SitesBLAST

SitesBLAST – Find functional sites

SitesBLAST

Comparing WP_010179546.1 NCBI__GCF_000255455.1:WP_010179546.1 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)

1a05A Crystal structure of the complex of 3-isopropylmalate dehydrogenase from thiobacillus ferrooxidans with 3-isopropylmalate (see paper)
44% identity, 88% coverage: 4:331/371 of query aligns to 3:333/357 of 1a05A

query
sites
1a05A

N

K

I

I

A

A

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I

L

F

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D

D

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active site: Y140 (≠ F142), K190 (= K189), D222 (= D221), D246 (= D245), D250 (≠ E249)
binding 3-isopropylmalic acid: R95 (= R97), R105 (= R107), R133 (= R135), Y140 (≠ F142), D246 (= D245)

Q56268 3-isopropylmalate dehydrogenase; 3-IPM-DH; Beta-IPM dehydrogenase; IMDH; EC 1.1.1.85 from Acidithiobacillus ferrooxidans (Thiobacillus ferrooxidans) (see paper)
44% identity, 88% coverage: 4:331/371 of query aligns to 3:333/358 of Q56268

query
sites
Q56268

N

K

I

I

A

A

V

I

L

F

G

A

G

G

D

D

G

G

V

I

G

G

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P

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E

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A

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A

A

A

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K

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A

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L

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A

A

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V

A

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E

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Y

A

Y

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H

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D

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F

L

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F

C

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T

E

E

A

G

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L

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V

G

G

A

G

T

A

A

A

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L

E

D

K

A

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G

D

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D

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E

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L

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R95 (= R97) binding substrate
R105 (= R107) binding substrate
R133 (= R135) binding substrate
D222 (= D221) binding Mg(2+); binding substrate
D246 (= D245) binding Mg(2+)

6xxyA Crystal structure of haemophilus influenzae 3-isopropylmalate dehydrogenase in complex with o-isobutenyl oxalylhydroxamate. (see paper)
46% identity, 94% coverage: 4:350/371 of query aligns to 5:358/358 of 6xxyA

query
sites
6xxyA

N

N

I

I

A

A

V

V

L

L

G

A

G

G

D

D

G

G

V

I

G

G

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E

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A

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A

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K

A

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A

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L

F

F

G

G

A
x
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I
x
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G

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P

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K

F

W

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T

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N

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L

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E

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G

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L

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x
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Y

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D

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Y

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x
N

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x
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N

N

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D

F

I

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S

S

E
x
D

E

E

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A

A

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L

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G

G

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x
M

G
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G

I

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L

A

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S

A

A

A

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L

L

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N

E

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E

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x
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S

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x
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P

V
x
D

A
x
I

T

A

N

G

K

K

G

G

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I

A

A

N
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N

P

P

I

I

G

A

A

Q

I

I

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L

S

S

A

A

A

A

M

M

L

M

L

L

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S

F

F

N

N

L

L

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N

V

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E

A

A

A

D

D

A

A

I

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E

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S

A

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K

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I

I

active site: Y144 (≠ F142), K194 (= K189), D226 (= D221), D250 (= D245)
binding magnesium ion: D250 (= D245), D254 (≠ E249)
binding nicotinamide-adenine-dinucleotide: S74 (≠ A73), V75 (≠ I74), G76 (= G75), E90 (= E90), L94 (= L93), Y224 (= Y219), N227 (≠ Q222), M230 (≠ A225), M263 (≠ K258), G264 (= G259), E280 (= E274), G283 (≠ H277), G284 (= G278), S285 (= S279), A286 (≠ Y280), P287 (= P281), D288 (≠ V282), I289 (≠ A283), N296 (= N290), D337 (= D330)
binding 2-(2-methylprop-2-enoxyamino)-2-oxidanylidene-ethanoic acid: E90 (= E90), R108 (= R107), R137 (= R135), K194 (= K189), V197 (= V192), D226 (= D221), D250 (= D245)

4iwhA Crystal structure of a 3-isopropylmalate dehydrogenase from burkholderia pseudomallei
44% identity, 93% coverage: 3:346/371 of query aligns to 4:354/358 of 4iwhA

query
sites
4iwhA

L

M

N

K

I

I

A

A

V

V

L

L

G

P

G

G

D

D

G

G

V

I

G

G

P

P

E

E

V

I

T

V

E

N

Q

E

A

A

V

V

K

K

A

V

L

L

E

N

A

A

V

L

A

D

E

E

Y

K

Y

F

Q

E

H

-

D

-

F

-

I

-

F

L

K

E

E

H

A

A

L

P

V

V

G

G

A

G

T

A

A

G

I

Y

E

E

K

A

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G

G

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H

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P

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D

E

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C

A

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K

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L

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F

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G

A

A

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G

D

D

P

W

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K

F

Y

D

D

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A

K

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P

E

E

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Q

G

A

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I

L

L

G

G

L

L

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K

E

H

L

L

N

E

L

L

Y

F

A

A

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R

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A

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Y

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L

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x
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-

A

-

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D

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I

A

A

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H

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A

A

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A

A

A

A

Q

Q

G

K

R

R

K

A

K

K

K

K

L

L

T

L

L

S

V

V

D

D

K
|
K

S

S

N

N

V

V

L

L

E

E

T

T

S

S

R

Q

L

F

W

W

R

R

R

D

T

V

V

M

M

I

N

D

M

V

A

S

K

K

Q

E

Y

Y

P

A

N

D

V

V

N

E

V

L

E

S

L

H

M

M

Y

Y

V

V

D
|
D

Q

N

A

A

A

A

A

M

K

Q

I

L

I

A

L

K

N

A

P

P

K

K

S

Q

F

F

D

D

V

V

I

I

L

V

T

T

A

G

N

N

L

M

I

F

G

G

D
|
D

F

I

I

L

S

S

E
x
D

E

E

A

A

S

S

A

M

L

L

V

T

G

G

S

S

K

I

G

G

I

M

M

L

A

P

S

S

A

A

A

S

L

L

G

D

E

K

-

N

K

N

Y

K

S

G

L

L

F

Y

E

E

P

P

I

S

H

H

G

G

S

S

Y

A

P

P

V

D

A

I

T

A

N

G

K

K

G

G

I

I

A

A

N

N

P

P

I

L

G

A

A

T

I

I

L

L

S

S

A

A

A

A

M

M

L

L

L

L

E

R

H

Y

-

S

F

L

N

N

L

R

Q

A

V

E

E

Q

A

A

D

D

A

R

I

I

K

E

R

R

S

A

I

V

T

K

K

T

A

V

M

L

E

E

L

Q

N

G

L

Y

T

R

T

T

P

G

D

D

L

I

N

A

K

T

Q

P

-

G

-

C

K

R

P

Q

L

V

S

G

T

T

E

A

K

A

I

M

G

G

D

D

F

A

I

V

active site: Y138 (≠ F142), K193 (= K189), D225 (= D221), D249 (= D245), D253 (≠ E249)
binding magnesium ion: D249 (= D245), D253 (≠ E249)

4xxvA Crystal structure of 3-isopropylmalate dehydrogenase from burkholderia thailandensis in complex with NAD
44% identity, 93% coverage: 3:346/371 of query aligns to 2:352/356 of 4xxvA

query
sites
4xxvA

L

M

N

K

I

I

A

A

V

V

L

L

G

P

G

G

D

D

G

G

V

I

G

G

P

P

E

E

V

I

T

V

E

N

Q

E

A

A

V

V

K

K

A

V

L

L

E

N

A

A

V

L

A

D

E

E

Y

K

Y

F

Q

E

H

-

D

-

F

-

I

-

F

L

K

E

E

H

A

A

L

P

V

V

G

G

A

G

T

A

A

G

I

Y

E

E

K

A

T

S

G

G

T

H

P

P

L

L

P

P

Q

D

E

A

T

T

I

L

T

A

I

L

C

A

K

K

A

E

S

A

D

D

T

A

V

I

L

L

F

F

G

G

A

A

I

V

G

G

D

D

P

W

K

K

F

Y

D

D

N

S

D

L

P

E

K

R

T

A

K

-

I

L

Y

R

P

P

E

E

Q

Q

G

A

L

I

L

L

G

G

L

L

R

R

S

K

E

H

L

L

N

E

L

L

Y

F

A

A

N

N

I

F

R

R

P

P

V

A

I

I

V

C

Y

Y

N

P

Y

Q

L

L

L

V

N

D

N

A

S

S

P

P

L

L

K

K

P

P

Q

E

N

L

A

V

R

A

G

G

T

L

N

D

I

I

L

L

I

I

Y

V

R

R

E

E

L

L

T

N

G

G

G

D

L

I

F
x
Y

Y

F

G

G

D

Q

-

P

-

R

-

G

-

V

-

R

-

A

-

A

-

P

K

D

G

G

T

P

T

F

D

A

N

G

G

E

H

R

K

E

A

G

Y

F

D

D

A

T

C

M

T

R

Y

Y

T

S

T

E

D

P

E

E

I

V

E

R

R

R

I

I

A

A

H

H

D

V

A

A

F

F

K

Q

A

A

A

A

Q

Q

G

K

R

R

K

A

K

K

K

K

L

L

T

L

L

S

V

V

D

D

K
|
K

S

S

N
|
N

V

V

L

L

E

E

T

T

S

S

R

Q

L

F

W

W

R

R

R

D

T

V

V

M

M

I

N

D

M

V

A

S

K

K

Q

E

Y

Y

P

A

N

D

V

V

N

E

V

L

E

S

L

H

M

M

Y
|
Y

V

V

D
|
D

Q
x
N

A

A

A

A

A

M

K

Q

I

L

I

A

L

K

N

A

P

P

K

K

S

Q

F

F

D

D

V

V

I

I

L

V

T

T

A

G

N

N

L

M

I

F

G

G

D
|
D

F

I

I

L

S

S

E
x
D

E

E

A

A

S

S

A

M

L

L

V

T

G

G

S

S

K

I

G

G

I

M

M

L

A

P

S

S

A

A

A

S

L

L

G

D

E

K

-

N

K

N

Y

K

S

G

L

L

F

Y

E

E

P

P

I

S

H

H

G

G

S

S

Y

A

P

P

V

D

A

I

T

A

N

G

K

K

G

G

I

I

A

A

N

N

P

P

I

L

G

A

A

T

I

I

L

L

S

S

A

A

A

A

M

M

L

L

L

L

E

R

H

Y

-

S

F

L

N

N

L

R

Q

A

V

E

E

Q

A

A

D

D

A

R

I

I

K

E

R

R

S

A

I

V

T

K

K

T

A

V

M

L

E

E

L

Q

N

G

L

Y

T

R

T

T

P

G

D

D

L

I

N

A

K

T

Q

P

-

G

-

C

K

R

P

Q

L

V

S

G

T

T

E

A

K

A

I

M

G

G

D

D

F

A

I

V

active site: Y136 (≠ F142), K191 (= K189), D223 (= D221), D247 (= D245), D251 (≠ E249)
binding nicotinamide-adenine-dinucleotide: N193 (= N191), Y221 (= Y219), N224 (≠ Q222)

3vkzA 3-isopropylmalate dehydrogenase from shewanella oneidensis mr-1 at atmospheric pressure (see paper)
44% identity, 94% coverage: 4:350/371 of query aligns to 4:360/364 of 3vkzA

query
sites
3vkzA

N

Q

I

I

A

A

V

V

L

L

G

A

G

G

D

D

G

G

V

I

G

G

P

P

E

E

V

V

T

M

E

A

Q

E

A

A

V

R

K

K

A

V

L

L

E

K

A

A

V

V

A

E

E

A

Y

R

Y

F

Q

G

H

L

D

N

F

I

I

E

F

Y

K

T

E

E

A

Y

L

D

V

V

G

G

A

G

T

I

A

A

I

I

E

D

K

N

T

H

G

G

T

C

P

P

L

L

P

P

Q

E

E

A

T

T

I

L

T

K

I

G

C

C

K

E

A

A

S

A

D

D

T

A

V

I

L

L

F

F

G

G

A

S

I

V

G

G

D

G

P

P

K

K

F

W

D

E

N

K

D

L

P

P

K

P

T

N

K

E

I

-

Y

Q

P

P

E

E

Q

R

G

G

-

A

L

L

L

L

G

P

L

L

R
|
R

S

G

E

H

L

F

N

E

L

L

Y

F

A

C

N

N

I

L

R

R

P

P

V

A

I

K

V

L

Y

H

N

D

Y

G

L

L

L

E

N

H

N

M

S

S

P

P

L

L

K

R

P

S

Q

D

-

I

N

S

A

A

R

R

G

G

T

F

N

D

I

V

L

L

I

C

Y

V

R
|
R

E

E

L

L

T

T

G

G

G

G

L

I

F
x
Y

Y

F

G

G

D

K

-

P

K

K

G

G

T

R

T

Q

D

G

N

E

G

G

H

E

-

S

-

E

K

E

A

A

Y

F

D

D

A

T

C

M

T

R

Y

Y

T

S

T

R

D

R

E

E

I

I

E

S

R

R

I

I

A

A

H

R

D

I

A

A

F

F

K

E

A

A

A

A

Q

R

G

G

R

R

K

R

K

K

K

K

L

V

T

T

L

S

V

V

D

D

K
|
K

S

A

N

N

V

V

L

L

E

A

T

C

S

S

R

V

L

L

W

W

R

R

R

Q

T

V

V

V

M

E

N

E

M

V

A

A

K

V

Q

D

Y

F

P

P

N

D

V

V

N

E

V

L

E

E

L

H

M

I

Y

Y

V

I

D
|
D

Q

N

A

A

A

T

A

M

K

Q

I

L

I

L

L

R

N

R

P

P

K

D

S

E

F

F

D

D

V

V

I

M

L

L

T

C

A

S

N

N

L

L

I

F

G

G

D
|
D

F

I

I

L

S

S

E
x
D

E

E

A

I

S

A

A

M

L

L

V

T

G

G

S

S

K

M

G

G

I

L

M

L

A

S

S

S

A

A

A

S

L

M

G

N

E

S

K

T

-

G

Y

F

S

G

L

L

F

F

E

E

P

P

I

A

H

G

G

G

S

S

Y

A

P

P

V

D

A

I

T

A

N

G

K

K

G

G

I

I

A

A

N

N

P

P

I

I

G

A

A

Q

I

I

L

L

S

S

A

A

A

A

M

L

L

M

L

L

E

R

H

H

F

S

N

L

L

K

Q

Q

V

E

E

E

-

A

A

A

D

S

A

A

I

I

K

E

R

R

S

A

I

V

T

T

K

K

A

A

M

L

E

N

L

S

N

G

L

Y

T

L

T

T

P

G

D

E

L

L

-

L

-

S

-

S

-

D

N

Q

K

R

Q

H

K

K

P

A

L

K

S

T

T

T

E

V

K

Q

I

M

G

G

D

D

F

F

I

I

A

A

D

D

Y

A

I

V

active site: Y143 (≠ F142), K193 (= K189), D225 (= D221), D249 (= D245), D253 (≠ E249)
binding calcium ion: D249 (= D245), D253 (≠ E249)
binding 3-isopropylmalic acid: R97 (= R97), R136 (= R135), Y143 (≠ F142), D249 (= D245)

2y41A Structure of isopropylmalate dehydrogenase from thermus thermophilus - complex with ipm and mn (see paper)
44% identity, 89% coverage: 3:332/371 of query aligns to 2:329/346 of 2y41A

query
sites
2y41A

L

M

N

K

I

V

A

A

V

V

L

L

G

P

G

G

D

D

G

G

V

I

G

G

P

P

E

E

V

V

T

T

E

E

Q

A

A

A

V

L

K

K

A

V

L

L

E

R

A

A

V

L

A

D

E

E

Y

A

Y

E

Q

G

H

L

D

G

F

L

I

A

F

Y

K

E

E

V

A

F

L

P

V

F

G

G

A

G

T

A

A

A

I

I

E

D

K

A

T

F

G

G

T

E

P

P

L

F

P

P

Q

E

E

P

T

T

I

R

T

K

I

G

C

V

K

E

A

E

S

A

D

E

T

A

V

V

L

L

F

L

G

G

A

S

I

V

G

G

D

G

P

P

K

K

F

W

D

D

N

G

D

L

P

P

K

R

T

-

K

K

I

I

Y

R

P

P

E

E

Q

T

G

G

L

L

L

L

G

S

L

L

R
|
R

S

K

E

S

L

Q

N

D

L

L

Y

F

A

A

N

N

I

L

R
|
R

P

P

V

A

I

K

V

V

Y

F

N

P

Y

G

L

L

L

E

N

R

N

L

S

S

P

P

L

L

K

K

P

E

Q

E

N

I

A

A

R

R

G

G

T

V

N

D

I

V

L

L

I

I

Y

V

R
|
R

E

E

L

L

T

T

G

G

G

G

L

I

F
x
Y

Y

F

G

G

D

E

-

P

K

R

G

G

T

M

T

S

D

E

N

A

G

-

H

-

K

E

A

A

Y

W

D

N

A

T

C

E

T

R

Y

Y

T

S

T

K

D

P

E

E

I

V

E

E

R

R

I

V

A

A

H

R

D

V

A

A

F

F

K

E

A

A

A

A

Q

R

G

K

R

R

K

R

K

K

K

H

L

V

T

V

L

S

V

V

D

D

K
|
K

S

A

N

N

V

V

L

L

E

E

T

V

S

G

R

E

L

F

W

W

R

R

R

K

T

T

V

V

M

E

N

E

M

V

A

G

K

R

Q

G

Y

Y

P

P

N

D

V

V

N

A

V

L

E

E

L

H

M

Q

Y

Y

V

V

D
|
D

Q

A

A

M

A

A

A

M

K

H

I

L

I

V

L

R

N

S

P

P

K

A

S

R

F

F

D

D

V

V

I

V

L

V

T

T

A

G

N

N

L

I

I

F

G

G

D
|
D

F

I

I

L

S

S

E
x
D

E

L

A

A

S

S

A

V

L

L

V

P

G

G

S

S

K

L

G

G

I

L

M

L

A

P

S

S

A

A

A

S

L

L

G

G

E

R

K

G

Y

T

S

P

L

V

F

F

E

E

P

P

I

V

H

H

G

G

S

S

Y

A

P

P

V

D

A

I

T

A

N

G

K

K

G

G

I

I

A

A

N

N

P

P

I

T

G

A

A

A

I

I

L

L

S

S

A

A

A

A

M

M

L

M

L

L

E

E

H

H

-

A

F

F

N

G

L

L

Q

V

V

E

E

L

A

A

D

R

A

K

I

V

K

E

R

D

S

A

I

V

T

A

K

K

A

A

M

L

E

-

L

L

N

E

L

T

T

P

T

P

P

P

D

D

L

L

N

G

active site: Y140 (≠ F142), K186 (= K189), D218 (= D221), D242 (= D245), D246 (≠ E249)
binding 3-isopropylmalic acid: R95 (= R97), R105 (= R107), R133 (= R135), Y140 (≠ F142), D242 (= D245)

2ztwA Structure of 3-isopropylmalate dehydrogenase in complex with the inhibitor and NAD+ (see paper)
44% identity, 89% coverage: 3:332/371 of query aligns to 1:328/345 of 2ztwA

query
sites
2ztwA

L

M

N

K

I

V

A

A

V

V

L

L

G

P

G

G

D

D

G

G

V
x
I

G

G

P

P

E

E

V

V

T

T

E

E

Q

A

A

A

V

L

K

K

A

V

L

L

E

R

A

A

V

L

A

D

E

E

Y

A

Y

E

Q

G

H

L

D

G

F

L

I

A

F

Y

K

E

E

V

A

F

L

P

V

F

G

G

A

G

T

A

A

A

I

I

E

D

K

A

T

F

G

G

T

E

P

P

L

F

P

P

Q

E

E

P

T

T

I

R

T

K

I

G

C

V

K

E

A

E

S

A

D

E

T

A

V

V

L

L

F

L

G

G

A

S

I

V

G

G

D

G

P

P

K

K

F

W

D

D

N

G

D

L

P

P

K

R

T

-

K

K

I

I

Y

R

P

P

E

E

Q

T

G

G

L

L

L

L

G

S

L

L

R

R

S

K

E

S

L

Q

N

D

L

L

Y

F

A

A

N

N

I

L

R

R

P

P

V

A

I

K

V

V

Y

F

N

P

Y

G

L

L

L

E

N

R

N

L

S

S

P

P

L

L

K

K

P

E

Q

E

N

I

A

A

R

R

G

G

T

V

N

D

I

V

L

L

I

I

Y

V

R

R

E

E

L

L

T

T

G

G

G

G

L

I

F
x
Y

Y

F

G

G

D

E

-

P

K

R

G

G

T

M

T

S

D

E

N

A

G

-

H

-

K

E

A

A

Y

W

D

N

A

T

C

E

T

R

Y

Y

T

S

T

K

D

P

E

E

I

V

E

E

R

R

I

V

A

A

H

R

D

V

A

A

F

F

K

E

A

A

A

A

Q

R

G

K

R

R

K

R

K

K

K

H

L

V

T

V

L

S

V

V

D

D

K
|
K

S

A

N

N

V

V

L

L

E

E

T

V

S

G

R

E

L

F

W

W

R

R

R

K

T

T

V

V

M

E

N

E

M

V

A
x
G

K

R

Q

G

Y
|
Y

P

P

N

D

V
|
V

N

A

V

L

E

E

L

H

M

Q

Y

Y

V

V

D
|
D

Q

A

A

M

A

A

A

M

K

H

I

L

I

V

L

R

N

S

P

P

K

A

S

R

F

F

D

D

V

V

I

V

L

V

T

T

A

G

N

N

L

I

I

F

G

G

D
|
D

F

I

I

L

S

S

E
x
D

E

L

A

A

S

S

A

V

L

L

V

P

G

G

S

S

K

L

G

G

I

L

M

L

A

P

S

S

A

A

A

S

L

L

G

G

E

R

K

G

Y

T

S

P

L

V

F

F

E

E

P

P

I

V

H
|
H

G
|
G

S

S

Y
x
A

P

P

V
x
D

A
x
I

T

A

N

G

K

K

G

G

I

I

A
|
A

N
|
N

P

P

I

T

G

A

A

A

I

I

L

L

S

S

A

A

A

A

M

M

L

M

L

L

E

E

H

H

-

A

F

F

N

G

L

L

Q

V

V

E

E

L

A

A

D

R

A

K

I

V

K

E

R

D

S

A

I

V

T

A

K

K

A

A

M

L

E

-

L

L

N

E

L

T

T

P

T

P

P

P

D

D

L

L

N

G

active site: Y139 (≠ F142), K185 (= K189), D217 (= D221), D241 (= D245), D245 (≠ E249)
binding magnesium ion: G203 (≠ A207), Y206 (= Y210), V209 (= V213)
binding nicotinamide-adenine-dinucleotide: I11 (≠ V13), H273 (= H277), G274 (= G278), A276 (≠ Y280), D278 (≠ V282), I279 (≠ A283), A285 (= A289), N286 (= N290)

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)
44% identity, 89% coverage: 3:332/371 of query aligns to 1:328/345 of Q5SIY4

query
sites
Q5SIY4

L

M

N

K

I

V

A

A

V

V

L

L

G

P

G

G

D

D

G

G

V

I

G

G

P

P

E

E

V

V

T

T

E

E

Q

A

A

A

V

L

K

K

A

V

L

L

E

R

A

A

V

L

A

D

E

E

Y

A

Y

E

Q

G

H

L

D

G

F

L

I

A

F

Y

K

E

E

V

A

F

L

P

V

F

G

G

A

G

T

A

A

A

I

I

E

D

K

A

T

F

G

G

T

E

P

P

L

F

P

P

Q

E

E

P

T

T

I

R

T

K

I

G

C

V

K

E

A

E

S

A

D

E

T

A

V

V

L

L

F

L

G

G

A

S

I

V

G

G

D
x
G

P
|
P

K
|
K

F
x
W

D
|
D

N
x
G

D
x
L

P
|
P

K
x
R

T

-

K
|
K

I
|
I

Y
x
R

P
|
P

E
|
E

Q

T

G

G

L

L

L

L

G

S

L

L

R

R

S

K

E

S

L

Q

N

D

L

L

Y

F

A

A

N

N

I

L

R

R

P

P

V

A

I

K

V

V

Y

F

N

P

Y

G

L

L

L

E

N

R

N

L

S

S

P

P

L

L

K

K

P

E

Q

E

N

I

A

A

R

R

G

G

T

V

N

D

I

V

L

L

I

I

Y

V

R

R

E

E

L

L

T

T

G

G

G

G

L

I

F
x
Y

Y

F

G

G

D

E

-

P

K

R

G

G

T

M

T

S

D

E

N

A

G

-

H

-

K

E

A

A

Y

W

D

N

A

T

C

E

T

R

Y

Y

T

S

T

K

D

P

E

E

I

V

E

E

R

R

I

V

A

A

H

R

D

V

A

A

F

F

K

E

A

A

A

A

Q

R

G

K

R

R

K

R

K

K

K

H

L

V

T

V

L

S

V

V

D

D

K

K

S

A

N

N

V

V

L

L

E

E

T

V

S

G

R

E

L

F

W

W

R

R

R

K

T

T

V

V

M

E

N

E

M

V

A

G

K

R

Q

G

Y

Y

P

P

N

D

V

V

N

A

V

L

E

E

L

H

M

Q

Y

Y

V

V

D

D

Q

A

A

M

A

A

A

M

K

H

I

L

I

V

L

R

N

S

P

P

K

A

S

R

F

F

D

D

V

V

I

V

L

V

T

T

A

G

N

N

L

I

I

F

G

G

D

D

F

I

I

L

S

S

E

D

E

L

A

A

S

S

A

V

L

L

V

P

G

G

S

S

K

L

G

G

I

L

M

L

A

P

S

S

A

A

A

S

L

L

G

G

E

R

K

G

Y

T

S

P

L

V

F

F

E

E

P

P

I

V

H

H

G
|
G

S
|
S

Y
x
A

P
|
P

V
x
D

A
x
I

T
x
A

N
x
G

K
|
K

G
|
G

I
|
I

A
|
A

N
|
N

P

P

I

T

G

A

A

A

I

I

L

L

S

S

A

A

A

A

M

M

L

M

L

L

E

E

H

H

-

A

F

F

N

G

L

L

Q

V

V

E

E

L

A

A

D

R

A

K

I

V

K

E

R

D

S

A

I

V

T

A

K

K

A

A

M

L

E

-

L

L

N

E

L

T

T

P

T

P

P

P

D

D

L

L

N

G

74:87 (vs. 76:90, 53% identical) binding NAD(+)
Y139 (≠ F142) mutation to F: Large decrease in activity and a small decrease in substrate affinity.
274:286 (vs. 278:290, 62% identical) binding NAD(+)

2y42D Structure of isopropylmalate dehydrogenase from thermus thermophilus - complex with nadh and mn (see paper)
44% identity, 89% coverage: 3:332/371 of query aligns to 2:329/355 of 2y42D

query
sites
2y42D

L

M

N

K

I

V

A

A

V

V

L

L

G

P

G

G

D

D

G

G

V
x
I

G

G

P

P

E

E

V

V

T

T

E

E

Q

A

A

A

V

L

K

K

A

V

L

L

E

R

A

A

V

L

A

D

E

E

Y

A

Y

E

Q

G

H

L

D

G

F

L

I

A

F

Y

K

E

E

V

A

F

L

P

V

F

G

G

A

G

T

A

A

A

I

I

E

D

K

A

T

F

G

G

T

E

P

P

L

F

P

P

Q

E

E

P

T

T

I

R

T

K

I

G

C

V

K

E

A

E

S

A

D

E

T

A

V

V

L

L

F

L

G

G

A

S

I

V

G

G

D

G

P

P

K

K

F

W

D
|
D

N

G

D

L

P

P

K

R

T

-

K

K

I

I

Y

R

P

P

E

E

Q

T

G

G

L

L

L

L

G

S

L

L

R

R

S

K

E

S

L

Q

N

D

L

L

Y

F

A

A

N

N

I

L

R

R

P

P

V

A

I

K

V

V

Y

F

N

P

Y

G

L

L

L

E

N

R

N

L

S

S

P

P

L

L

K

K

P

E

Q

E

N

I

A

A

R

R

G

G

T

V

N

D

I

V

L

L

I

I

Y

V

R

R

E

E

L

L

T

T

G

G

G

G

L

I

F
x
Y

Y

F

G

G

D

E

-

P

K

R

G

G

T

M

T

S

D

E

N

A

G

-

H

-

K

E

A

A

Y

W

D

N

A

T

C

E

T

R

Y

Y

T

S

T

K

D

P

E

E

I

V

E

E

R

R

I

V

A

A

H

R

D

V

A

A

F

F

K

E

A

A

A

A

Q

R

G

K

R

R

K

R

K

K

K

H

L

V

T

V

L

S

V

V

D

D

K
|
K

S

A

N

N

V

V

L

L

E

E

T

V

S

G

R

E

L

F

W

W

R

R

R

K

T

T

V

V

M

E

N

E

M

V

A

G

K

R

Q

G

Y

Y

P

P

N

D

V

V

N

A

V

L

E

E

L

H

M

Q

Y

Y

V

V

D
|
D

Q

A

A

M

A

A

A

M

K

H

I

L

I

V

L

R

N

S

P

P

K

A

S

R

F

F

D

D

V

V

I

V

L

V

T

T

A

G

N

N

L

I

I

F

G

G

D
|
D

F

I

I

L

S

S

E
x
D

E

L

A

A

S

S

A

V

L

L

V

P

G

G

S

S

K

L

G

G

I

L

M

L

A

P

S

S

A

A

A

S

L

L

G

G

E

R

K

G

Y

T

S

P

L

V

F

F

E

E

P

P

I

V

H
|
H

G
|
G

S

S

Y
x
A

P

P

V
x
D

A
x
I

T

A

N

G

K

K

G

G

I

I

A

A

N
|
N

P

P

I

T

G

A

A

A

I

I

L

L

S

S

A

A

A

A

M

M

L

M

L

L

E

E

H

H

-

A

F

F

N

G

L

L

Q

V

V

E

E

L

A

A

D

R

A

K

I

V

K

E

R

D

S

A

I

V

T

A

K

K

A

A

M

L

E

-

L

L

N

E

L

T

T

P

T

P

P

P

D

D

L

L

N

G

active site: Y140 (≠ F142), K186 (= K189), D218 (= D221), D242 (= D245), D246 (≠ E249)
binding manganese (ii) ion: D242 (= D245), D246 (≠ E249)
binding nicotinamide-adenine-dinucleotide: I12 (≠ V13), D79 (= D80), H274 (= H277), G275 (= G278), A277 (≠ Y280), D279 (≠ V282), I280 (≠ A283), N287 (= N290)

3vmkA 3-isopropylmalate dehydrogenase from shewanella benthica db21 mt-2 (see paper)
42% identity, 94% coverage: 4:350/371 of query aligns to 10:366/369 of 3vmkA

query
sites
3vmkA

N

Q

I

I

A

A

V

V

L

L

G

A

G

G

D

D

G

G

V

I

G

G

P

P

E

E

V

V

T

M

E

A

Q

E

A

A

V

R

K

K

A

V

L

L

E

A

A

A

V

V

A

E

E

K

Y

R

Y

F

Q

D

H

L

D

S

F

I

I

E

F

Y

K

S

E

E

A

Y

L

D

V

V

G

G

A

G

T

A

A

A

I

I

E

D

K

N

T

H

G

G

T

C

P

P

L

L

P

P

Q

E

E

A

T

T

I

L

T

K

I

G

C

C

K

E

A

A

S

A

D

D

T

A

V

V

L

L

F

F

G

G

A

S

I

V

G

G

D

G

P

P

K

K

F

W

D

E

N

H

D

L

P

P

K

P

T

N

K

D

I

-

Y

Q

P

P

E

E

Q

R

G

G

-

A

L

L

L

L

G

P

L

L

R
|
R

S

G

E

H

L

F

N

E

L

L

Y

F

A

C

N

N

I

M

R

R

P

P

V

A

I

K

V

L

Y

H

N

P

Y

G

L

L

L

E

N

H

N

M

S

S

P

P

L

L

K

R

P

S

Q

D

-

I

N

S

A

E

R

K

G

G

T

F

N

D

I

I

L

L

I

C

Y

V

R
|
R

E

E

L

L

T

T

G

G

G

G

L

I

F
x
Y

Y

F

G

G

D

K

-

P

K

K

G

G

T

R

T

Q

D

G

N

E

G

G

H

E

-

N

-

E

K

E

A

A

Y

F

D

D

A

T

C

M

T

R

Y

Y

T

S

T

R

D

K

E

E

I

I

E

R

R

R

I

I

A

A

H

K

D

I

A

A

F

F

K

E

A

S

A

A

Q

Q

G

G

R

R

K

R

K

K

K

K

L

V

T

T

L

S

V

V

D

D

K
|
K

S

A

N
|
N

V

V

L

L

E

A

T

C

S

S

R

V

L

L

W

W

R

R

R

E

T

V

V

V

M

E

N

E

M

V

A

A

K

K

Q

D

Y

Y

P

P

N

D

V

V

N

E

V

L

E

E

L

H

M

I

Y

Y

V

I

D
|
D

Q

N

A

A

A

T

A

M

K

Q

I

L

I

L

L

R

N

R

P

P

K

N

S

E

F

F

D

D

V

V

I

M

L

L

T

C

A

S

N

N

L

L

I

F

G

G

D
|
D

F

I

I

V

S

S

E
x
D

E

E

A

I

S

A

A

M

L

L

V

T

G

G

S

S

K

M

G

G

I

L

M

L

A

A

S

S

A

I

A

S

L

M

-

N

G

S

E

Q

K

G

Y

F

S

G

L

M

F

Y

E

E

P

P

I

A

H

G

G

G

S

S

Y

A

P

P

V

D

A

I

T

A

N

G

K

Q

G

G

I

I

A

A

N

N

P

P

I

V

G

A

A

Q

I

I

L

L

S

S

A

A

A

A

M

L

L

L

L

L

E

R

H

H

-

S

F

L

N

K

L

L

Q

E

V

D

E

A

A

A

D

L

A

A

I

I

K

E

R

A

S

A

I

V

T

S

K

K

A

A

M

L

E

S

L

D

N

G

L

Y

T

L

T

T

P

C

D

E

L

L

-

L

-

P

-

A

-

S

N

E

K

R

Q

S

K

Q

P

A

L

K

S

S

T

T

E

S

K

Q

I

M

G

G

D

D

F

Y

I

I

A

A

D

Q

Y

A

I

I

active site: Y149 (≠ F142), K199 (= K189), D231 (= D221), D255 (= D245), D259 (≠ E249)
binding 3-isopropylmalic acid: R103 (= R97), R142 (= R135), Y149 (≠ F142), K199 (= K189), N201 (= N191), D255 (= D245)

1cnzA 3-isopropylmalate dehydrogenase (ipmdh) from salmonella typhimurium (see paper)
43% identity, 94% coverage: 4:350/371 of query aligns to 6:359/363 of 1cnzA

query
sites
1cnzA

N

H

I

I

A

A

V

V

L

L

G

P

G

G

D

D

G

G

V

I

G

G

P

P

E

E

V

V

T

M

E

A

Q

Q

A

A

V

L

K

K

A

V

L

M

E

D

A

A

V

V

A

R

E

S

Y

R

Y

F

Q

D

H

M

D

R

F

I

I

T

F

T

K

S

E

H

A

Y

L

D

V

V

G

G

A

G

T

I

A

A

I

I

E

D

K

N

T

H

G

G

T

H

P

P

L

L

P

P

Q

K

E

A

T

T

I

V

T

E

I

G

C

C

K

E

A

Q

S

A

D

D

T

A

V

I

L

L

F

F

G

G

A

S

I

V

G

G

D

G

P

P

K

K

F

W

D

E

N

N

D

L

P

P

K

P

T

E

K

S

I

-

Y

Q

P

P

E

E

Q

R

G

G

-

A

L

L

L

L

G

P

L

L

R

R

S

K

E

H

L

F

N

K

L

L

Y

F

A

S

N

N

I

L

R

R

P

P

V

A

I

K

V

L

Y

Y

N

Q

Y

G

L

L

L

E

N

A

N

F

S

C

P

P

L

L

K

R

P

A

Q

D

-

I

N

A

A

A

R

N

G

G

T

F

N

D

I

I

L

L

I

C

Y

V

R

R

E

E

L

L

T

T

G

G

G

G

L

I

F
x
Y

Y

F

G

G

D

Q

-

P

K

K

G

G

T

R

T

E

D

G

N

S

G

G

H

Q

-

Y

-

E

K

K

A

A

Y

F

D

D

A

T

C

E

T

V

Y

Y

T

H

T

R

D

F

E

E

I

I

E

E

R

R

I

I

A

A

H

R

D

I

A

A

F

F

K

E

A

S

A

A

Q

R

G

K

R

R

K

R

K

R

K

K

L

V

T

T

L

S

V

I

D

D

K
|
K

S

A

N

N

V

V

L

L

E

Q

T

S

S

S

R

I

L

L

W

W

R

R

R

E

T

I

V

V

M

N

N

D

M

V

A

A

K

K

Q

T

Y

Y

P

P

N

D

V

V

N

E

V

L

E

A

L

H

M

M

Y

Y

V

I

D
|
D

Q

N

A

A

A

T

A

M

K

Q

I

L

I

I

L

K

N

D

P

P

K

S

S

Q

F

F

D

D

V

V

I

L

L

L

T

C

A

S

N

N

L

L

I

F

G

G

D
|
D

F

I

I

L

S

S

E
x
D

E

E

A

C

S

A

A

M

L

I

V

T

G

G

S

S

K

M

G

G

I

M

M

L

A

P

S

S

A

A

A

S

L

L

G

N

E

E

K

Q

-

G

Y

F

S

G

L

L

F

Y

E

E

P

P

I

A

H

G

G

G

S

S

Y

A

P

P

V

D

A

I

T

A

N

G

K

K

G

N

I

I

A

A

N

N

P

P

I

I

G

A

A

Q

I

I

L

L

S

S

A

L

A

A

M

L

L

L

L

L

E

R

H

Y

-

S

F

L

N

D

L

A

Q

N

V

D

E

A

A

A

D

T

A

A

I

I

K

E

R

Q

S

A

I

I

T

N

K

R

A

A

M

L

E

E

L

E

N

G

L

V

T

R

T

T

P

G

D

D

L

L

N

A

K

R

-

G

Q

A

K

A

P

A

L

V

S

S

T

T

E

D

K

E

I

M

G

G

D

D

F

I

I

I

A

A

D

R

Y

Y

I

V

active site: Y145 (≠ F142), K195 (= K189), D227 (= D221), D251 (= D245)
binding manganese (ii) ion: D251 (= D245), D255 (≠ E249)

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)
43% identity, 94% coverage: 4:350/371 of query aligns to 6:359/363 of P37412

query
sites
P37412

N

H

I

I

A

A

V

V

L

L

G

P

G

G

D

D

G

G

V

I

G

G

P

P

E

E

V

V

T

M

E

A

Q

Q

A

A

V

L

K

K

A

V

L

M

E

D

A

A

V

V

A

R

E

S

Y

R

Y

F

Q

D

H

M

D

R

F

I

I

T

F

T

K

S

E

H

A

Y

L

D

V

V

G

G

A

G

T

I

A

A

I

I

E

D

K

N

T

H

G

G

T

H

P

P

L

L

P

P

Q

K

E

A

T

T

I

V

T

E

I

G

C

C

K

E

A

Q

S

A

D

D

T

A

V

I

L

L

F

F

G

G

A

S

I

V

G

G

D

G

P

P

K

K

F

W

D

E

N

N

D

L

P

P

K

P

T

E

K

S

I

-

Y

Q

P

P

E

E

Q

R

G

G

-

A

L

L

L

L

G

P

L

L

R

R

S

K

E

H

L

F

N

K

L

L

Y

F

A

S

N

N

I

L

R

R

P

P

V

A

I

K

V

L

Y

Y

N

Q

Y

G

L

L

L

E

N

A

N

F

S

C

P

P

L

L

K

R

P

A

Q

D

-

I

N

A

A

A

R

N

G

G

T

F

N

D

I

I

L

L

I

C

Y

V

R

R

E

E

L

L

T

T

G

G

G

G

L

I

F

Y

Y

F

G

G

D

Q

-

P

K

K

G

G

T

R

T

E

D

G

N

S

G

G

H

Q

-

Y

-

E

K

K

A

A

Y

F

D

D

A

T

C

E

T

V

Y

Y

T

H

T

R

D

F

E

E

I

I

E

E

R

R

I

I

A

A

H

R

D

I

A

A

F

F

K

E

A

S

A

A

Q

R

G

K

R

R

K

R

K

R

K

K

L

V

T

T

L

S

V

I

D

D

K

K

S

A

N

N

V

V

L

L

E

Q

T

S

S

S

R

I

L

L

W

W

R

R

R

E

T

I

V

V

M

N

N

D

M

V

A

A

K

K

Q

T

Y

Y

P

P

N

D

V

V

N

E

V

L

E

A

L

H

M

M

Y

Y

V

I

D
|
D

Q

N

A

A

A

T

A

M

K

Q

I

L

I

I

L

K

N

D

P

P

K

S

S

Q

F

F

D

D

V

V

I

L

L

L

T

C

A

S

N

N

L

L

I

F

G

G

D
|
D

F

I

I

L

S

S

E
x
D

E

E

A

C

S

A

A

M

L

I

V

T

G

G

S

S

K

M

G

G

I

M

M

L

A

P

S

S

A

A

A

S

L

L

G

N

E

E

K

Q

-

G

Y

F

S

G

L

L

F

Y

E

E

P

P

I

A

H

G

G

G

S

S

Y

A

P

P

V

D

A

I

T

A

N

G

K

K

G

N

I

I

A

A

N

N

P

P

I

I

G

A

A

Q

I

I

L

L

S

S

A

L

A

A

M

L

L

L

L

L

E

R

H

Y

-

S

F

L

N

D

L

A

Q

N

V

D

E

A

A

A

D

T

A

A

I

I

K

E

R

Q

S

A

I

I

T

N

K

R

A

A

M

L

E

E

L

E

N

G

L

V

T

R

T

T

P

G

D

D

L

L

N

A

K

R

-

G

Q

A

K

A

P

A

L

V

S

S

T

T

E

D

K

E

I

M

G

G

D

D

F

I

I

I

A

A

D

R

Y

Y

I

V

D227 (= D221) binding Mn(2+)
D251 (= D245) binding Mn(2+)
D255 (≠ E249) binding Mn(2+)

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)
43% identity, 89% coverage: 2:331/371 of query aligns to 43:377/404 of Q9SA14

query
sites
Q9SA14

K

R

L

Y

N

N

I

I

A

T

V

L

L

L