SitesBLAST

SitesBLAST – Find functional sites

SitesBLAST

Comparing 408370 DVUA0016 homocitrate synthase 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)

6ktqA Crystal structure of catalytic domain of homocitrate synthase from sulfolobus acidocaldarius (sahcs(dram)) in complex with alpha- ketoglutarate/zn2+/coa (see paper)
31% identity, 95% coverage: 15:379/384 of query aligns to 15:362/399 of 6ktqA

query
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6ktqA

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binding 2-oxoglutaric acid: R30 (= R30), R154 (≠ T150), T156 (≠ G152), E158 (= E154), S184 (≠ R180), T188 (= T184), H216 (= H211), H218 (= H213)
binding coenzyme a: V67 (≠ L70), R96 (= R91), A97 (≠ C92), F116 (≠ G111), H128 (≠ L123), E158 (= E154)
binding zinc ion: E31 (= E31), H216 (= H211), H218 (= H213)

Q9FN52 Methylthioalkylmalate synthase 3, chloroplastic; 2-isopropylmalate synthase 2; Methylthioalkylmalate synthase-like; EC 2.3.3.17 from Arabidopsis thaliana (Mouse-ear cress) (see paper)
28% identity, 94% coverage: 19:379/384 of query aligns to 82:448/503 of Q9FN52

query
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Q9FN52

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G263 (= G186) mutation to E: In gsm2-1; loss of activity and lack of C6, C7 and C8 aliphatic glucosinolates.

6e1jA Crystal structure of methylthioalkylmalate synthase (bjumam1.1) from brassica juncea (see paper)
29% identity, 82% coverage: 19:332/384 of query aligns to 15:353/409 of 6e1jA

query
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6e1jA

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binding coenzyme a: Q30 (= Q34), F60 (≠ W64), S63 (≠ A65), I95 (vs. gap), R97 (= R91), F121 (≠ G111), K132 (≠ R122), L133 (= L123), S322 (= S301), G323 (= G302), I324 (≠ V303), D327 (≠ H306), K331 (≠ R310)
binding 4-(methylsulfanyl)-2-oxobutanoic acid: P192 (≠ S182), T194 (= T184), H225 (= H211), H227 (= H213)
binding manganese (ii) ion: D27 (≠ E31), V82 (≠ L84), E84 (vs. gap), H225 (= H211), H227 (= H213)

Sites not aligning to the query:

binding coenzyme a: 359, 362, 363

Q9FG67 Methylthioalkylmalate synthase 1, chloroplastic; 2-isopropylmalate synthase 3; EC 2.3.3.17 from Arabidopsis thaliana (Mouse-ear cress) (see paper)
28% identity, 93% coverage: 22:379/384 of query aligns to 85:448/506 of Q9FG67

query
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Q9FG67

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R

M

V

A

T

V

T

S

V

S

L

I

E

R

H

F

A

A

A

K

H

S

L

L

G

G

F

F

L

N

H

D

V

I

T

Q

L

F

G

G

L

C

E

E

D

D

A

G

G

G

R

R

A

S

A

D

P

K

D

D

L

F

L

L

E

C

A

K

L

I

A

L

R

G

T

E

A

A

A

I

R

K

T

A

G

G

A

V

H

T

R

V

L

V

R

T

C

I

S

G

D

D

T

T

V

V

G

G

L

I

L

N

T

M

P

P

D

H

G

E

M

Y

V

G

R

E

L

L

V

V

L

T

L

Y

A

L

R

K

R

A

A

N

S

T

A

P

-

G

-

I

-

D

L

V

P

V

V

V

A
|
A

V

V

H

H

C

C

H

H

N

N

D

D

L

L

G

G

L

L

A

A

T

T

A

A

N

N

A

S

L

I

A

A

A

G

L

I

D

R

A

A

G

G

A

A

D

R

G

Q

A

V

D

E

V

V

S

T

L

I

L

N

G

G

L

I

G

G

E

E

R

R

A

S

G

G

I

N

T

A

R

S

A

L

E

E

L

V

A

V

A

M

A

A

L

L

-

K

-

C

-

R

-

G

-

A

V

Y

V

V

L

I

R

N

G

G

E

V

S

Y

Y

T

R

K

L

I

D

D

-

T

-

R

M

Q

L

I

R

M

G

A

V

T

C

S

R

K

R

M

L

V

A

Q

A

E

S

Y

L

T

E

G

M

L

R

Y

L

V

P

Q

P

A

H

H

W

K

A

P

V

I

A

V

G

G

E

A

N

N

L

C

F

F

A

V

V

H

E

E

S

S

G

G

V

I

H

H

L

Q

H

D

G

G

V

I

Q

L

R

K

D

N

P

R

A

S

L

T

F

Y

E

E

P

I

F

L

P

S

P

P

A

E

L

D

V

I

G

G

A

I

E

V

R

K

R

-

L

-

G

-

V

-

G

-

K

-

C

-

G

-

S

-

A

-

G

-

V

-

A

-

M

-

A

S

H

Q

S

N

H

S

G

G

L

L

T

V

L

L

Q

-

G

G

D

K

A

L

L

S

R

G

R

R

H

H

V

-

R

-

A

A

V

V

R

K

D

D

K

R

A

L

C

K

S

E

L

L

G

G

R

Y

P

E

L

L

T

D

D

D

A

E

E

K

F

L

S102 (≠ Y39) mutation to F: In gsm1-1; loss of conversion of C3 to C4 glucosinolates.
A290 (= A209) mutation to T: In gsm1-2; loss of conversion of C3 to C4 glucosinolates.

O87198 Homocitrate synthase; HCS; EC 2.3.3.14 from Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27) (see paper)
31% identity, 89% coverage: 24:366/384 of query aligns to 6:358/376 of O87198

query
sites
O87198

L

I

I

I

D

D

S

S

T

T

L

L

R
|
R

E
|
E

G

G

A

E

Q

Q

A

F

Y

E

G

K

V

A

Y

N

F

F

D

S

A

T

A

Q

D

D

R

K

E

V

S

E

I

I

L

A

Q

K

-

A

-

L

-

D

-

E

-

F

G

G

V

I

A

E

A

Y

S

I

G

E

V

V

T

T

E

T

A

P

E

V

A

A

G

S

W

P

A

Q

G

S

Q

R

D

K

D

D

-

A

-

E

L

V

A

L

A

A

T

S

L

L

R

G

L

L

G

K

A

A

R

K

V

V

A

V

P

T

S
x
H

L

I

R

Q

L

-

A

-

V

-

W

-

C

C

R

R

C

L

C

D

T

A

A

A

D

K

L

V

D

-

K

-

A

A

A

V

E

E

A

T

G

G

A

V

R

Q

R

G

V

I

H
x
D

I

L

G

L

V

F

P

G

S

T

S

S

D

K

A

Y

H

-

M

-

R

-

L

L

R

R

L

A

G

A

M

H

G

G

R

R

D

D

-

I

-

P

-

R

-

I

-

E

E

E

V

A

L

K

Q

E

R

V

V

I

T

A

T

Y

V

I

L

R

E

E

H

A

A

A

A

P

H

H

L

V

G

-

F

-

L

-

H

E

V

V

T
x
R

L

F

G
x
S

L

A

E

E

D

D

A

T

G

F

R

R

A

S

A

E

P

E

-

Q

D

D

L

L

-

A

-

V

-

Y

E

E

A

A

L

V

A

A

R

P

T

Y

A

V

A

D

R

R

T

V

G

G

A

-

H

-

R

-

L

-

R

-

C

L

S

A

D

D

T
|
T

V

V

G

G

L

V

L

A

T

T

P

P

D

R

G

Q

M

V

V

Y

R

A

L

L

V

V

L

R

L

E

A

V

R

R

A

V

S

V

A

G

-

P

-

R

L

V

P

D

V

I

A

E

V

F

H
|
H

C

G

H
|
H

N

N

D

D

L

T

G

G

L

C

A

A

T

I

A

A

N

N

A

A

L

Y

A

E

A

A

L

I

D

E

A

A

G

G

A

A

D

T

G

H

A

V

D

D

V

T

S

T

L

I

L

L

G

G

L

I

G

G

E

E

R

R

A

N

G

G

I

I

T

T

R

P

A

L

E

G

L

F

A

L

A

A

A

R

L

M

V

Y

V

T

L

L

R

Q

G

P

E

E

-

Y

-

V

-

R

S

K

Y

Y

R

K

L

L

D

E

M

M

L

L

R

P

G

E

V

L

C

D

R

R

R

M

L

V

A

A

A

R

S

M

L

V

E

G

M

V

R

E

L

I

P

P

P

F

H

N

W

N

A

Y

V

I

A

T

G

G

E

E

N

T

L

A

F

F

A

S

V

H

E

K

S

A

G

G

V

M

H

H

L

L

H

K

G

A

V

I

Q

Y

R

I

D

N

P

P

A

E

L

A

F

Y

E

E

P

P

F

Y

P

P

A

E

L

V

V

F

G

G

A

V

E

K

R

R

R

K

L

L

G

I

V

I

G

A

G

S

K

R

-

L

C

T

G

G

S

R

A

H

G

A

V

I

A

K

A

A

M

R

A

A

H

E

S

E

H

L

G

G

L

L

T

H

L

Y

Q

G

G

E

D

E

A

E

L

L

R

H

R

R

-

V

-

T

-

Q

H

H

V

I

R

K

A

A

V

L

R

A

D

D

K

R

R12 (= R30) binding
E13 (= E31) binding
H72 (≠ S83) binding ; mutation to L: Significant decrease in sensitivity to lysine inhibition. Large decrease in affinity for 2-oxoglutarate. Almost no effect on affinity for acetyl-CoA and on turnover number.
D92 (≠ H109) binding
R133 (≠ T150) binding
S135 (≠ G152) binding
T166 (= T184) binding ; binding
H195 (= H211) binding
H197 (= H213) binding

3ivtB Homocitrate synthase lys4 bound to 2-og (see paper)
29% identity, 81% coverage: 24:334/384 of query aligns to 32:346/400 of 3ivtB

query
sites
3ivtB

L

I

I

I

D

E

S

S

T

T

L

L

R
|
R

E
|
E

G

G

A

E

Q
|
Q

A

F

Y

A

G

N

V

A

Y

F

F

F

D

D

A

T

A

E

D

K

R

K

E

I

S

Q

I

I

L

A

Q

K

G

A

V

L

A

D

A

N

S

F

G

G

V

V

T

D

E

Y

A

I

E

E

-

L

-

T

-

S

-

P

-

V

A

A

G

S

W

E

A

Q

G

S

Q

R

D

Q

D

D

L

C

A

E

A

A

T

I

L

C

R

K

L

L

G

G

A

L

R

K

V

C

A

-

P

-

S

-

L

-

R

K

L

I

A

L

V

T

W
x
H

C

I

R

R

C

C

C

H

T

M

A

D

D

D

L

A

D

R

K

V

A

A

A

V

E

E

A

T

G

G

A

V

R

D

R

G

V

V

H

D

I

V

G

V

V

I

P

G

S

T

S

S

D

Q

A

Y

H

L

M

R

R

K

L

Y

R

S

L

H

G

G

M

K

G

D

R

M

D

T

E

Y

V

I

L

I

Q

D

R

S

V

A

T

T

T

E

V

V

L

I

E

N

H

F

A

V

A

K

H

S

L

K

G

G

F

-

L

I

H

E

V

V

T
x
R

L

F

G
x
S

L

S

E

E

D

D

A

S

G

F

R

R

A

S

A

D

P

L

D

V

L

D

L

L

E

L

A

S

L

L

A

Y

R

K

T

A

A

V

A

D

R

K

T

I

G

G

A

V

H

N

R

R

L

V

R

G

C

I

S

A

D

D

T
|
T

V

V

G

G

L

C

L

A

T

T

P

P

D

R

G

Q

M

V

V

Y

R

D

L

L

V

I

L

R

L

T

A

L

R

R

R

G

A

V

S

V

A

S

L

C

P

D

V

I

A

E

V

C

H
|
H

C

F

H
|
H

N

N

D

D

L

T

G

G

L

M

A

A

T

I

A

A

N

N

A

A

L

Y

A

C

A

A

L

L

D

E

A

A

G

G

A

A

D

T

G

H

A

I

D

D

V

T

S

S

L

I

L

L

G

G

L

I

G

G

E

E

R

R

A

N

G

G

I

I

T

T

R

P

A

L

E

G

E

A

L

L

A

L

A

A

A

R

L

M

V

Y

V

V

L

T

R

D

G

R

E

E

-

Y

-

I

-

T

-

H

S

K

Y

Y

R

K

L

L

D

N

M

Q

L

L

R

R

G

E

V

L

C

E

R

N

R

L

L

V

A

A

A

D

S

A

L

V

E

E

M

V

R

Q

L

I

P

P

P

F

H

N

W

N

A

Y

V

I

A

T

G

G

E

M

N

C

L

A

F

F

A

T

V

H

E

K

S

A

G

G

V

I

H

H

L

A

H

K

G

A

V

I

Q

L

R

A

D

N

P

P

A

S

L

T

F

Y

E

E

P

I

F

L

P

K

P

P

A

E

L

D

V

F

G

G

A

M

E

S

R

R

R

Y

L

V

G

H

V

V

G

G

G

S

K

R

active site: Q42 (= Q34)
binding 2-oxoglutaric acid: R38 (= R30), H98 (≠ W89), R158 (≠ T150), S160 (≠ G152), T192 (= T184), H219 (= H211), H221 (= H213)
binding zinc ion: E39 (= E31), H219 (= H211), H221 (= H213)

Q9Y823 Homocitrate synthase, mitochondrial; HCS; EC 2.3.3.14 from Schizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast) (see 2 papers)
29% identity, 81% coverage: 24:334/384 of query aligns to 37:351/418 of Q9Y823

query
sites
Q9Y823

L

I

I

I

D

E

S

S

T

T

L

L

R
|
R

E
|
E

G

G

A

E

Q
|
Q

A

F

Y

A

G

N

V

A

Y

F

F

F

D

D

A

T

A

E

D

K

R

K

E

I

S

Q

I

I

L

A

Q

K

G

A

V

L

A

D

A

N

S

F

G

G

V

V

T

D

E

Y

A

I

E
|
E

-

L

-

T

-

S

-

P

-

V

A

A

G

S

W

E

A

Q

G

S

Q

R

D

Q

D

D

L

C

A

E

A

A

T

I

L

C

R

K

L

L

G

G

A

L

R

K

V

C

A

-

P

-

S

-

L

-

R

K

L

I

A

L

V

T

W
x
H

C

I

R

R

C

C

C

H

T

M

A

D

D

D

L

A

D

R

K

V

A

A

A

V

E

E

A

T

G

G

A

V

R

D

R

G

V

V

H
x
D

I

V

G

V

V

I

P

G

S

T

S

S

D

Q

A

Y

H

L

M

R

R

K

L

Y

R

S

L

H

G

G

M

K

G

D

R

M

D

T

E

Y

V

I

L

I

Q

D

R

S

V

A

T

T

T

E

V

V

L

I

E

N

H

F

A

V

A

K

H

S

L

K

G

G

F

-

L

I

H

E

V

V

T
x
R

L

F

G
x
S

L

S

E
|
E

D

D

A

S

G

F

R

R

A

S

A

D

P

L

D

V

L

D

L

L

E

L

A

S

L

L

A

Y

R

K

T

A

A

V

A

D

R

K

T

I

G

G

A

V

H

N

R

R

L

V

R

G

C

I

S

A

D

D

T
|
T

V

V

G

G

L

C

L

A

T

T

P

P

D

R

G

Q

M

V

V

Y

R

D

L

L

V

I

L

R

L

T

A

L

R

R

R

G

A

V

S

V

A

S

L

C

P

D

V

I

A
x
E

V

C

H
|
H

C

F

H
|
H

N

N

D

D

L

T

G

G

L

M

A

A

T

I

A

A

N

N

A

A

L

Y

A

C

A

A

L

L

D

E

A

A

G

G

A

A

D

T

G

H

A

I

D

D

V

T

S

S

L

I

L

L

G

G

L

I

G

G

E

E

R

R

A

N

G

G

I

I

T

T

R

P

A

L

E

G

E

A

L

L

A

L

A

A

A

R

L

M

V

Y

V

V

L

T

R

D

G

R

E

E

-

Y

-

I

-

T

-

H

S

K

Y

Y

R

K

L

L

D

N

M

Q

L

L

R
|
R

G

E

V

L

C

E

R

N

R

L

L

V

A

A

A

D

S

A

L

V

E

E

M

V

R

Q

L

I

P

P

P

F

H

N

W

N

A

Y

V

I

A

T

G

G

E

M

N

C

L

A

F

F

A

T

V

H

E

K

S

A

G

G

V

I

H

H

L

A

H

K

G

A

V

I

Q

L

R

A

D

N

P

P

A

S

L

T

F
x
Y

E

E

P

I

F

L

P

K

P

P

A

E

L

D

V

F

G

G

A

M

E

S

R

R

R

Y

L

V

G

H

V

V

G

G

G

S

K

R

R43 (= R30) binding ; mutation R->A,K,Q: Abolishes the catalytic activity.
E44 (= E31) binding ; binding ; binding
Q47 (= Q34) mutation to A: Abolishes the catalytic activity.
E74 (= E61) mutation to A: Abolishes the catalytic activity.; mutation to Q: Results in a moderate decrease in the turnover number and a slight increase in the Km value for each substrate.
H103 (≠ W89) binding ; mutation to A: Substantially impairs catalytic efficiency.
D123 (≠ H109) binding ; mutation to N: Does not affect the catalytic activity but impairs L-lysine inhibition.
R163 (≠ T150) binding ; mutation R->A,Q: Abolishes the catalytic activity.; mutation to K: Severely diminishes affinity for 2-oxoglutarate and substantially impairs catalytic efficiency.
S165 (≠ G152) binding ; mutation to A: Results in a moderate decrease in catalytic efficiency.
E167 (= E154) mutation E->A,Q: Abolishes the catalytic activity.
T197 (= T184) binding ; binding ; mutation to A: Exhibits a 25-fold decrease in catalytic efficiency.; mutation to S: Results in a modest decrease in catalytic efficiency.; mutation to V: Abolishes the catalytic activity.
E222 (≠ A209) mutation to Q: Does not affect the catalytic activity but impairs L-lysine inhibition.
H224 (= H211) binding ; binding
H226 (= H213) binding ; binding
R288 (= R271) mutation to K: Does not affect the catalytic activity but impairs L-lysine inhibition.
Y332 (≠ F315) mutation to A: Abolishes the catalytic activity.; mutation to F: Results in a decrease in catalytic efficiency.

Sites not aligning to the query:

364 Q→R: Does not affect the catalytic activity but impairs L-lysine inhibition.

3ivsA Homocitrate synthase lys4 (see paper)
28% identity, 88% coverage: 24:361/384 of query aligns to 14:343/364 of 3ivsA

query
sites
3ivsA

L

I

I

I

D

E

S

S

T

T

L

L

R

R

E
|
E

G

G

A

E

Q
|
Q

A

F

Y

A

G

N

V

A

Y

F

F

F

D

D

A

T

A

E

D

K

R

K

E

I

S

Q

I

I

L

A

Q

K

G

A

V

L

A

D

A

N

S

F

G

G

V

V

T

D

E

Y

A

I

E

E

-

L

-

T

-

S

-

P

-

V

A

A

G

S

W

E

A

Q

G

S

Q

R

D

Q

D

D

L

C

A

E

A

A

T

I

L

C

R

K

L

L

G

G

A

L

R

K

V

C

A

-

P

-

S

-

L

-

R

K

L

I

A

L

V

T

W

H

C

I

R

R

C

C

C

H

T

M

A

D

D

D

L

A

D

R

K

V

A

A

A

V

E

E

A

T

G

G

A

V

R

D

R

G

V

V

H

D

I

V

G

V

V

I

P

-

S

-

D

-

A

-

H

-

M

-

R

-

L

-

R

-

L

-

G

-

M

-

G

G

R

T

D

T

E

Y

V

I

L

I

Q

D

R

S

V

A

T

T

T

E

V

V

L

I

E

N

H

F

A

V

A

K

H

S

L

K

G

G

F

-

L

I

H

E

V

V

T

R

L

F

G

S

L

S

E

E

D

D

A

S

G

F

R

R

A

S

A

D

P

L

D

V

L

D

L

L

E

L

A

S

L

L

A

Y

R

K

T

A

A

V

A

D

R

K

T

I

G

G

A

V

H

N

R

R

L

V

R

G

C

I

S

A

D

D

T

T

V

V

G

G

L

C

L

A

T

T

P

P

D

R

G

Q

M

V

V

Y

R

D

L

L

V

I

L

R

L

T

A

L

R

R

R

G

A

V

S

V

A

S

L

C

P

D

V

I

A

E

V

C

H
|
H

C

F

H
|
H

N

N

D

D

L

T

G

G

L

M

A

A

T

I

A

A

N

N

A

A

L

Y

A

C

A

A

L

L

D

E

A

A

G

G

A

A

D

T

G

H

A

I

D

D

V

T

S

S

L

I

L

L

G

G

L

I

G

G

E

E

R

R

A

N

G

G

I

I

T

T

R

P

A

L

E

G

E

A

L

L

A

L

A

A

A

R

L

M

V

Y

V

V

L

T

R

D

G

R

E

E

-

Y

-

I

-

T

-

H

S

K

Y

Y

R

K

L

L

D

N

M

Q

L

L

R

R

G

E

V

L

C

E

R

N

R

L

L

V

A

A

A

D

S

A

L

V

E

E

M

V

R

Q

L

I

P

P

P

F

H

N

W

N

A

Y

V

I

A

T

G

G

E

M

N

C

L

A

F

F

A

T

V

H

E

K

S

A

G

G

V

I

H

H

L

A

H

K

G

A

V

I

Q

L

R

A

D

N

P

P

A

S

L

T

F

Y

E

E

P

I

F

L

P

K

P

P

A

E

L

D

V

F

G

G

A

M

E

S

R

R

R

Y

L

V

G

H

V

V

G

G

G

S

K

R

-

L

C

T

G

G

S

W

A

N

G

A

V

I

A

K

A

S

M

R

A

A

H

E

S

Q

H

L

G

N

L

L

T

H

L

L

Q

Q

G

A

D

K

A

E

L

L

R

T

R

V

H

R

V

I

R

K

active site: Q24 (= Q34)
binding cobalt (ii) ion: E21 (= E31), H188 (= H211), H190 (= H213)

3mi3A Homocitrate synthase lys4 bound to lysine (see paper)
29% identity, 81% coverage: 24:334/384 of query aligns to 14:317/370 of 3mi3A

query
sites
3mi3A

L

I

I

I

D

E

S

S

T

T

L

L

R
|
R

E
|
E

G

G

A

E

Q
|
Q

A

F

Y

A

G

N

V

A

Y

F

F

F

D

D

A

T

A

E

D

K

R

K

E

I

S

Q

I

I

L

A

Q

K

G

A

V

L

A

D

A

N

S

F

G

G

V

V

T

D

E

Y

A

I

E

E

-

L

-

T

-

S

-

P

-

V

A

A

G

S

W

E

A

Q

G

S

Q

R

D

Q

D

D

L

C

A

E

A

A

T

I

L

C

R

K

L

L

G

G

A

L

R

K

V

C

A

-

P

-

S

-

L

-

R

K

L

I

A

L

V

T

W

H

C

I

R

R

C

C

C

H

T

M

A

D

D

D

L

A

D

R

K

V

A

A

A

V

E

E

A

T

G

G

A

V

R

D

R

G

V

V

H
x
D

I

V

G

V

V

I

P

G

S

T

S

S

D

M

A

T

H

Y

M

-

R

-

L

-

R

-

L

-

G

-

M

-

G

-

R

-

D

-

E

-

V

I

L

I

Q

D

R

S

V

A

T

T

T

E

V

V

L

I

E

N

H

F

A

V

A

K

H

S

L

K

G

G

F

-

L

I

H

E

V

V

T

R

L

F

G

S

L

S

E

E

D

D

A

S

G

F

R

R

A

S

A

D

P

L

D

V

L

D

L

L

E

L

A

S

L

L

A

Y

R

K

T

A

A

V

A

D

R

K

T

I

G

G

A

V

H

N

R

R

L

V

R

G

C

I

S

A

D

D

T
|
T

V

V

G

G

L

C

L

A

T

T

P

P

D

R

G

Q

M

V

V

Y

R

D

L

L

V

I

L

R

L

T

A

L

R

R

R

G

A

V

S

V

A

S

L

C

P

D

V

I

A

E

V

C

H
|
H

C

F

H
|
H

N

N

D

D

L

T

G

G

L

M

A

A

T

I

A

A

N

N

A

A

L

Y

A

C

A

A

L

L

D

E

A

A

G

G

A

A

D

T

G

H

A

I

D

D

V

T

S

S

L

I

L

L

G

G

L

I

G

G

E

E

R

R

A

N

G

G

I

I

T

T

R

P

A

L

E

G

E

A

L

L

A

L

A

A

A

R

L

M

V

Y

V

V

L

T

R

D

G

R

E

E

-

Y

-

I

-

T

-

H

S

K

Y

Y

R

K

L

L

D

N

M

Q

L

L

R

R

G

E

V

L

C

E

R

N

R

L

L

V

A

A

A

D

S

A

L

V

E

E

M

V

R

Q

L

I

P

P

P

F

H

N

W

N

A

Y

V

I

A

T

G

G

E

M

N

C

L

A

F

F

A

T

V

H

E

K

S

A

G

G

V

I

H

H

L

A

H

K

G

A

V

I

Q

L

R

A

D

N

P

P

A

S

L

T

F

Y

E

E

P

I

F

L

P

K

P

P

A

E

L

D

V

F

G

G

A

M

E

S

R

R

R

Y

L

V

G

H

V

V

G

G

G

S

K

R

active site: Q24 (= Q34)
binding lysine: R20 (= R30), D100 (≠ H109), T163 (= T184), H190 (= H211), H192 (= H213)
binding zinc ion: E21 (= E31), H190 (= H211), H192 (= H213)

2ztjA Crystal structure of homocitrate synthase from thermus thermophilus complexed with alpha-ketoglutarate (see paper)
33% identity, 80% coverage: 24:329/384 of query aligns to 6:309/312 of 2ztjA

query
sites
2ztjA

L

I

I

I

D

D

S

S

T

T

L

L

R
|
R

E
|
E

G

G

A

E

Q
|
Q

A

F

Y

E

G

K

V

A

Y

N

F

F

D

S

A

T

A

Q

D

D

R

K

E

V

S

E

I

I

L

A

Q

K

-

A

-

L

-

D

-

E

-

F

G

G

V

I

A

E

A

Y

S

I

G

E

V

V

T

T

E

T

A

P

E

V

A

A

G

S

W

P

A

Q

G

S

Q

R

D

K

D

D

-

A

-

E

L

V

A

L

A

A

T

S

L

L

R

G

L

L

G

K

A

A

R

K

V

V

A

V

P

T

S
x
H

L

I

R

Q

L

-

A

-

V

-

W

-

C

C

R

R

C

-

T

-

A

-

D

-

L

L

D

D

K

A

A

A

A

K

E

V

A

A

G

-

A

-

R

-

V

V

H

E

I

T

G

G

V

V

P

Q

S

G

S

I

D

D

A

-

H

-

M

-

R

-

L

L

R
x
L

L

F

G

G

M

T

G

G

R

R

D

D

-

I

-

P

-

R

-

I

-

E

E

E

V

A

L

K

Q

E

R

V

V

I

T

A

T

Y

V

I

L

R

E

E

H

A

A

A

A

P

H

H

L

V

G

-

F

-

L

-

H

E

V

V

T
x
R

L

F

G

S

L

A

E

E

D

D

A

T

G

F

R

R

A

S

A

E

P

E

-

Q

D

D

L

L

-

A

-

V

-

Y

E

E

A

A

L

V

A

A

R

P

T

Y

A

V

A

D

R

R

T

V

G

G

A

-

H

-

R

-

L

-

R

-

C

L

S
x
A

D

D

T
|
T

V

V

G

G

L

V

L

A

T

T

P

P

D

R

G

Q

M

V

V

Y

R

A

L

L

V

V

L

R

L

E

A

V

R

R

A

V

S

V

A

G

-

P

-

R

L

V

P

D

V

I

A

E

V

F

H
|
H

C

G

H
|
H

N

N

D

D

L

T

G

G

L

C

A

A

T

I

A

A

N

N

A

A

L

Y

A

E

A

A

L

I

D

E

A

A

G

G

A

A

D

T

G

H

A

V

D

D

V

T

S

T

L

I

L

L

G

G

L

I

G

G

E

E

R

R

A

N

G

G

I

I

T

T

R

P

A

L

E

G

L

F

A

L

A

A

A

R

L

M

V

Y

V

T

L

L

R

Q

G

P

E

E

-

Y

-

V

-

R

S

K

Y

Y

R

K

L

L

D

E

M

M

L

L

R

P

G

E

V

L

C

D

R

R

R

M

L

V

A

A

A

R

S

M

L

V

E

G

M

V

R

E

L

I

P

P

P

F

H

N

W

N

A

Y

V

I

A

T

G

G

E

E

N

T

L

A

F

F

A

S

V

H

E

K

S

A

G

G

V

M

H

H

L

L

H

K

G

A

V

I

Q

Y

R

I

D

N

P

P

A

E

L

A

F

Y

E

E

P

P

F

Y

P

P

A

E

L

V

V

F

G

G

A

V

E

K

R

R

R

K

L

L

active site: Q16 (= Q34)
binding 2-oxoglutaric acid: R12 (= R30), H72 (≠ S83), L94 (≠ R122), R125 (≠ T150), A156 (≠ S182), T158 (= T184), H187 (= H211), H189 (= H213)
binding copper (ii) ion: E13 (= E31), H187 (= H211), H189 (= H213)

2zyfA Crystal structure of homocitrate synthase from thermus thermophilus complexed with magnesuim ion and alpha-ketoglutarate (see paper)
32% identity, 80% coverage: 24:329/384 of query aligns to 6:311/314 of 2zyfA

query
sites
2zyfA

L

I

I

I

D

D

S

S

T

T

L

L

R
|
R

E
|
E

G

G

A

E

Q
|
Q

A

F

Y

E

G

K

V

A

Y

N

F

F

D

S

A

T

A

Q

D

D

R

K

E

V

S

E

I

I

L

A

Q

K

-

A

-

L

-

D

-

E

-

F

G

G

V

I

A

E

A

Y

S

I

G

E

V

V

T

T

E

T

A

P

E

V

A

A

G

S

W

P

A

Q

G

S

Q

R

D

K

D

D

-

A

-

E

L

V

A

L

A

A

T

S

L

L

R

G

L

L

G

K

A

A

R

K

V

V

A

V

P

T

S
x
H

L

I

R

Q

L

-

A

-

V

-

W

-

C

C

R

R

C

L

C

D

T

A

A

A

D

K

L

V

D

-

K

-

A

A

A

V

E

E

A

T

G

G

A

V

R

Q

R

G

V

I

H

D

I

L

G
x
L

V

F

P

G

S

T

S

S

D

K

A

G

H

R

M

D

R

I

L

P

R

R

L

I

G

-

M

-

G

-

R

I

D

E

E

E

V

A

L

K

Q

E

R

V

V

I

T

A

T

Y

V

I

L

R

E

E

H

A

A

A

A

P

H

H

L

V

G

-

F

-

L

-

H

E

V

V

T
x
R

L

F

G

S

L

A

E

E

D

D

A

T

G

F

R

R

A

S

A

E

P

E

-

Q

D

D

L

L

-

A

-

V

-

Y

E

E

A

A

L

V

A

A

R

P

T

Y

A

V

A

D

R

R

T

V

G

G

A

-

H

-

R

-

L

-

R

-

C

L

S

A

D

D

T
|
T

V

V

G

G

L

V

L

A

T

T

P

P

D

R

G

Q

M

V

V

Y

R

A

L

L

V

V

L

R

L

E

A

V

R

R

A

V

S

V

A

G

-

P

-

R

L

V

P

D

V

I

A

E

V

F

H
|
H

C

G

H
|
H

N

N

D

D

L

T

G

G

L

C

A

A

T

I

A

A

N

N

A

A

L

Y

A

E

A

A

L

I

D

E

A

A

G

G

A

A

D

T

G

H

A

V

D

D

V

T

S

T

L

I

L

L

G

G

L

I

G

G

E

E

R

R

A

N

G

G

I

I

T

T

R

P

A

L

E

G

L

F

A

L

A

A

A

R

L

M

V

Y

V

T

L

L

R

Q

G

P

E

E

-

Y

-

V

-

R

S

K

Y

Y

R

K

L

L

D

E

M

M

L

L

R

P

G

E

V

L

C

D

R

R

R

M

L

V

A

A

A

R

S

M

L

V

E

G

M

V

R

E

L

I

P

P

P

F

H

N

W

N

A

Y

V

I

A

T

G

G

E

E

N

T

L

A

F

F

A

S

V

H

E

K

S

A

G

G

V

M

H

H

L

L

H

K

G

A

V

I

Q

Y

R

I

D

N

P

P

A

E

L

A

F

Y

E

E

P

P

F

Y

P

P

A

E

L

V

V

F

G

G

A

V

E

K

R

R

R

K

L

L

active site: Q16 (= Q34)
binding 2-oxoglutaric acid: R12 (= R30), H72 (≠ S83), L94 (≠ G111), R127 (≠ T150), T160 (= T184), H189 (= H211)
binding magnesium ion: E13 (= E31), H189 (= H211), H191 (= H213)

Q9JZG1 2-isopropylmalate synthase; Alpha-IPM synthase; Alpha-isopropylmalate synthase; EC 2.3.3.13 from Neisseria meningitidis serogroup B (strain MC58) (see 2 papers)
30% identity, 87% coverage: 22:354/384 of query aligns to 7:353/517 of Q9JZG1

query
sites
Q9JZG1

V

V

M

I

L

I

I

F

D

D

S

T

T

T

L

L

R

R

E
x
D

G

G

A

E

Q

Q

A

S

Y

P

G

G

V

A

Y

A

F

M

D

T

A

K

A

E

D

E

R

K

E

I

S

R

I

V

L

A

Q

R

G

Q

V

L

A

E

A

K

S

L

G

G

V

V

T

D

E

I

A

I

E

E

A

A

G

G

W

F

A

A

G

A

Q

A

D

S

-

P

-

G

D

D

L

F

A

E

A

A

T

V

L

N

R

A

L

I

G

A

A

K

R

T

V

I

A

T

P

K

S

S

L

T

R

-

L

V

A

C

V

S

W

L

C

S

R

R

C

A

C

I

T

E

A

R

D

D

L

I

D

R

K

Q

A

A

A

G

E

E

A

A

G

V

A

A

-

P

-

A

-

P

-

K

R

K

R

R

V

I

H

H

I

T

G

F

V

I

P

A

S

T

S

S

D

P

A

I

H

H

M

M

R

E

L

Y

R

K

L

L

G

K

M

M

G

K

R

P

D

K

E

Q

V

V

L

I

Q

E

R

A

V

A

T

V

T

K

V

A

L

V

E

K

H

I

A

A

A

R

H

E

L

Y

G

T

F

-

L

D

H

D

V

V

T

E

L

F

G

S

L

C

E

E

D

D

A

A

G

L

R

R

A

S

A

E

P

I

D

D

L

F

L

L

E

A

A

E

L

I

A

C

R

G

T

A

A

V

A

I

R

E

T

A

G

G

A

A

H

T

R

T

L

I

R

N

C

I

S

P

D

D

T

T

V

V

G

G

L

Y

L

S

T

I

P

P

D

Y

G

K

M

T

V

E

R

E

L

F

V

F

-

R

-

E

L

L

L

I

A

A

R

K

R

T

A

P

S

N

A

G

L

G

P

K

V

V

-

V

-

W

A

S

V

A

H
|
H

C

C

H
|
H

N

N

D

D

L

L

G

G

L

L

A

A

T

V

A

A

N

N

A

S

L

L

A

A

L

L

D

K

A

G

G

G

A

A

D

R

G

Q

A

V

D

E

V

C

S

T

L

V

L

N

G

G

L

L

G

G

E

E

R

R

A

A

G

G

I
x
N

T

A

R

S

A

V

E

E

L

I

A

V

A

M

A

A

L

L

V

K

V

V

-

R

-

H

-

D

L

L

R

F

G

G

E

L

S

E

Y

T

R

G

L

I

D

D

M

T

L

T

R

Q

G

I

V

V

-

P

C

S

R

S

R

K

L

L

A

V

A

S

S

T

L

I

E

T

-

G

M

Y

R

P

L

V

P

Q

P

P

H

N

W

K

A

A

V

I

A

V

G

G

E

A

N

N

L

A

F

F

A

S

V

H

E

E

S

S

G

G

V

I

H

H

L

Q

H

D

G

G

V

V

Q

L

R

K

D

H

P

R

A

E

L

T

F

Y

E

E

P

I

F

M

P

S

P

A

A

E

L

S

V

V

G

G

-

W

A

A

E

T

R

N

R

R

L

L

G

S

V

L

G

G

G

K

K

L

C

S

G

G

S

R

A

N

G

A

V

F

A

K

A

T

M

K

A

L

H

A

S

D

H

L

G

G

L

I

T

E

L

L

Q

E

G

S

D

E

D16 (≠ E31) binding
H204 (= H211) binding
H206 (= H213) binding
N240 (≠ I247) binding

Sites not aligning to the query:

366:517 Required for the condensation reaction. Not required to bind substrate

3a9iA Crystal structure of homocitrate synthase from thermus thermophilus complexed with lys (see paper)
31% identity, 79% coverage: 24:326/384 of query aligns to 5:307/347 of 3a9iA

query
sites
3a9iA

L

I

I

I

D

D

S

S

T

T

L

L

R
|
R

E
|
E

G

G

A

E

Q

Q

A

F

Y

E

G

K

V

A

Y

N

F

F

D

S

A

T

A

Q

D

D

R

K

E

V

S

E

I

I

L

A

Q

K

-

A

-

L

-

D

-

E

-

F

G

G

V

I

A

E

A

Y

S

I

G

E

V

V

T

T

E

T

A

P

E

V

A

A

G

S

W

P

A

Q

G

S

Q

R

D

K

D

D

-

A

-

E

L

V

A

L

A

A

T

S

L

L

R

G

L

L

G

K

A

A

R

K

V

V

A

V

P

T

S

H

L

I

R

Q

L

-

A

-

V

-

W

-

C

C

R

R

C

L

C

D

T

A

A

A

D

K

L

V

D

-

K

-

A

A

A

V

E

E

A

T

G

G

A

V

R

Q

R

G

V

I

H
x
D

I

L

G

L

V

F

P

G

S

T

S

S

D

K

A

Y

H

-

M

-

R

-

L

L

R

D

L

I

G

P

M

R

G

I

R

I

D

E

E

E

V

A

L

K

Q

E

R

V

V

I

T

A

T

Y

V

I

L

R

E

E

H

A

A

A

A

P

H

H

L

V

G

-

F

-

L

-

H

E

V

V

T

R

L

F

G
x
S

L

A

E

E

D

D

A

T

G

F

R

R

A

S

A

E

P

E

-

Q

D

D

L

L

-

A

-

V

-

Y

E

E

A

A

L

V

A

A

R

P

T

Y

A

V

A

D

R

R

T

V

G

G

A

-

H

-

R

-

L

-

R

-

C

L

S

A

D

D

T
|
T

V

V

G

G

L

V

L

A

T

T

P

P

D

R

G

Q

M

V

V

Y

R

A

L

L

V

V

L

R

L

E

A

V

R

R

A

V

S

V

A

G

-

P

-

R

L

V

P

D

V

I

A

E

V

F

H
|
H

C

G

H
|
H

N

N

D

D

L

T

G

G

L

C

A

A

T

I

A

A

N

N

A

A

L

Y

A

E

A

A

L

I

D

E

A

A

G

G

A

A

D

T

G

H

A

V

D

D

V

T

S

T

L

I

L

L

G

G

L

I

G

G

E

E

R

R

A

N

G

G

I

I

T

T

R

P

A

L

E

G

L

F

A

L

A

A

A

R

L

M

V

Y

V

T

L

L

R

Q

G

P

E

E

-

Y

-

V

-

R

S

K

Y

Y

R

K

L

L

D

E

M

M

L

L

R

P

G

E

V

L

C

D

R

R

R

M

L

V

A

A

A

R

S

M

L

V

E

G

M

V

R

E

L

I

P

P

P

F

H

N

W

N

A

Y

V

I

A

T

G

G

E

E

N

T

L

A

F

F

A

S

V

H

E

K

S

A

G

G

V

M

H

H

L

L

H

K

G

A

V

I

Q

Y

R

I

D

N

P

P

A

E

L

A

F

Y

E

E

P

P

F

Y

P

P

A

E

L

V

V

F

G

G

A

V

E

K

binding cobalt (ii) ion: E12 (= E31), H188 (= H211), H190 (= H213)
binding lysine: R11 (= R30), D91 (≠ H109), S128 (≠ G152), T159 (= T184), H188 (= H211), H190 (= H213)

Q8F3Q1 (R)-citramalate synthase CimA; LiCMS; EC 2.3.3.21 from Leptospira interrogans serogroup Icterohaemorrhagiae serovar Lai (strain 56601) (see 2 papers)
25% identity, 87% coverage: 24:358/384 of query aligns to 10:356/516 of Q8F3Q1

query
sites
Q8F3Q1

L

I

I

L

D

D

S

V

T

T

L

L

R
|
R

E
x
D

G

G

A

E

Q

Q

A

T

Y

R

G

G

V

V

Y

S

F

F

D

S

A

T

A

S

D

E

R

K

E

L

S

N

I

I

-

A

-

K

-

F

-

L

L

L

Q

Q

G

K

-

L

-

N

-

V

-

D

-

R

-

V

-

E

V

I

A

A

A

S

S

A

G

R

V

V

T

S

E

K

A

G

E

E

-

L

-

E

-

T

-

V

-

Q

-

K

-

I

A

M

G

E

W

W

A

A

G

A

Q

T

D

E

D

Q

L

L

A

T

A

E

T

R

L

I

R

E

L

I

G
x
L

A

G

R
x
F

V

V

A

D

P

G

S

N

L

-

R

K

L

T

A

V

V

D

W

W

C

I

R

K

C

-

T

-

A

-

D

-

L

-

D

-

K

-

A

-

E

D

A

S

G

G

A

A

R

K

R

V

V

L

H

N

I

L

G
x
L

V

T

P

K

S

G

S

S

D

L

A

H

H

H

M

L

R

E

L

K

R

Q

L

L

G

G

M

K

G

T

R

P

D

K

E

E

V

F

L

F

Q

T

R

D

V

V

T

S

T

F

V

V

L

I

E

E

H

Y

A

A

A

I

H

K

L

S

G

G

F

-

L

L

H

K

V

I

T

N

L

V

G
x
Y

L

L

E
|
E

D

D

A

W

G

S

-

N

-

G

-

F

R

R

A

N

A

S

P

P

D

D

L

Y

L

V

E

K

A

S

L

L

A

V

R

E

T

H

A

L

A

S

R

K

T

E

G

H

A

I

H

E

R

R

L

I

R

F

C

L

S

P

D

D

T
|
T

V

L

G

G

L

V

L

L

T

S

P

P

D

E

G

E

M

T

V

F

R

Q

L

G

V

V

-

D

L

S

L

L

A

I

R

Q

R

K

A

Y

S

P

A

D

L

I

P

H

V

F

A

E

V

F

H

H

C

G

H

H

N

N

D

D

L

Y

G

D

L

L

A

S

T

V

A

A

N

N

A

S

L

L

A

Q

A

A

L

I

D

R

A

A

G

G

A

V

D

K

G

G

A

L

D

H

V

A

S

S

L

I

L

N

G

G

L

L

G

G

E

E

R

R

A

A

G

G

I

N

T

T

R

P

A

L

E

E

E

A

L

L

A

V

A

T

L

I

V

H

V

D

L

K

R

S

G

N

E

S

S

K

Y

T

R

N

L

I

D

N

M

E

-

I

-

A

L

I

R

T

G

E

V

A

C

S

R

R

R

L

L

V

A

E

A

V

S

F

L

S

E

G

M

K

R

R

L

I

P

S

P

A

H

N

W

R

A

P

V

I

A

V

G

G

E

E

N

D

L

V

F

F

A

T

V

Q

E

T

S

A

G

G

V

V

H
|
H

L

A

H
x
D

G

G

V

D

Q

K

R

K

D

G

P
x
N

A
x
L

L
x
Y

F

A

E

N

P

P

F

I

P

L

P

P

A

E

L

R

V

F

G

G

A

R

E

K

R

R

R

S

L

Y

G

A

V

L

G

G

G

K

K

L

C

A

G

G

S

K

A

A

G

S

V

I

A

S

A

E

M

N

A

V

H

K

S

Q

H

L

G

G

L

M

T

V

L

L

Q

S

G

E

D

V

A

V

L

L

R

Q

R

K

R16 (= R30) mutation R->K,Q: Loss of activity.
RD 16:17 (≠ RE 30:31) binding
D17 (≠ E31) mutation to A: 34-fold increase in Km for pyruvate and 315-fold decrease in kcat.; mutation to N: 4.4-fold increase in Km for pyruvate and 480-fold decrease in kcat.
L81 (≠ G77) mutation to A: 4.7-fold increase in Km for pyruvate and 15.7-fold decrease in kcat.; mutation to V: 3.3-fold increase in Km for pyruvate and 10.1-fold decrease in kcat.
F83 (≠ R79) mutation to A: 5-fold increase in Km for acetyl-CoA and 120-fold decrease in kcat.
L104 (≠ G111) mutation to V: 1.8-fold increase in Km for pyruvate and 3.4-fold decrease in kcat.
Y144 (≠ G152) binding ; mutation to L: 259-fold increase in Km for pyruvate and 76-fold decrease in kcat.; mutation to V: 114-fold increase in Km for pyruvate and 5.3-fold decrease in kcat.
E146 (= E154) mutation E->D,Q: Minor effects on the binding of acetyl-CoA, but causes a strong decrease in kcat.
T179 (= T184) binding ; mutation to A: 16.4-fold increase in Km for pyruvate and 186-fold decrease in kcat.
H302 (= H304) mutation H->A,N: Loss of activity.
D304 (≠ H306) mutation to A: 5.2-fold increase in Km for acetyl-CoA and 16.6-fold decrease in kcat.
N310 (≠ P312) mutation to A: 2.2-fold increase in Km for acetyl-CoA and 1.7-fold decrease in kcat.
L311 (≠ A313) mutation to A: 8-fold increase in Km for acetyl-CoA and 6-fold decrease in kcat.
Y312 (≠ L314) mutation to A: Loss of activity.

Sites not aligning to the query:

430 Y→L: No change in Km for acetyl-CoA and 2.3-fold decrease in kcat. Severely impairs inhibition by isoleucine.
431 D→A: 1.8-fold decrease in Km for acetyl-CoA and 5-fold decrease in kcat.
451 L→V: 1.5-fold increase in Km for acetyl-CoA and 4.3 decrease in kcat.
454 Y→A: 1.4 decrease in Km for acetyl-CoA and 17-fold decrease in kcat. Still inhibited by isoleucine and weakly inhibited by leucine.
458 I→A: 1.3-fold decrease in Km for acetyl-CoA and 14-fold decrease in kcat. Abolishes inhibition by isoleucine.
464 T→A: 1.8-fold decrease in Km for acetyl-CoA and 4.3-fold decrease in kcat.
468 V→A: No change in Km for acetyl-CoA and 2-fold decrease in kcat. Increases inhibition by isoleucine and leucine becomes an effective inhibitor.
493 P→A: 1.5-fold decrease in Km for acetyl-CoA and 2.6-fold decrease in kcat.
495 Q→A: 1.6-fold decrease in Km for acetyl-CoA and 2.8-fold decrease in kcat.

3rmjB Crystal structure of truncated alpha-isopropylmalate synthase from neisseria meningitidis (see paper)
30% identity, 73% coverage: 22:301/384 of query aligns to 4:296/308 of 3rmjB

query
sites
3rmjB

V

V

M

I

L

I

I

F

D

D

S

T

T

T

L

L

R

R

E
x
D

G

G

A

E

Q
|
Q

A

S

Y

P

G

G

V

A

Y

A

F

M

D

T

A

K

A

E

D

E

R

K

E

I

S

R

I

V

L

A

Q

R

G

Q

V

L

A

E

A

K

S

L

G

G

V

V

T

D

E

I

A

I

E

E

A

A

G

G

W

F

A

A

G

A

Q

A

D

S

-

P

-

G

D

D

L

F

A

E

A

A

T

V

L

N

R

A

L

I

G

A

A

K

R

T

V

I

A

T

P

K

S

S

L

T

R

V

L

C

A

S

V

L

W

-

C

S

R

R

C

A

C

I

T

E

A

R

D

D

L

I

D

R

K

Q

A

A

A

G

E

E

A

A

G

V

A

A

-

P

-

A

-

P

-

K

R

K

R

R

V

I

H

H

I

T

G

F

V

I

P

A

S

T

S

S

D

P

A

I

H

H

M

M

R

E

L

Y

R

K

L

L

G

K

M

M

G

K

R

P

D

K

E

Q

V

V

L

I

Q

E

R

A

V

A

T

V

T

K

V

A

L

V

E

K

H

I

A

A

A

R

H

E

L

Y

G

T

F

-

L

D

H

D

V

V

T

E

L

F

G

S

L

C

E

E

D

D

A

A

G

L

R

R

A

S

A

E

P

I

D

D

L

F

L

L

E

A

A

E

L

I

A

C

R

G

T

A

A

V

A

I

R

E

T

A

G

G

A

A

H

T

R

T

L

I

R

N

C

I

S

P

D

D

T

T

V

V

G

G

L

Y

L

S

T

I

P

P

D

Y

G

K

M

T

V

E

R

E

L

F

V

F

-

R

-

E

L

L

L

I

A

A

R

K

R

T

A

P

S

N

A

G

L

G

P

K

V

V

-

V

-

W

A

S

V

A

H
|
H

C

C

H
|
H

N

N

D

D

L

L

G

G

L

L

A

A

T

V

A

A

N

N

A

S

L

L

A

A

L

L

D

K

A

G

G

G

A

A

D

R

G

Q

A

V

D

E

V

C

S

T

L

V

L

N

G

G

L

L

G

G

E

E

R

R

A

A

G

G

I
x
N

T

A

R

S

A

V

E

E

L

I

A

V

A

M

A

A

L

L

V

K

V

V

-

R

-

H

-

D

L

L

R

F

G

G

E

L

S

E

Y

T

R

G

L

I

D

D

M

T

L

T

R

Q

G

I

V

V

-

P

C

S

R

S

R

K

L

L

A

V

A

S

S

T

L

I

E

T

-

G

M

Y

R

P

L

V

P

Q

P

P

H

N

W

K

A

A

V

I

A

V

G

G

E

A

N

N

L

A

F

F

A

S

V

H

E

E

S

T

active site: Q16 (= Q34)
binding manganese (ii) ion: D13 (≠ E31), H201 (= H211), H203 (= H213), N237 (≠ I247)

4ov4A Isopropylmalate synthase binding with ketoisovalerate (see paper)
25% identity, 94% coverage: 20:381/384 of query aligns to 2:376/379 of 4ov4A

query
sites
4ov4A

R

K

C

T

V

I

M

H

L

I

I

Q

D

D

S

V

T

T

L

L

R
|
R

E
x
D

G

G

A

N

Q
|
Q

A

A

Y

L

G

K

V

R

Y

P

F

W

D

T

A

I

A

D

D

E

R

K

E

I

S

E

I

V

L

F

Q

D

G

L

V

L

A

V

A

E

S

L

G

N

V

V

T

D

E

G

A

I

E

E

A

V

G

G

W

F

A

P

G

S

Q

S

D

N

D

E

L

T

A

E

A

F

-

H

T

T

L

C

R

Q

L

V

G

L

A

S

R

K

V

R

A

A

P

P

S

K

L

G

R

K

-

P

L

I

A

A

V

A

W

L

C

S

R

R

C

A

C

N

T

Q

A

N

D

E

L

I

D

A

K

V

A

T

A

W

E

E

A

A

G

I

A

Q

R

K

-

A

-

D

-

C

-

P

R

R

V

M

H

H

I

I

G

V

V

Y

P

P

S

V

S

S

D

D

A

F

H

S

M

I

R

K

L

H

R

V

L

L

G

K

M

I

G

S

R

E

D

K

E

E

V

V

L

L

Q

Q

R

K

V

I

T

R

T

N

V

S

L

I

E

S

H

F

A

A

A

R

H

S

L

I

G

-

F

-

L

-

H

-

V

V

T

G

L

P

G

G

L

I

E

E

-

I

-

Q

D

F

A

S

G

G

R

E

A

H

A

F

P

G

D

D

L

A

L

I

E

E

A

N

L

F

A

A

R

F

T

T

-

K

-

E

-

A

-

F

-

L

-

T

A

A

A

I

R

E

T

A

G

G

A

A

H

N

R

I

L

I

R

N

C

L

S
x
P

D

N

T
|
T

V

V

G

E

L

R

L

Y

T

R

P

P

D

M

G

V

M

F

V

V

R

N

L

M

V

V

L

K

L

E

A

I

R

K

-

D

-

V

R

K

A

D

S

K

A

A

L

I

P

-

V

I

A

S

V

I

H
|
H

C

T

H
|
H

N

N

D

D

L

L

G

G

L

M

A

A

T

T

A

A

N

T

A

S

L

V

A

E

A

S

L

V

D

Y

A

V

G

G

A

A

D

E

G

Q

A

I

D

E

V

V

S

A

L

L

L

N

G

G

L

L

G

G

E

E

R

R

A

A

G

G

I

N

T

T

R

N

A

L

E

Y

E

E

L

T

A

A

A

I

A

A

L

L

V

-

V

H

L

Q

R

N

G

G

E

E

S

N

Y

L

R

N

L

I

D

N

M

F

L

Q

R

R

-

I

-

Y

G

P

V

T

C

A

R

K

R

R

L

I

A

S

A

E

S

L

L

T

E

G

M

I

R

P

L

I

P

G

P

E

H

K

W

T

A

P

V

I

A

I

G

G

E

E

N

D

L

I

F

F

A

S

V

H

E

R

S

S

G

G

V

I

H

H

L

Q

H

H

G

-

V

-

Q

-

R

Q

D

S

P

K

A

G

L

A

F

Y

E

R

P

T

F

F

P

S

P

P

A

E

L

F

V

V

G

G

-

R

-

M

A

D

E

K

R

E

R

T

L

I

G

S

V

F

G

T

G

N

K

Q

C

S

G

G

S

H

A

K

G

A

V

I

A

E

A

F

M

L

A

L

H

H

S

Q

H

R

G

G

L

I

T

Q

L

V

Q

S

G

K

D

E

A

G

L

I

R

-

R

H

H

H

V

L

R

F

A

S

V

L

R

A

D

K

K

S

A

I

C

S

S

S

-

R

-

E

L

N

G

N

R

R

P

E

L

I

T

T

D

E

A

A

E

E

F

L

L

V

C

A

active site: Q16 (= Q34)
binding 3-methyl-2-oxobutanoic acid: R12 (= R30), P174 (≠ S182), T176 (= T184), H205 (= H211), H207 (= H213)
binding zinc ion: D13 (≠ E31), H205 (= H211), H207 (= H213)

4ov9A Structure of isopropylmalate synthase binding with alpha- isopropylmalate (see paper)
24% identity, 94% coverage: 20:381/384 of query aligns to 2:378/380 of 4ov9A

query
sites
4ov9A

R

K

C

T

V

I

M

H

L

I

I

Q

D

D

S

V

T

T

L

L

R
|
R

E
x
D

G

G

A

N

Q
|
Q

A

A

Y

L

G

K

V

R

Y

P

F

W

D

T

A

I

A

D

D

E

R

K

E

I

S

E

I

V

L

F

Q

D

G

L

V

L

A

V

A

E

S

L

G

N

V

V

T

D

E

G

A

I

E

E

A

V

G

G

W

F

A

P

G

S

Q

S

D

N

D

E

L

T

A

E

A

F

-

H

T

T

L

C

R

Q

L

V

G

L

A

S

R

K

V

R

A

A

P

P

S

K

L

G

R

K

-

P

L

I

A

A

V

A

W
x
L

C

S

R

R

C

A

C

N

T

Q

A

N

D

E

L

I

D

A

K

V

A

T

A

W

E

E

A

A

G

I

A

Q

R

K

-

A

-

D

-

C

-

P

R

R

V

M

H

H

I

I

G

V

V

Y

P

P

S

V

S

S

D

D

A

F

H

S

M

I

R

K

L

H

R

V

L

L

G

K

M

I

G

S

R

E

D

K

E

E

V

V

L

L

Q

Q

R

K

V

I

T

R

T

N

V

S

L

I

E

S

H

F

A

A

A

R

H

S

L

I

G

-

F

-

L

-

H

-

V

V

T

G

L

P

G

G

L

I

E

E

-

I

-

Q

D

F

A

S

G

G

R

E

A

H

A

F

P

G

D

D

L

A

L

I

E

E

A

N

L

F

A

A

R

F

T

T

-

K

-

E

-

A

-

F

-

L

-

T

A

A

A

I

R

E

T

A

G

G

A

A

H

N

R

I

L

I

R

N

C

L

S

P

D

N

T
|
T

V

V

G

E

L

R

L

Y

T

R

P

P

D

M

G

V

M

F

V

V

R

N

L

M

V

V

L

K

L

E

A

I

R

K

-

D

-

V

R

K

A

D

S

K

A

A

L

I

P

-

V

I

A

S

V

I

H
|
H

C

T

H
|
H

N

N

D

D

L

L

G

G

L

M

A

A

T

T

A

A

N

T

A

S

L

V

A

E

A

S

L

V

D

Y

A

V

G

G

A

A

D

E

G

Q

A

I

D

E

V

V

S

A

L

L

L

N

G

G

L

L

G

G

E

E

R

R

A

A

G

G

I

N

T

T

R

N

A

L

E

Y

E

E

L

T

A

A

A

I

A

A

L

L

V

-

V

H

L

Q

R

N

G

G

E

E

S

N

Y

L

R

N

L

I

D

N

M

F

L

Q

R

R

-

I

-

Y

G

P

V

T

C

A

R

K

R

R

L

I

A

S

A

E

S

L

L

T

E

G

M

I

R

P

L

I

P

G

P

E

H

K

W

T

A

P

V

I

A

I

G

G

E

E

N

D

L

I

F

F

A

S

V

H

E

R

S

S

G

G

V

I

H

H

L

-

H

Q

G

T

V

L

Q

H

R

Q

D

S

P

K

A

G

L

A

F

Y

E

R

P

T

F

F

P

S

P

P

A

E

L

F

V

V

G

G

-

R

-

M

A

D

E

K

R

E

R

T

L

I

G

S

V

F

G

T

G

N

K

Q

C

S

G

G

S

H

A

K

G

A

V

I

A

E

A

F

M

L

A

L

H

H

S

Q

H

R

G

G

L

I

T

Q

L

V

Q

S

G

K

D

E

A

G

L

I

R

-

R

H

H

H

V

L

R

F

A

S

V

L

R

A

D

K

K

S

A

I

C

S

S

S

-

R

-

E

L

N

G

N

R

R

P

E

L

I

T

T

D

E

A

A

E

E

F

L

L

V

C

A

active site: Q16 (= Q34)
binding (2S)-2-hydroxy-2-(propan-2-yl)butanedioic acid: R12 (= R30), L73 (≠ W89), T176 (= T184), H205 (= H211), H207 (= H213)
binding zinc ion: D13 (≠ E31), H205 (= H211), H207 (= H213)

3bliA Crystal structure of the catalytic domain of licms in complexed with pyruvate and acetyl-coa (see paper)
26% identity, 77% coverage: 24:318/384 of query aligns to 4:307/311 of 3bliA

query
sites
3bliA

L

I

I

L

D

D

S

V

T

T

L

L

R
|
R

E
x
D

G

G

A

E

Q
|
Q

A

T

Y

R

G

G

V

V

Y

S

F

F

D

S

A

T

A

S

D

E

R

K

E

L

S

N

I

I

-

A

-

K

-

F

-

L

L

L

Q

Q

G

K

-

L

-

N

-

V

-

D

-

R

-

V

-

E

V

I

A

A

A

S

S

A

G
x
R

V
|
V

T

S

E

K

A

G

E

E

-

L

-

E

-

T

-

V

-

Q

-

K

-

I

A

M

G

E

W

W

A

A

G

A

Q

T

D

E

D

Q

L

L

A

T

A

E

T

R

L

I

R

E

L

I

G

L

A

G

R

F

V

V

A

D

P

G

S

N

L

-

R

K

L

T

A

V

V

D

W

W

C

I

R

K

C

-

T

-

A

-

D

-

L

-

D

-

K

-

A

-

E

D

A

S

G

G

A

A

R

K

R

V

V

L

H

N

I

L

G

L

V

T

P

K

S

G

S

S

D

L

A

H

H

H

M

L

R

E

L

K

R

Q

L

L

G

G

M

K

G

T

R

P

D

K

E

E

V

F

L

F

Q

T

R

D

V

V

T

S

T

F

V

V

L

I

E

E

H

Y

A

A

A

I

H

K

L

S

G

G

F

-

L

L

H

K

V

I

T

N

L

V

G
x
Y

L

L

E
|
E

D

D

A

W

G

S

-

N

-

G

-

F

R

R

A

N

A

S

P

P

D

D

L

Y

L

V

E

K

A

S

L

L

A

V

R

E

T

H

A

L

A

S

R

K

T

E

G

H

A

I

H

E

R

R

L

I

R

F

C

L

S
x
P

D

D

T
|
T

V

L

G

G

L

V

L

L

T

S

P

P

D

E

G

E

M

T

V

F

R

Q

L

G

V

V

-

D

L

S

L

L

A

I

R

Q

R

K

A

Y

S

P

A

D

L

I

P

H

V

F

A

E

V

F

H
|
H

C

G

H
|
H

N

N

D

D

L

Y

G

D

L

L

A

S

T

V

A

A

N

N

A

S

L

L

A

Q

A

A

L

I

D

R

A

A

G

G

A

V

D

K

G

G

A

L

D

H

V

A

S

S

L

I

L

N

G

G

L

L

G

G

E

E

R

R

A

A

G

G

I

N

T

T

R

P

A

L

E

E

E

A

L

L

A

V

A

T

L

I

V

H

V

D

L

K

R

S

G

N

E

S

S

K

Y

T

R

N

L

I

D

N

M

E

-

I

-

A

L

I

R

T

G

E

V

A

C

S

R

R

R

L

L

V

A

E

A

V

S

F

L

S

E

G

M

K

R

R

L

I

P

S

P

A

H

N

W

R

A

P

V

I

A

V

G

G

E

E

N

D

L

V

F

F

A

T

V

Q

E

T

S

A

G

G

V

V

H

N

L

L

H

Y

G

A

V

-

Q

-

R

-

D

N

P

P

A

I

L

L

F

P

E

E

P

R

F

F

active site: Q14 (= Q34)
binding acetyl coenzyme *a: Q14 (= Q34), R47 (≠ G56), V48 (= V57), E140 (= E154)
binding pyruvic acid: R10 (= R30), Y138 (≠ G152), P171 (≠ S182), T173 (= T184)
binding zinc ion: D11 (≠ E31), H201 (= H211), H203 (= H213)

P13703 Hydroxymethylglutaryl-CoA lyase; HL; HMG-CoA lyase; 3-hydroxy-3-methylglutarate-CoA lyase; EC 4.1.3.4 from Pseudomonas mevalonii (see paper)
33% identity, 38% coverage: 97:242/384 of query aligns to 84:235/301 of P13703

query
sites
P13703

L

F

D

E

K

A

A

A

A

Q

E

R

A

A

G

G

A

C

R

R

R

E

V

V

H

A

I

V

G

F

V

A

P

A

S

A

S

S

D

E

A

A

H

F

M

S

R

R

L

N

R

N

L

I

G

N

M

C

G

S

R

I

D

D

E

E

V

S

L

F

Q

E

R

R

V

F

T

T

T

P

V

V

L

L

E

R

H

A

A

A

A

N

H

E

L

A

-

S

-

I

-

R

-

V

-

R

G

G

F

Y

L

V

H

S

V

C

T

V

L

L

G

G

L

C

E

P

D

F

A

S

G

G

R

A

A

V

A

A

P

P

D

E

L

A

L

V

E

A

A

K

L

V

A

A

R

R

T

R

A

L

A

Y

R

E

T

L

G

G

A

C

H

Y

R

E

L

I

R

S

C

L

S

G

D

D

T

T

V

I

G

G

L

A

L

G

T

R

P

P

D

D

G

E

M

T

V

A

R

Q

L

L

V

F

L

E

L

L

A

C

R

A

R

R

A

-

S

-

A

Q

L

L

P

P

V

V

A

A

V

A

-

L

-

A

-

G

H

H

C

F

H

H

N

D

D

T

L

W

G

G

L

M

A

A

T

I

A

A

N

N

A

V

L

H

A

A

L

L

D

A

A

Q

G

G

A

V

D

R

G

T

A

F

D

D

V

S

S

S

L

V

L

A

G

G

L

L

G

G

Sites not aligning to the query:

237 active site

P35914 Hydroxymethylglutaryl-CoA lyase, mitochondrial; HL; HMG-CoA lyase; 3-hydroxy-3-methylglutarate-CoA lyase; EC 4.1.3.4 from Homo sapiens (Human) (see 11 papers)
25% identity, 63% coverage: 2:242/384 of query aligns to 7:264/325 of P35914

query
sites
P35914

A

A

W

L

R

P

R

R

H

L

V

V

G

G

L

L

A

A

S

S

-

L

-

R

-

A

-

V

-

S

-

T

G

S

L

S

Q

M

G

G

H

T

L

L

R

P

R

K

C

R

V

V

M

K

L

I

I

V

D
x
E

S

V

T

G

L

P

R
|
R

E
x
D

G

G

A

L

Q

Q

A

N

Y

E

G
x
K

V

N

Y

I

F

V

D

S

A

T

A

P

D

V

R

K

E

I

S

K

I

L

L

I

Q

D

G

M

V

L

A

S

A

E

S

A

G

G

V

L

T

S

E

V

A

I

E
|
E

A

T

-

T

-

S

-

F

-

V

-

S

-

P

G

K

W

W

A

V

G

P

Q

Q

D

M

D

G

L

D

A

H

A

T

T

E

L

V

R

L

L

K

G

G

A

I

R

Q

V

K

A

F

P

P

S

G

L

I

R

N

L

Y

A

P

V

V

W

L

C

-

R

-

C

-

T

T

A

P

D

N

L

L

-

K

-

G

-

F

D

E

K

A

A

A

A

V

E

A

A

A

G

G

A

A

R

K

R

E

V

V

H

V

I

I

G

F

V

G

P

A

S

A

S

S

D

E

A

L

H

F

M

T

R

K

L

K

R

N

L

I

G

N

M

C

G
x
S

R

I

D

E

E

E

V

S

L

F

Q

Q

R

R

V

F

T

D

T

A

V

I

L

L

E

K

-

A

H

Q

A

S

A

A

H

N

L

I

-

S

-

V

-

R

G

G

F

Y

L

V

H

S

V

C

T

A

L

L

G

G

L
x
C

E

P

D

Y

A

E

G

G

R

K

A

I

A

S

P

P

D

A

L

K

L

V

E

A

A

E

L

V

A

T

R

K

T

K

A
x
F

A

Y

R

S

T

M

G

G

A

C

H

Y

R

E

L
x
I

R

S

C

L

S
x
G

D
|
D

T

T

V

I

G

G

L

V

L

G

T

T

P

P

D

-

G

G

M

I

V

M

R

K

L

D

V

M

L

L

L

S

A

A

-

V

-

M

R

Q

R

E

A

V

S

P

A

L

L

A

P

A

V

L

A

A

V

V

H
|
H

C

C

H

H

N

D

D

T

L

Y

G

G

L

Q

A

A

T

L

A

A

N

N

A

T

L

L

A

M

A

A

L

L

D

Q

A

M

G

G

A

V

D

S

G

V

A

V

D

D

V

S

S

S

L

V

L

A

G

G

L

L

G

G

E37 (≠ D26) to K: in HMGCLD; activity lower than 5% respect to the wild-type; mutation to D: Normal activity.
R41 (= R30) to Q: in HMGCLD; loss of activity and of proton exchange; dbSNP:rs121964997; mutation to M: Reduced activity, and loss of proton exchange.
D42 (≠ E31) to E: in HMGCLD; reduced activity; to G: in HMGCLD; loss of activity; dbSNP:rs1467902610; to H: in HMGCLD; loss of activity; mutation D->A,N: Loss of activity, and reduced proton exchange rate.
K48 (≠ G37) to N: in HMGCLD; abolishes almost all enzymatic activity
E72 (= E61) mutation to A: Loss of activity, and reduced affinity for metal cofactor and substrate.
S142 (≠ G126) to F: in HMGCLD; activity lower than 5% respect to the wild-type
C174 (≠ L153) to Y: in HMGCLD; activity lower than 5% respect to the wild-type; dbSNP:rs765475941
F192 (≠ A171) to S: in HMGCLD; activity lower than 5% respect to the wild-type
I200 (≠ L179) to F: in HMGCLD; activity lower than 5% respect to the wild-type
G203 (≠ S182) to E: in HMGCLD; complete loss of activity; dbSNP:rs1553131940
D204 (= D183) mutation to A: Reduced activity, and reduced affinity for metal cofactor and substrate.
H233 (= H211) to R: in HMGCLD; loss of activity; dbSNP:rs727503963; mutation to A: Loss of activity, and reduced proton exchange rate.

Sites not aligning to the query:

279 E→A: Reduced thermal stability, but normal activity.
280 D→A: Normal activity.
323 modified: Interchain; C→S: Abolishes interchain homodimerization. Exhibits no DTT stimulated activity.

Query Sequence

>408370 DVUA0016 homocitrate synthase
MAWRRRHVGLASGLQGHLRRCVMLIDSTLREGAQAYGVYFDAADRESILQGVAASGVTEA
EAGWAGQDDLAATLRLGARVAPSLRLAVWCRCCTADLDKAAEAGARRVHIGVPSSDAHMR
LRLGMGRDEVLQRVTTVLEHAAHLGFLHVTLGLEDAGRAAPDLLEALARTAARTGAHRLR
CSDTVGLLTPDGMVRLVLLARRASALPVAVHCHNDLGLATANALAALDAGADGADVSLLG
LGERAGITRAEELAAALVVLRGESYRLDMLRGVCRRLAASLEMRLPPHWAVAGENLFAVE
SGVHLHGVQRDPALFEPFPPALVGAERRLGVGGKCGSAGVAAMAHSHGLTLQGDALRRHV
RAVRDKACSLGRPLTDAEFLCAGR

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