

V

V

E

R

L

L

Q

S

H

H

M

M

Y

Y

V

V

D
|
D

N

N

A

A

M

M

Q

Q

I

L

I

I

R

R

W

A

P

P

K

A

Q

Q

F

F

D

D

V

V

I

L

V

L

T

T

T

G

N

N

M

M

F

F

G

G

D
|
D

I

I

L

L

S

S

D

D

A

E

C

A

A

S

M

Q

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

G

G

E

K

G

I

R

G

A

L

M

Y

Y

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

N

D

I

K

A

A

N

N

P

P

I

L

A

A

T

T

I

I

N

L

S

S

A

V

G

A

M

M

F

L

T

R

Y

H

S

S

F

L

D

N

M

A

P

E

E

P

V

W

E

A

E

Q

A

R

I

V

D

E

K

A

A

A

V

V

R

Q

A

R

V

V

L

L

A

D

K

Q

G

G

Y

L

R

R

T

T

R

A

D

D

I

I

Y

A

S

A

E

P

G

G

T

T

K

P

L

V

V

I

S

G

T

T

E

K

E

A

M

M

G

G

D

A

L

A

I

V

A

V

E

N

E

A

L

L

K

N

R95 (= R97) binding substrate
R105 (= R107) binding substrate
R133 (= R135) binding substrate
D222 (= D224) binding Mg(2+); binding substrate
D246 (= D248) binding Mg(2+)

4xxvA Crystal structure of 3-isopropylmalate dehydrogenase from burkholderia thailandensis in complex with NAD
57% identity, 98% coverage: 4:356/359 of query aligns to 2:356/356 of 4xxvA

query
sites
4xxvA

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

V

V

K

N

Q

E

A

A

V

V

K

K

V

V

M

L

E

N

A

A

A

L

A

D

E

E

K

K

F

F

G

-

F

-

G

-

L

-

E

E

L

L

N

E

Y

H

G

A

L

P

I

V

G

G

A

A

A

G

I

Y

D

E

E

A

T

S

G

G

V

H

P

P

F

L

P

P

E

D

E

A

T

T

K

L

E

A

L

L

I

A

L

K

S

E

S

A

D

D

A

A

V

I

L

L

L

F

G

G

A

A

V

V

G

G

G

D

P

W

K

K

W

Y

D

D

N

S

L

L

P

E

F

R

E

A

I

L

R

R

P

P

E

E

R

Q

A

A

L

I

L

L

G

G

M

L

R

R

K

K

L

H

L

L

N

E

A

L

F

F

A

A

N

N

L

F

R

R

P

P

A

A

R

I

L

C

Y

Y

D

P

E

Q

L

L

I

V

D

D

A

A

S

S

T

P

L

L

K

K

P

P

E

E

V

L

V

V

R

A

G

G

V

L

D

D

I

I

M

L

V

I

I

V

R

R

E

E

L

L

T

N

S

G

G

D

I

I

Y
|
Y

F

F

G

G

I

Q

P

P

K

R

G

G

I

V

F

R

V

A

D

A

G

P

D

D

-

G

-

P

-

F

-

A

-

G

E

E

R

R

V

E

G

G

I

F

N

D

T

T

L

M

R

R

Y

Y

Y

S

E

E

H

P

E

E

V

V

E

R

R

R

I

I

A

A

K

H

V

V

A

A

F

F

E

Q

V

A

A

A

R

Q

K

K

R

R

N

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

A

T

T

S

V

Q

L

F

W

W

R

R

E

D

V

V

V

M

E

I

R

D

V

V

H

S

E

K

N

E

Y

Y

P

A

D

D

V

V

E

E

L

L

Q

S

H

H

M

M

Y
|
Y

V

V

D
|
D

N
|
N

A

A

M

M

Q

Q

I

L

I

A

R

K

W

A

P

P

K

K

Q

Q

F

F

D

D

V

V

I

I

V

V

T

T

T

G

N

N

M

M

F

F

G

G

D
|
D

I

I

L

L

S

S

D
|
D

A

E

C

A

A

S

M

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

-

K

G

N

K

N

I

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

N

G

I

I

A

A

N

N

P

P

I

L

A

A

T

T

I

I

N

L

S

S

A

A

G

A

M

M

M

L

F

L

T

R

Y

Y

S

S

F

L

D

N

M

R

P

A

E

E

V

Q

E

A

E

D

A

R

I

I

D

E

K

R

A

A

V

V

R

K

A

T

V

V

L

L

A

E

K

Q

G

G

Y

Y

R

R

T

T

R

G

D

D

I

I

Y

A

S

T

E

P

G

G

T

C

K

R

L

Q

V

V

S

G

T

T

E

A

M

M

G

G

D

D

L

A

I

V

A

V

E

A

L

L

active site: Y136 (= Y142), K191 (= K192), D223 (= D224), D247 (= D248), D251 (= D252)
binding nicotinamide-adenine-dinucleotide: N193 (= N194), Y221 (= Y222), N224 (= N225)

4iwhA Crystal structure of a 3-isopropylmalate dehydrogenase from burkholderia pseudomallei
56% identity, 99% coverage: 2:356/359 of query aligns to 2:358/358 of 4iwhA

query
sites
4iwhA

R

H

K

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

V

V

K

N

Q

E

A

A

V

V

K

K

V

V

M

L

E

N

A

A

A

L

A

D

E

E

K

K

F

F

G

-

F

-

G

-

L

-

E

E

L

L

N

E

Y

H

G

A

L

P

I

V

G

G

A

A

A

G

I

Y

D

E

E

A

T

S

G

G

V

H

P

P

F

L

P

P

E

D

E

A

T

T

K

L

E

A

L

L

I

A

L

K

S

E

S

A

D

D

A

A

V

I

L

L

L

F

G

G

A

A

V

V

G

G

G

D

P

W

K

K

W

Y

D

D

N

S

L

L

P

E

F

R

E

A

I

L

R

R

P

P

E

E

R

Q

A

A

L

I

L

L

G

G

M

L

R

R

K

K

L

H

L

L

N

E

A

L

F

F

A

A

N

N

L

F

R

R

P

P

A

A

R

I

L

C

Y

Y

D

P

E

Q

L

L

I

V

D

D

A

A

S

S

T

P

L

L

K

K

P

P

E

E

V

L

V

V

R

A

G

G

V

L

D

D

I

I

M

L

V

I

I

V

R

R

E

E

L

L

T

N

S

G

G

D

I

I

Y
|
Y

F

F

G

G

I

Q

P

P

K

R

G

G

I

V

F

R

V

A

D

A

G

P

D

D

-

G

-

P

-

F

-

A

-

G

E

E

R

R

V

E

G

G

I

F

N

D

T

T

L

M

R

R

Y

Y

Y

S

E

E

H

P

E

E

V

V

E

R

R

R

I

I

A

A

K

H

V

V

A

A

F

F

E

Q

V

A

A

A

R

Q

K

K

R

R

N

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

A

T

T

S

V

Q

L

F

W

W

R

R

E

D

V

V

V

M

E

I

R

D

V

V

H

S

E

K

N

E

Y

Y

P

A

D

D

V

V

E

E

L

L

Q

S

H

H

M

M

Y

Y

V

V

D
|
D

N

N

A

A

M

M

Q

Q

I

L

I

A

R

K

W

A

P

P

K

K

Q

Q

F

F

D

D

V

V

I

I

V

V

T

T

T

G

N

N

M

M

F

F

G

G

D
|
D

I

I

L

L

S

S

D
|
D

A

E

C

A

A

S

M

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

-

K

G

N

K

N

I

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

N

G

I

I

A

A

N

N

P

P

I

L

A

A

T

T

I

I

N

L

S

S

A

A

G

A

M

M

M

L

F

L

T

R

Y

Y

S

S

F

L

D

N

M

R

P

A

E

E

V

Q

E

A

E

D

A

R

I

I

D

E

K

R

A

A

V

V

R

K

A

T

V

V

L

L

A

E

K

Q

G

G

Y

Y

R

R

T

T

R

G

D

D

I

I

Y

A

S

T

E

P

G

G

T

C

K

R

L

Q

V

V

S

G

T

T

E

A

M

M

G

G

D

D

L

A

I

V

A

V

E

A

L

L

active site: Y138 (= Y142), K193 (= K192), D225 (= D224), D249 (= D248), D253 (= D252)
binding magnesium ion: D249 (= D248), D253 (= D252)

6xxyA Crystal structure of haemophilus influenzae 3-isopropylmalate dehydrogenase in complex with o-isobutenyl oxalylhydroxamate. (see paper)
54% identity, 99% coverage: 1:356/359 of query aligns to 1:358/358 of 6xxyA

query
sites
6xxyA

M

M

R

E

K

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

V

M

K

A

Q

E

A

A

V

I

K

K

V

V

M

L

E

N

A

R

A

V

A

Q

E

E

K

K

F

F

G

G

F

F

G

K

L

L

E

N

L

F

N

N

Y

E

G

F

L

F

I

V

G

G

A

A

I

I

D

E

E

H

T

C

G

G

V

Y

P

P

F

L

P

P

E

A

E

E

T

T

K

L

E

K

L

G

I

C

L

D

S

Q

S

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

N

N

L

L

P

P

F

P

E

D

I

Q

R

Q

P

P

E
|
E

R

R

-

G

A

A

L
|
L

L

L

G

P

M

L

R

R

K

K

L

H

L

F

N

K

A

L

F

F

A

C

N

N

L

L

R
|
R

P

P

A

A

R

T

L

L

Y

Y

D

K

E

G

L

L

I

E

D

K

A

F

S

C

T

P

L

L

K

R

P

A

E

D

V

I

V

A

-

A

R

K

G

G

V

F

D

D

I

M

M

V

V

V

I

V

R
|
R

E

E

L

L

T

T

S

G

G

G

I

I

Y
|
Y

F

F

G

G

I

Q

P

P

K

K

G

G

I

R

F

E

V

G

D

D

G

G

D

V

E

Q

R

T

V

K

G

A

I

F

N

D

T

T

L

E

R

V

Y

Y

E

K

H

Y

E

E

V

I

E

E

R

R

I

I

A

A

K

R

V

A

A

A

F

F

E

E

V

A

A

A

R

M

K

K

R

R

N

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

A

S

T

S

V

I

L

L

W

W

R

R

E

E

V

T

V

V

E

T

R

E

V

M

H

A

E

K

N

D

Y

Y

P

P

D

E

V

V

E

T

L

L

Q

E

H

H

M

I

Y
|
Y

V

I

D
|
D

N
|
N

A

A

A

T

M
|
M

Q

Q

I

L

I

I

R

K

W

S

P

P

K

E

Q

S

F

F

D

D

V

V

I

L

V

L

T

C

T

S

N

N

M

I

F

F

G

G

D
|
D

I

I

L

I

S

S

D
|
D

A

E

C

A

A

A

M

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

G

E

K

E

-

G

I

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

N

G

I

I

A

A

N
|
N

P

P

I

I

A

A

T

Q

I

I

N

L

S

S

A

A

G

A

M

M

F

L

T

R

Y

Y

S

S

F

F

D

N

M

L

P

N

E

E

V

A

E

A

E

D

A

A

I

I

D

E

K

S

A

A

V

V

R

Q

A

K

V

V

L

L

A

A

K

S

G

G

Y

H

R

R

T

T

R

A

D
|
D

I

L

Y

A

S

D

E

D

G

S

T

T

K

P

L

-

V

V

S

S

T

T

E

A

E

E

M

M

G

G

D

T

L

L

I

I

A

T

E

Q

E

A

L

I

active site: Y144 (= Y142), K194 (= K192), D226 (= D224), D250 (= D248)
binding magnesium ion: D250 (= D248), D254 (= D252)
binding nicotinamide-adenine-dinucleotide: S74 (≠ A74), V75 (= V75), G76 (= G76), E90 (= E90), L94 (= L93), Y224 (= Y222), N227 (= N225), M230 (= M228), M263 (≠ L261), G264 (= G262), E280 (= E277), G283 (≠ H280), G284 (= G281), S285 (= S282), A286 (= A283), P287 (= P284), D288 (= D285), I289 (= I286), N296 (= N293), D337 (= D334)
binding 2-(2-methylprop-2-enoxyamino)-2-oxidanylidene-ethanoic acid: E90 (= E90), R108 (= R107), R137 (= R135), K194 (= K192), V197 (= V195), D226 (= D224), D250 (= D248)

1cnzA 3-isopropylmalate dehydrogenase (ipmdh) from salmonella typhimurium (see paper)
54% identity, 98% coverage: 2:353/359 of query aligns to 3:356/363 of 1cnzA

query
sites
1cnzA

R

K

K

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

V

M

K

A

Q

Q

A

A

V

L

K

K

V

V

M

M

E

D

A

A

A

V

A

R

E

S

K

R

F

F

G

D

F

M

G

R

L

I

E

T

L

T

N

S

Y

H

G

Y

L

D

I

V

G

G

A

I

A

A

I

I

D

D

E

N

T

H

G

G

V

H

P

P

F

L

P

P

E

K

E

A

T

T

K

V

E

E

L

G

I

C

L

E

S

Q

S

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

N

N

L

L

P

P

F

P

E

E

I

S

R

Q

P

P

E

E

R

R

-

G

A

A

L

L

G

P

M

L

R

R

K

K

L

H

L

F

N

K

A

L

F

F

A

S

N

N

L

L

R

R

P

P

A

A

R

K

L

L

Y

Y

D

Q

E

G

L

L

I

E

D

A

A

F

S

C

T

P

L

L

K

R

P

A

E

D

V

I

V

A

-

A

R

N

G

G

V

F

D

D

I

I

M

L

V

C

I

V

R

R

E

E

L

L

T

T

S

G

G

G

I

I

Y
|
Y

F

F

G

G

I

Q

P

P

K

K

G

G

I

R

F

E

V

G

D

S

G

G

D

Q

E

Y

R

E

V

K

G

A

I

F

N

D

T

T

L

E

R

V

Y

Y

Y

H

E

R

H

F

E

E

V

I

E

E

R

R

I

I

A

A

K

R

V

I

A

A

F

F

E

E

V

S

A

A

R

R

K

K

R

R

N

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

A

S

T

S

V

I

L

L

W

W

R

R

E

E

V

I

V

V

E

N

R

D

V

V

H

A

E

K

N

T

Y

Y

P

P

D

D

V

V

E

E

L

L

Q

A

H

H

M

M

Y

Y

V

I

D
|
D

N

N

A

A

A

T

M

M

Q

Q

I

L

I

I

R

K

W

D

P

P

K

S

Q

Q

F

F

D

D

V

V

I

L

V

L

T

C

T

S

N

N

M

L

F

F

G

G

D
|
D

I

I

L

L

S

S

D
|
D

A

E

C

C

A

A

M

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

G

E

K

Q

-

G

I

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

N

N

I

I

A

A

N

N

P

P

I

I

A

A

T

Q

I

I

N

L

S

S

A

L

G

A

M

L

F

L

T

R

Y

Y

S

S

F

L

D

D

M

A

P

N

E

D

V

A

E

A

E

T

A

A

I

I

D

E

K

Q

A

A

V

I

R

N

A

R

V

A

L

L

A

E

K

E

G

G

Y

V

R

R

T

T

R

G

D

D

I

L

Y

-

S

A

E

R

G

G

T

A

K

A

L

A

V

V

S

S

T

T

E

D

E

E

M

M

G

G

D

D

L

I

I

I

A

A

active site: Y145 (= Y142), K195 (= K192), D227 (= D224), D251 (= D248)
binding manganese (ii) ion: D251 (= D248), D255 (= D252)

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)
54% identity, 98% coverage: 2:353/359 of query aligns to 3:356/363 of P37412

query
sites
P37412

R

K

K

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

V

M

K

A

Q

Q

A

A

V

L

K

K

V

V

M

M

E

D

A

A

A

V

A

R

E

S

K

R

F

F

G

D

F

M

G

R

L

I

E

T

L

T

N

S

Y

H

G

Y

L

D

I

V

G

G

A

I

A

A

I

I

D

D

E

N

T

H

G

G

V

H

P

P

F

L

P

P

E

K

E

A

T

T

K

V

E

E

L

G

I

C

L

E

S

Q

S

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

N

N

L

L

P

P

F

P

E

E

I

S

R

Q

P

P

E

E

R

R

-

G

A

A

L

L

G

P

M

L

R

R

K

K

L

H

L

F

N

K

A

L

F

F

A

S

N

N

L

L

R

R

P

P

A

A

R

K

L

L

Y

Y

D

Q

E

G

L

L

I

E

D

A

A

F

S

C

T

P

L

L

K

R

P

A

E

D

V

I

V

A

-

A

R

N

G

G

V

F

D

D

I

I

M

L

V

C

I

V

R

R

E

E

L

L

T

T

S

G

G

G

I

I

Y

Y

F

F

G

G

I

Q

P

P

K

K

G

G

I

R

F

E

V

G

D

S

G

G

D

Q

E

Y

R

E

V

K

G

A

I

F

N

D

T

T

L

E

R

V

Y

Y

Y

H

E

R

H

F

E

E

V

I

E

E

R

R

I

I

A

A

K

R

V

I

A

A

F

F

E

E

V

S

A

A

R

R

K

K

R

R

N

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

A

S

T

S

V

I

L

L

W

W

R

R

E

E

V

I

V

V

E

N

R

D

V

V

H

A

E

K

N

T

Y

Y

P

P

D

D

V

V

E

E

L

L

Q

A

H

H

M

M

Y

Y

V

I

D
|
D

N

N

A

A

A

T

M

M

Q

Q

I

L

I

I

R

K

W

D

P

P

K

S

Q

Q

F

F

D

D

V

V

I

L

V

L

T

C

T

S

N

N

M

L

F

F

G

G

D
|
D

I

I

L

L

S

S

D
|
D

A

E

C

C

A

A

M

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

G

E

K

Q

-

G

I

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

N

N

I

I

A

A

N

N

P

P

I

I

A

A

T

Q

I

I

N

L

S

S

A

L

G

A

M

L

F

L

T

R

Y

Y

S

S

F

L

D

D

M

A

P

N

E

D

V

A

E

A

E

T

A

A

I

I

D

E

K

Q

A

A

V

I

R

N

A

R

V

A

L

L

A

E

K

E

G

G

Y

V

R

R

T

T

R

G

D

D

I

L

Y

-

S

A

E

R

G

G

T

A

K

A

L

A

V

V

S

S

T

T

E

D

E

E

M

M

G

G

D

D

L

I

I

I

A

A

D227 (= D224) binding Mn(2+)
D251 (= D248) binding Mn(2+)
D255 (= D252) binding Mn(2+)

3vkzA 3-isopropylmalate dehydrogenase from shewanella oneidensis mr-1 at atmospheric pressure (see paper)
51% identity, 99% coverage: 3:357/359 of query aligns to 2:361/364 of 3vkzA

query
sites
3vkzA

K

S

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

V

M

K

A

Q

E

A

A

V

R

K

K

V

V

M

L

E

K

A

A

A

V

A

E

E

A

K

R

F

F

G

G

F

L

G

N

L

I

E

E

L

Y

N

T

Y

E

G

Y

L

D

I

V

G

G

A

I

A

A

I

I

D

D

E

N

T

H

G

G

V

C

P

P

F

L

P

P

E

E

E

A

T

T

K

L

E

K

L

G

I

C

L

E

S

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

N

K

L

L

P

P

F

P

E

N

I

E

R

Q

P

P

E

E

R

R

-

G

A

A

L

L

G

P

M

L

R
|
R

K

G

L

H

L

F

N

E

A

L

F

F

A

C

N

N

L

L

R

R

P

P

A

A

R

K

L

L

Y

H

D

D

E

G

L

L

I

E

D

H

A

M

S

S

T

P

L

L

K

R

P

S

E

D

V

I

-

S

V

A

R

R

G

G

V

F

D

D

I

V

M

L

V

C

I

V

R
|
R

E

E

L

L

T

T

S

G

G

G

I

I

Y
|
Y

F

F

G

G

I

K

P

P

K

K

G

G

I

R

F

Q

V

G

D

E

G

G

D

E

E

S

R

E

V

E

G

A

I

F

N

D

T

T

L

M

R

R

Y

Y

Y

S

E

R

H

R

E

E

V

I

E

S

R

R

I

I

A

A

K

R

V

I

A

A

F

F

E

E

V

A

A

A

R

R

K

G

R

R

N

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

A

C

T

S

V

V

L

L

W

W

R

R

E

Q

V

V

E

E

R

E

V

V

H

A

E

V

N

D

Y

F

P

P

D

D

V

V

E

E

L

L

Q

E

H

H

M

I

Y

Y

V

I

D
|
D

N

N

A

A

A

T

M

M

Q

Q

I

L

R

R

W

R

P

P

K

D

Q

E

F

F

D

D

V

V

I

M

V

L

T

C

T

S

N

N

M

L

F

F

G

G

D
|
D

I

I

L

L

S

S

D
|
D

A

E

C

I

A

A

M

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

G

S

K

T

-

G

I

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

N

G

I

I

A

A

N

N

P

P

I

I

A

A

T

Q

I

I

N

L

S

S

A

A

G

A

M

L

M

M

F

L

T

R

Y

H

S

S

F

L

D

K

M

Q

P

E

E

E

V

A

E

A

E

S

A

A

I

I

D

E

K

R

A

A

V

V

R

T

A

K

V

A

L

L

A

N

K

S

G

G

Y

Y

R

L

T

T

R

G

D

E

I

L

Y

L

S

S

-

S

-

D

E

Q

G

R

T

H

K

K

L

A

V

K

S

T

T

T

E

V

E

Q

M

M

G

G

D

D

L

F

I

I

A

A

E

D

E

A

L

V

K

K

active site: Y143 (= Y142), K193 (= K192), D225 (= D224), D249 (= D248), D253 (= D252)
binding calcium ion: D249 (= D248), D253 (= D252)
binding 3-isopropylmalic acid: R97 (= R97), R136 (= R135), Y143 (= Y142), D249 (= D248)

3vmkA 3-isopropylmalate dehydrogenase from shewanella benthica db21 mt-2 (see paper)
50% identity, 99% coverage: 3:356/359 of query aligns to 8:366/369 of 3vmkA

query
sites
3vmkA

K

S

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

V

M

K

A

Q

E

A

A

V

R

K

K

V

V

M

L

E

A

A

A

A

V

A

E

E

K

K

R

F

F

G

D

F

L

G

S

L

I

E

E

L

Y

N

S

Y

E

G

Y

L

D

I

V

G

G

A

A

I

I

D

D

E

N

T

H

G

G

V

C

P

P

F

L

P

P

E

E

E

A

T

T

K

L

E

K

L

G

I

C

L

E

S

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

N

H

L

L

P

P

F

P

E

N

I

D

R

Q

P

P

E

E

R

R

-

G

A

A

L

L

G

P

M

L

R
|
R

K

G

L

H

L

F

N

E

A

L

F

F

A

C

N

N

L

M

R

R

P

P

A

A

R

K

L

L

Y

H

D

P

E

G

L

L

I

E

D

H

A

M

S

S

T

P

L

L

K

R

P

S

E

D

V

I

V

S

-

E

R

K

G

G

V

F

D

D

I

I

M

L

V

C

I

V

R
|
R

E

E

L

L

T

T

S

G

G

G

I

I

Y
|
Y

F

F

G

G

I

K

P

P

K

K

G

G

I

R

F

Q

V

G

D

E

G

G

D

E

E

N

R

E

V

E

G

A

I

F

N

D

T

T

L

M

R

R

Y

Y

Y

S

E

R

H

K

E

E

V

I

E

R

R

R

I

I

A

A

K

K

V

I

A

A

F

F

E

E

V

S

A

A

R

Q

K

G

R

R

N

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

A

C

T

S

V

V

L

L

W

W

R

R

E

E

V

V

E

E

R

E

V

V

H

A

E

K

N

D

Y

Y

P

P

D

D

V

V

E

E

L

L

Q

E

H

H

M

I

Y

Y

V

I

D
|
D

N

N

A

A

A

T

M

M

Q

Q

I

L

R

R

W

R

P

P

K

N

Q

E

F

F

D

D

V

V

I

M

V

L

T

C

T

S

N

N

M

L

F

F

G

G

D
|
D

I

I

L

V

S

S

D
|
D

A

E

C

I

A

A

M

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

G

S

K

Q

-

G

I

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

N

G

I

I

A

A

N

N

P

P

I

V

A

A

T

Q

I

I

N

L

S

S

A

A

G

A

M

L

F

L

T

R

Y

H

S

S

F

L

D

K

M

L

P

E

E

D

V

A

E

A

E

L

A

A

I

I

D

E

K

A

A

A

V

V

R

S

A

K

V

A

L

L

A

S

K

D

G

G

Y

Y

R

L

T

T

R

C

D

E

I

L

Y

L

-

P

-

A

S

S

E

E

G

R

T

S

K

Q

L

A

V

K

S

S

T

T

E

S

E

Q

M

M

G

G

D

D

L

Y

I

I

A

A

E

Q

E

A

L

I

active site: Y149 (= Y142), K199 (= K192), D231 (= D224), D255 (= D248), D259 (= D252)
binding 3-isopropylmalic acid: R103 (= R97), R142 (= R135), Y149 (= Y142), K199 (= K192), N201 (= N194), D255 (= D248)

2y42D Structure of isopropylmalate dehydrogenase from thermus thermophilus - complex with nadh and mn (see paper)
55% identity, 90% coverage: 3:326/359 of query aligns to 1:320/355 of 2y42D

query
sites
2y42D

K

S

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

V

T

K

E

Q

A

A

A

V

L

K

K

V

V

M

L

E

R

A

A

A

L

A

D

E

E

K

A

F

E

G

G

F

L

G

G

L

L

E

A

L

Y

N

E

Y

V

G

F

L

P

I

F

G

G

A

A

I

I

D

D

E

A

T

F

G

G

V

E

P

P

F

F

P

P

E

E

E

P

T

T

K

R

E

K

L

G

I

V

L

E

S

E

S

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

N

G

L

L

P

P

F

R

E

K

I

I

R

R

P

P

E

E

R

T

A

G

L

L

G

S

M

L

R

R

K

K

L

S

L

Q

N

D

A

L

F

F

A

A

N

N

L

L

R

R

P

P

A

A

R

K

L

V

Y

F

D

P

E

G

L

L

I

E

D

R

A

L

S

S

T

P

L

L

K

K

P

E

E

E

V

I

V

A

R

R

G

G

V

V

D

D

I

V

M

L

V

I

I

V

R

R

E

E

L

L

T

T

S

G

G

G

I

I

Y
|
Y

F

F

G

G

I

E

P

P

K

R

G

G

I

M

F

-

V

-

D

-

G

-

D

S

E

E

R

A

V

E

G

A

I

W

N

N

T

T

L

E

R

R

Y

Y

Y

S

E

K

H

P

E

E

V

V

E

E

R

R

I

V

A

A

K

R

V

V

A

A

F

F

E

E

V

A

A

A

R

R

K

K

R

R

N

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

A

V

T

G

V

E

L

F

W

W

R

R

E

K

V

T

V

V

E

E

R

E

V

V

H

G

E

R

N

G

Y

Y

P

P

D

D

V

V

E

A

L

L

Q

E

H

H

M

Q

Y

Y

V

V

D
|
D

N

A

A

M

A

A

M

M

Q

H

I

L

I

V

R

R

W

S

P

P

K

A

Q

R

F

F

D

D

V

V

I

V

V

V

T

T

T

G

N

N

M

I

F

F

G

G

D
|
D

I

I

L

L

S

S

D
|
D

A

L

C

A

A

S

M

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

G

R

K

G

I

T

G

P

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

N

G

I

I

A

A

N
|
N

P

P

I

T

A

A

T

A

I

I

N

L

S

S

A

A

G

A

M

M

F

L

T

E

Y

H

S

A

F

F

D

G

M

L

P

V

E

E

V

L

E

A

E

R

A

K

I

V

D

E

K

D

A

A

V

V

R

A

A

K

V

A

L

L

active site: Y140 (= Y142), K186 (= K192), D218 (= D224), D242 (= D248), D246 (= D252)
binding manganese (ii) ion: D242 (= D248), D246 (= D252)
binding nicotinamide-adenine-dinucleotide: I12 (= I14), D79 (= D81), H274 (= H280), G275 (= G281), A277 (= A283), D279 (= D285), I280 (= I286), N287 (= N293)

2ztwA Structure of 3-isopropylmalate dehydrogenase in complex with the inhibitor and NAD+ (see paper)
55% identity, 90% coverage: 4:326/359 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

V

T

K

E

Q

A

A

A

V

L

K

K

V

V

M

L

E

R

A

A

A

L

A

D

E

E

K

A

F

E

G

G

F

L

G

G

L

L

E

A

L

Y

N

E

Y

V

G

F

L

P

I

F

G

G

A

A

I

I

D

D

E

A

T

F

G

G

V

E

P

P

F

F

P

P

E

E

E

P

T

T

K

R

E

K

L

G

I

V

L

E

S

E

S

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

N

G

L

L

P

P

F

R

E

K

I

I

R

R

P

P

E

E

R

T

A

G

L

L

G

S

M

L

R

R

K

K

L

S

L

Q

N

D

A

L

F

F

A

A

N

N

L

L

R

R

P

P

A

A

R

K

L

V

Y

F

D

P

E

G

L

L

I

E

D

R

A

L

S

S

T

P

L

L

K

K

P

E

E

E

V

I

V

A

R

R

G

G

V

V

D

D

I

V

M

L

V

I

I

V

R

R

E

E

L

L

T

T

S

G

G

G

I

I

Y
|
Y

F

F

G

G

I

E

P

P

K

R

G

G

I

M

F

-

V

-

D

-

G

-

D

S

E

E

R

A

V

E

G

A

I

W

N

N

T

T

L

E

R

R

Y

Y

Y

S

E

K

H

P

E

E

V

V

E

E

R

R

I

V

A

A

K

R

V

V

A

A

F

F

E

E

V

A

A

A

R

R

K

K

R

R

N

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

A

V

T

G

V

E

L

F

W

W

R

R

E

K

V

T

V

V

E

E

R

E

V

V

H
x
G

E

R

N

G

Y
|
Y

P

P

D

D

V
|
V

E

A

L

L

Q

E

H

H

M

Q

Y

Y

V

V

D
|
D

N

A

A

M

A

A

M

M

Q

H

I

L

I

V

R

R

W

S

P

P

K

A

Q

R

F

F

D

D

V

V

I

V

V

V

T

T

T

G

N

N

M

I

F

F

G

G

D
|
D

I

I

L

L

S

S

D
|
D

A

L

C

A

A

S

M

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

G

R

K

G

I

T

G

P

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

N

G

I

I

A
|
A

N
|
N

P

P

I

T

A

A

T

A

I

I

N

L

S

S

A

A

G

A

M

M

F

L

T

E

Y

H

S

A

F

F

D

G

M

L

P

V

E

E

V

L

E

A

E

R

A

K

I

V

D

E

K

D

A

A

V

V

R

A

A

K

V

A

L

L

active site: Y139 (= Y142), K185 (= K192), D217 (= D224), D241 (= D248), D245 (= D252)
binding magnesium ion: G203 (≠ H210), Y206 (= Y213), V209 (= V216)
binding nicotinamide-adenine-dinucleotide: I11 (= I14), H273 (= H280), G274 (= G281), A276 (= A283), D278 (= D285), I279 (= I286), A285 (= A292), N286 (= N293)

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)
55% identity, 90% coverage: 4:326/359 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

V

T

K

E

Q

A

A

A

V

L

K

K

V

V

M

L

E

R

A

A

A

L

A

D

E

E

K

A

F

E

G

G

F

L

G

G

L

L

E

A

L

Y

N

E

Y

V

G

F

L

P

I

F

G

G

A

A

I

I

D

D

E

A

T

F

G

G

V

E

P

P

F

F

P

P

E

E

E

P

T

T

K

R

E

K

L

G

I

V

L

E

S

E

S

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

N
x
G

L
|
L

P
|
P

F
x
R

E
x
K

I
|
I

R
|
R

P
|
P

E
|
E

R

T

A

G

L

L

G

S

M

L

R

R

K

K

L

S

L

Q

N

D

A

L

F

F

A

A

N

N

L

L

R

R

P

P

A

A

R

K

L

V

Y

F

D

P

E

G

L

L

I

E

D

R

A

L

S

S

T

P

L

L

K

K

P

E

E

E

V

I

V

A

R

R

G

G

V

V

D

D

I

V

M

L

V

I

I

V

R

R

E

E

L

L

T

T

S

G

G

G

I

I

Y
|
Y

F

F

G

G

I

E

P

P

K

R

G

G

I

M

F

-

V

-

D

-

G

-

D

S

E

E

R

A

V

E

G

A

I

W

N

N

T

T

L

E

R

R

Y

Y

Y

S

E

K

H

P

E

E

V

V

E

E

R

R

I

V

A

A

K

R

V

V

A

A

F

F

E

E

V

A

A

A

R

R

K

K

R

R

N

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

A

V

T

G

V

E

L

F

W

W

R

R

E

K

V

T

V

V

E

E

R

E

V

V

H

G

E

R

N

G

Y

Y

P

P

D

D

V

V

E

A

L

L

Q

E

H

H

M

Q

Y

Y

V

V

D

D

N

A

A

M

A

A

M

M

Q

H

I

L

I

V

R

R

W

S

P

P

K

A

Q

R

F

F

D

D

V

V

I

V

V

V

T

T

T

G

N

N

M

I

F

F

G

G

D

D

I

I

L

L

S

S

D

D

A

L

C

A

A

S

M

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

G

R

K

G

I

T

G

P

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

N
x
G

I
|
I

A
|
A

N
|
N

P

P

I

T

A

A

T

A

I

I

N

L

S

S

A

A

G

A

M

M

F

L

T

E

Y

H

S

A

F

F

D

G

M

L

P

V

E

E

V

L

E

A

E

R

A

K

I

V

D

E

K

D

A

A

V

V

R

A

A

K

V

A

L

L

74:87 (vs. 77:90, 79% identical) binding NAD(+)
Y139 (= Y142) mutation to F: Large decrease in activity and a small decrease in substrate affinity.
274:286 (vs. 281:293, 85% identical) binding NAD(+)

2y41A Structure of isopropylmalate dehydrogenase from thermus thermophilus - complex with ipm and mn (see paper)
55% identity, 90% coverage: 3:326/359 of query aligns to 1:320/346 of 2y41A

query
sites
2y41A

K

S

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

V

T

K

E

Q

A

A

A

V

L

K

K

V

V

M

L

E

R

A

A

A

L

A

D

E

E

K

A

F

E

G

G

F

L

G

G

L

L

E

A

L

Y

N

E

Y

V

G

F

L

P

I

F

G

G

A

A

I

I

D

D

E

A

T

F

G

G

V

E

P

P

F

F

P

P

E

E

E

P

T

T

K

R

E

K

L

G

I

V

L

E

S

E

S

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

N

G

L

L

P

P

F

R

E

K

I

I

R

R

P

P

E

E

R

T

A

G

L

L

G

S

M

L

R
|
R

K

K

L

S

L

Q

N

D

A

L

F

F

A

A

N

N

L

L

R
|
R

P

P

A

A

R

K

L

V

Y

F

D

P

E

G

L

L

I

E

D

R

A

L

S

S

T

P

L

L

K

K

P

E

E

E

V

I

V

A

R

R

G

G

V

V

D

D

I

V

M

L

V

I

I

V

R
|
R

E

E

L

L

T

T

S

G

G

G

I

I

Y
|
Y

F

F

G

G

I

E

P

P

K

R

G

G

I

M

F

-

V

-

D

-

G

-

D

S

E

E

R

A

V

E

G

A

I

W

N

N

T

T

L

E

R

R

Y

Y

Y

S

E

K

H

P

E

E

V

V

E

E

R

R

I

V

A

A

K

R

V

V

A

A

F

F

E

E

V

A

A

A

R

R

K

K

R

R

N

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

A

V

T

G

V

E

L

F

W

W

R

R

E

K

V

T

V

V

E

E

R

E

V

V

H

G

E

R

N

G

Y

Y

P

P

D

D

V

V

E

A

L

L

Q

E

H

H

M

Q

Y

Y

V

V

D
|
D

N

A

A

M

A

A

M

M

Q

H

I

L

I

V

R

R

W

S

P

P

K

A

Q

R

F

F

D

D

V

V

I

V

V

V

T

T

T

G

N

N

M

I

F

F

G

G

D
|
D

I

I

L

L

S

S

D
|
D

A

L

C

A

A

S

M

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

G

R

K

G

I

T

G

P

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

N

G

I

I

A

A

N

N

P

P

I

T

A

A

T

A

I

I

N

L

S

S

A

A

G

A

M

M

F

L

T

E

Y

H

S

A

F

F

D

G

M

L

P

V

E

E

V

L

E

A

E

R

A

K

I

V

D

E

K

D

A

A

V

V

R

A

A

K

V

A

L

L

active site: Y140 (= Y142), K186 (= K192), D218 (= D224), D242 (= D248), D246 (= D252)
binding 3-isopropylmalic acid: R95 (= R97), R105 (= R107), R133 (= R135), Y140 (= Y142), D242 (= D248)

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)
44% identity, 100% coverage: 1:359/359 of query aligns to 1:370/371 of P18869

query
sites
P18869

M

M

R

C

K

A

F

K

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

V

V

K

A

Q

S

A

A

V

L

K

E

V

V

M

L

E

K

A

V

A

E

E

K

K

K

F

R

G

P

-

E

F

L

G

K

L

L

E

E

L

F

N

E

Y

E

G

H

L

K

I

I

G

G

A

A

A

S

I

I

D

D

E

A

T

Y

G

G

V
x
T

P

P

F

L

P

T

E

D

E

E

T

T

K

V

E

K

L

A

I

C

L

L

S

E

S

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

N

N

L

-

P

-

F

P

E

N

I

C

R

R

P

P

E

E

R

Q

A

G

L

L

G

K

M

L

R

R

K

K

L

S

L

M

N

G

A

V

F

W

A

A

N

N

L

L

R

R

P

P

A

C

R

N

L

F

Y

A

D

S

E

K

-

S

L

L

I

V

D

K

A

Y

S

S

T

P

L

L

K

K

P

P

E

E

V

I

V

V

R

E

G

G

V

V

D

D

I

F

M

C

V

V

I

V

R

R

E

E

L

L

T

T

S

G

G

G

I

C

Y

Y

F

F

G

G

I

E

P

R

K

T

G

E

I

-

F

-

V

-

D

D

G

N

D

G

E

S

R

G

V

Y

G

A

I

M

N

D

T

T

L

W

R

P

Y

Y

Y

S

E

L

H

E

E

E

V

V

E

S

R

R

I

I

A

A

K

R

V

L

A

A

F

A

E

W

V

L

A

A

R

E

K

T

R

S

N

N

-

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

A

T

T

S

V

R

L

L

W

W

R

R

E

K

V

T

V

V

E

A

R

K

V

I

-

F

H

K

E

E

N

E

Y

Y

P

P

D

H

V

L

E

T

L

L

Q

K

H

N

M

Q

Y

L

V

I

D

D

N

S

A

A

M

M

Q

L

I

L

I

V

R

K

W

S

P

P

K

R

Q

T

F

L

D

N

-

G

V

V

I

V

V

L

T

T

T

D

N

N

M

L

F

F

G

G

D

D

I

I

L

I

S

S

D

D

A

E

C

A

A

S

M

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

G

K

V

I

V

G

G

-

K

-

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

N

G

I

I

A

V

N

N

P

P

I

V

A

G

T

T

I

I

N

L

S

S

A

A

G

S

M

L

F

L

T

R

Y

Y

S

G

F

L

D

N

M

A

P

P

E

K

V

E

E

A

E

E

A

A

I

I

D

E

K

A

A

A

V

V

R

R

A

K

V

V

L

L

-

D

-

T

-

S

-

I

-

G

A

G

K

R

G

G

Y

L

R

Y

T

T

R

R

D

D

I

L

Y

G

S

G

E

E

G

A

T

-

K

-

L

-

V

-

S

S

T

T

E

A

E

D

M

I

G

T

D

K

L

A

I

V

A

V

E

E

L

L

K

E

N

K

L

I

T55 (≠ V54) modified: Phosphothreonine

4yb4A Crystal structure of homoisocitrate dehydrogenase from thermus thermophilus in complex with homoisocitrate, magnesium ion (ii) and nadh
39% identity, 99% coverage: 4:359/359 of query aligns to 2:333/333 of 4yb4A

query
sites
4yb4A

F

Y

K

R

I

I

A

C

V

L

L

I

P

E

G

G

D

D

G

G

I
|
I

G

G

P

H

E

E

I

V

V

I

K

P

Q

A

A

A

V

R

K

R

V

V

M

L

E

E

A

A

A

T

A

-

E

-

K

-

F

-

G

G

F

L

G

P

L

L

E

E

L

F

N

V

Y

E

G

A

L

E

I

A

G

G

G

W

A

E

A

T

I

F

D

E

E

R

T

R

G

G

V

T

P

S

F

V

P

P

E

E

T

T

K

V

E

E

L

K

I

I

L

L

S

S

S

C

D

H

A

A

V

T

L

L

L

F

G

G

A

A

V
x
A

G
x
T

G
x
S

P

P

K

T

W

R

D

K

N

V

L

P

P

G

F

F

E

F

I

-

R

-

P

-

E

-

R

G

A

A

L

I

L
x
R

G

Y

M

L

R
|
R

K

R

L

R

L

L

N

D

A

L

F

Y

A

A

N

N

L

V

R
|
R

P

P

A

A

R

K

L

-

Y

-

D

-

E

-

L

-

I

-

D

-

A

-

S

S

T

R

L

P

K

V

P

P

E

G

V

S

V

R

R

P

G

G

V

V

D

D

I

L

M

V

V

I

I

V

R
|
R

E

E

L

N

T

T

S

E

G

G

I

L

Y
|
Y

F

-

G

-

I

-

P

-

K

-

G

-

I

-

F

-

V

V

D

E

G

Q

D

E

E

R

R

R

-

Y

-

L

-

D

V

V

G

A

I

I

N

A

T

D

L

A

R

V

Y

I

Y

S

E

K

H

K

E

A

V

S

E

E

R

R

I

I

A

G

K

R

V

A

A

A

F

L

E

R

V

I

A

A

R

E

K

G

R

R

N

P

K

R

K

K

V

T

T

L

S

H

V

I

-

A

D

H

K
|
K

A

A

N

N

V

V

L

L

E

P

A

L

T

T

V

Q

-

G

L

L

W

F

R

L

E

D

V

T

V

V

E

K

R

E

V

V

H

A

E

K

N

D

Y

F

P

P

D

L

V

V

E

N

L

V

Q

Q

H

D

M

I

Y
x
I

V

V

D
|
D

N
|
N

A

C

A

A

M

M

Q

Q

I

L

I

V

R

M

W

R

P

P

K

E

Q

R

F

F

D

D

V

V

I

I

V

V

T

T

N

N

M

L

F

L

G

G

D
|
D

I

I

L

L

S

S

D
|
D

A

L

C

A

A

A

M

G

L

L

T

V

G

G

S

G

L
|
L

G

G

M

L

L

A

P

P

S

S

A

G

S

N

I

I

G

G

G

D

K

T

I

T

G

A

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

N

G

I

I

A

A

N
|
N

P

P

I

T

A

A

T

A

I

I

N

L

S

S

A

A

G

A

M

M

F

L

T

D

Y

Y

S

-

F

L

D

G

M

E

P

K

E

E

V

A

E

A

E

K

A

R

I

V

D

E

K

K

A

A

V

V

R

D

A

L

V

V

L

L

A

E

K

R

G

G

Y

P

R

R

T

T

R

P

D
|
D

I

L

Y

G

S

G

E

D

G

A

T

T

K

-

L

-

V

-

S

-

T

T

E

E

E

A

M

F

G

T

D

E

L

A

I

V

A

V

E

E

E

A

L

L

K

K

N

S

L

L

active site: Y124 (= Y142), K170 (= K192), D203 (= D224), D227 (= D248), D231 (= D252)
binding (1R,2S)-1-hydroxybutane-1,2,4-tricarboxylic acid: S71 (≠ G77), R84 (≠ L94), R87 (= R97), R97 (= R107), R117 (= R135), Y124 (= Y142), D227 (= D248)
binding 1,4-dihydronicotinamide adenine dinucleotide: I12 (= I14), A69 (≠ V75), T70 (≠ G76), S71 (≠ G77), I201 (≠ Y222), N204 (= N225), L240 (= L261), E256 (= E277), H259 (= H280), G260 (= G281), S261 (= S282), A262 (= A283), D264 (= D285), I265 (= I286), N272 (= N293), D312 (= D334)

Query Sequence

>WP_013537107.1 NCBI__GCF_000185805.1:WP_013537107.1
MRKFKIAVLPGDGIGPEIVKQAVKVMEAAAEKFGFGLELNYGLIGGAAIDETGVPFPEET
KELILSSDAVLLGAVGGPKWDNLPFEIRPERALLGMRKLLNAFANLRPARLYDELIDAST
LKPEVVRGVDIMVIRELTSGIYFGIPKGIFVDGDERVGINTLRYYEHEVERIAKVAFEVA
RKRNKKVTSVDKANVLEATVLWREVVERVHENYPDVELQHMYVDNAAMQIIRWPKQFDVI
VTTNMFGDILSDACAMLTGSLGMLPSASIGGKIGLYEPIHGSAPDIAGQNIANPIATINS
AGMMFTYSFDMPEVEEAIDKAVRAVLAKGYRTRDIYSEGTKLVSTEEMGDLIAEELKNL

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