SitesBLAST

SitesBLAST – Find functional sites

SitesBLAST

Comparing GFF3323 FitnessBrowser__WCS417:GFF3323 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)

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)
60% identity, 98% coverage: 2:295/299 of query aligns to 28:321/325 of P35914

query
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P35914

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E37 (= E11) to K: in HMGCLD; activity lower than 5% respect to the wild-type; mutation to D: Normal activity.
R41 (= R15) to Q: in HMGCLD; loss of activity and of proton exchange; dbSNP:rs121964997; mutation to M: Reduced activity, and loss of proton exchange.
D42 (= D16) 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 (≠ A22) to N: in HMGCLD; abolishes almost all enzymatic activity
E72 (= E46) mutation to A: Loss of activity, and reduced affinity for metal cofactor and substrate.
S142 (= S116) to F: in HMGCLD; activity lower than 5% respect to the wild-type
C174 (= C148) to Y: in HMGCLD; activity lower than 5% respect to the wild-type; dbSNP:rs765475941
F192 (≠ L166) to S: in HMGCLD; activity lower than 5% respect to the wild-type
I200 (≠ V174) to F: in HMGCLD; activity lower than 5% respect to the wild-type
G203 (= G177) to E: in HMGCLD; complete loss of activity; dbSNP:rs1553131940
D204 (= D178) mutation to A: Reduced activity, and reduced affinity for metal cofactor and substrate.
H233 (= H207) to R: in HMGCLD; loss of activity; dbSNP:rs727503963; mutation to A: Loss of activity, and reduced proton exchange rate.
E279 (= E253) mutation to A: Reduced thermal stability, but normal activity.
D280 (= D254) mutation to A: Normal activity.

Sites not aligning to the query:

323 modified: Interchain; C→S: Abolishes interchain homodimerization. Exhibits no DTT stimulated activity.

3mp3B Crystal structure of human lyase in complex with inhibitor hg-coa (see paper)
60% identity, 98% coverage: 2:295/299 of query aligns to 1:294/296 of 3mp3B

query
sites
3mp3B

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binding (3R,5S,9R,21S)-1-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]-3,5,9,21-tetrahydroxy-8,8-dimethyl-10,14,19-trioxo-2,4,6-trioxa-18-thia-11,15-diaza-3,5-diphosphatricosan-23-oic acid 3,5-dioxide: R14 (= R15), D15 (= D16), Q18 (= Q19), F49 (= F50), V50 (= V51), S51 (= S52), P52 (= P53), K53 (= K54), W54 (= W55), H61 (≠ S62), L79 (= L80), P81 (= P82), N82 (= N83), K84 (≠ R85), G85 (= G86), F100 (= F101), N111 (= N112), I112 (= I113), N113 (= N114), R122 (= R123), Y140 (= Y141), S142 (= S143), T178 (= T179), H206 (= H207), H208 (= H209)
binding magnesium ion: D15 (= D16), H206 (= H207), H208 (= H209)

2cw6A Crystal structure of human hmg-coa lyase: insights into catalysis and the molecular basis for hydroxymethylglutaric aciduria (see paper)
60% identity, 98% coverage: 2:295/299 of query aligns to 1:294/296 of 2cw6A

query
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2cw6A

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binding 3-hydroxypentanedioic acid: R14 (= R15), Q18 (= Q19), F100 (= F101)
binding magnesium ion: D15 (= D16), H206 (= H207), H208 (= H209), N248 (= N249)

3mp5B Crystal structure of human lyase r41m in complex with hmg-coa (see paper)
59% identity, 98% coverage: 2:295/299 of query aligns to 1:294/296 of 3mp5B

query
sites
3mp5B

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G

N

N

V

L

A

A

T

T

E

E

D

D

V

L

V

V

Y

Y

L

M

L

L

N

E

G

G

L

L

G

G

I

I

E

H

T

T

G

G

I

V

D

N

L

L

E

Q

A

K

L

L

I

L

G

E

A

A

G

G

Q

N

Q

F

I

I

S

C

S

Q

V

A

L

L

G

N

R

R

P

K

T

T

G

S

S

S

R

K

V

V

A

A

K

Q

A

A

binding 3-hydroxy-3-methylglutaryl-coenzyme a: D15 (= D16), Q18 (= Q19), S51 (= S52), P52 (= P53), K53 (= K54), W54 (= W55), H61 (≠ S62), L79 (= L80), F100 (= F101), N111 (= N112), I112 (= I113), N113 (= N114), R122 (= R123), Y140 (= Y141), S142 (= S143), G176 (= G177), T178 (= T179), H206 (= H207), H208 (= H209), C239 (= C240)
binding magnesium ion: D15 (= D16), H206 (= H207), H208 (= H209)

P13703 Hydroxymethylglutaryl-CoA lyase; HL; HMG-CoA lyase; 3-hydroxy-3-methylglutarate-CoA lyase; EC 4.1.3.4 from Pseudomonas mevalonii (see paper)
62% identity, 95% coverage: 7:291/299 of query aligns to 4:288/301 of P13703

query
sites
P13703

V

V

R

K

L

V

V

F

E

E

V

V

G

G

P

P

R

R

D

D

G

G

L

L

Q

Q

N

N

E

E

A

R

Q

Q

P

P

I

L

S

S

V

V

S

A

D

A

K

R

V

V

R

G

L

L

V

I

D

G

A

E

L

L

S

A

A

G

A

T

G

G

L

L

S

R

Y

H

I

I

E

E

V

A

G

G

S

A

F

F

V

V

S

S

P

P

K

R

W

W

V

V

P

P

Q

Q

M

M

A

A

G

G

S

S

A

D

E

E

V

V

F

L

A

R

Q

Q

I

L

Q

P

R

S

K

N

P

D

G

G

V

V

T

S

Y

Y

G

T

A

A

L

L

A

V

P

P

N

N

L

R

R

Q

G

G

F

F

E

E

D

A

A

A

V

Q

S

R

A

A

G

G

V

C

K

R

E

E

V

V

A

A

V

V

F

F

A

A

S

S

E

E

A

A

F

F

S

S

Q

R

R

N

N

N

I

I

N

N

C

C

S

S

I

I

S

D

E

E

S

S

L

F

E

E

R

R

F

F

A

T

P

P

I

V

M

L

A

R

A

A

K

N

Q

E

N

A

G

S

V

I

S

R

V

V

R

R

G

G

Y

Y

V

V

S

S

C

C

V

V

L

L

G

G

C

C

P

P

Y

F

E

S

G

G

Q

A

I

V

A

A

P

P

E

E

Q

A

V

V

A

A

A

K

V

V

A

A

R

R

E

R

L

L

Y

Y

A

E

M

L

G

G

C

C

Y

Y

E

E

V

I

S

S

L

L

G

G

D

D

T

T

I

I

G

G

T

A

G

G

T

R

A

P

G

D

A

E

T

T

R

A

R

Q

L

L

F

F

E

E

V

L

V

C

G

A

A

R

Q

Q

V

L

P

P

R

V

D

A

K

A

L

L

A

A

G

G

H

H

F

F

H

H

D

D

T

T

Y

W

G

G

Q

M

A

A

I

I

A

A

N

N

I

V

Y

H

A

A

S

A

L

L

L

A

E

Q

G

G

I

V

S

R

V

T

F

F

D

D

S

S

I

V

A

A

G

G

L

L

G

G

C
|
C

P

P

Y

Y

A

S

K

P

G

G

A

A

S

S

G

G

N

N

V

V

A

A

T

T

E

E

D

D

V

L

Y

Y

L

L

N

H

G

G

L

L

G

G

I

Y

E

S

T

T

G

G

I

V

D

D

L

L

E

E

A

A

L

V

I

A

G

Q

A

V

G

G

Q

V

Q

R

I

I

S

S

S

A

V

Q

L

L

G

G

R

T

P

A

T

N

G

R

S

S

R

R

C237 (= C240) active site

Q8TB92 3-hydroxy-3-methylglutaryl-CoA lyase, cytoplasmic; 3-hydroxy-3-methylglutaryl-CoA lyase-like protein 1; HMGCL-like 1; Endoplasmic reticulum 3-hydroxy-3-methylglutaryl-CoA lyase; er-cHL; EC 4.1.3.4 from Homo sapiens (Human) (see 2 papers)
56% identity, 98% coverage: 3:295/299 of query aligns to 74:366/370 of Q8TB92

query
sites
Q8TB92

L

L

P

P

S

E

H

F

V

V

R

K

L

I

V

V

E

E

V

V

G

G

P

P

R
|
R

D

D

G

G

L

L

Q

Q

N

N

E

E

A

K

Q

V

P

I

I

V

S

P

V

T

S

D

D

I

K

K

V

I

R

E

L

F

V

I

D

N

A

R

L

L

S

S

A

Q

A

T

G

G

L

L

S

S

Y

V

I

I

E

E

V

V

G

T

S

S

F

F

V

V

S

S

P

S

K

R

W

W

V

V

P

P

Q

Q

M

M

A

A

G

D

S

H

A

T

E

E

V

V

F

M

A

K

Q

G

I

I

Q

H

R

Q

K

Y

P

P

G

G

V

V

T

R

Y

Y

G

P

A

V

L

L

A

T

P

P

N

N

L

L

R

Q

G

G

F

F

E

H

D

H

A

A

V

V

S

A

A

A

G

G

V

A

K

T

E

E

V

I

A

S

V

V

F

F

A

G

A

A

S

S

E

E

A

S

F

F

S

S

Q

K

R

K

N

N

I

I

N

N

C

C

S

S

I

I

S

E

E

E

S

S

L

M

E

G

R

K

F

F

A

E

P

E

I

V

M

V

A

K

A

S

A

A

K

R

Q

H

N

M

G

N

V

I

S

P

V

A

R

R

G

G

Y

Y

V

V

S

S

C

C

V

A

L

L

G

G

C

C

P

P

Y

Y

E

E

G

G

Q

S

I

I

A

T

P

P

E

Q

Q

K

V

V

A

T

A

E

V

V

A

S

R

K

E

R

L
|
L

Y

Y

A

G

M

M

G

G

C

C

Y

Y

E

E

V

I

S

S

L

L

G

G

D

D

T

T

I

I

G

G

T

V

G

G

T

T

A

P

G

G

A

S

T

M

R

K

R

R

L

M

F

L

E

E

V

S

V

V

G

M

A

K

Q

E

V

I

P

P

R

P

D

G

K

A

L

L

A

A

G

V

H
|
H

F

C

H

H

D

D

T

T

Y

Y

G

G

Q

Q

A

A

I

L

A

A

N

N

I

I

Y

L

A

T

S

A

L

L

L

Q

E

M

G

G

I

I

S

N

V

V

F

V

D

D

S

S

S

A

I

V

A

S

G

G

L

L

G

G

C

C

P

P

Y

Y

A

A

K

K

G

G

A

A

S

S

G

G

N

N

V

V

A

A

T

T

E

E

D

D

V

L

V

I

Y

Y

L

M

L

L

N

N

G

G

L

L

G

G

I

L

E

N

T

T

G

G

I

V

D

N

L

L

E

Y

A

K

L

V

I

M

G

E

A

A

G

G

Q

D

Q

F

I

I

S

C

S

K

V

A

L

V

G

N

R

K

P

T

T

T

G

N

S

S

R

K

V

V

A

A

K

Q

A

A

R86 (= R15) mutation to Q: Abolishes catalytic activity.
L237 (= L166) mutation to S: Abolishes catalytic activity.
H278 (= H207) mutation to R: Abolishes catalytic activity.

Sites not aligning to the query:

2 modified: N-myristoyl glycine; G→A: Abolishes myristoylation and induces a subcellular location change.

1ydnA Crystal structure of the hmg-coa lyase from brucella melitensis, northeast structural genomics target lr35. (see paper)
53% identity, 91% coverage: 6:277/299 of query aligns to 3:274/283 of 1ydnA

query
sites
1ydnA

H

H

V

V

R

E

L

I

V

V

E

E

V

M

G

A

P

A

R

R

D
|
D

G

G

L

L

Q

Q

N

N

E

E

A

K

Q

R

P

F

I

V

S

P

V

T

S

A

D

D

K

K

V

I

R

A

L

L

V

I

D

N

A

R

L

L

S

S

A

D

A

C

G

G

L

Y

S

A

Y

R

I

I

E

E

V

A

G

T

S

S

F

F

V

V

S

S

P

P

K

K

W

W

V

V

P

P

Q

Q

M

L

A

A

G

D

S

S

A

R

E

E

V

V

F

M

A

A

Q

G

I

I

Q

R

R

R

K

A

P

D

G

G

V

V

T

R

Y

Y

G

S

A

V

L

L

A

V

P

P

N

N

L

M

R

K

G

G

F

Y

E

E

D

A

A

A

V

A

S

A

A

A

G

H

V

A

K

D

E

E

V

I

A

A

V

V

F

F

A

I

A

S

A

A

S

S

E

E

A

G

F

F

S

S

Q

K

R

A

N

N

I

I

N

N

C

C

S

T

I

I

S

A

E

E

S

S

L

I

E

E

R

R

F

L

A

S

P

P

I

V

M

I

A

G

A

A

K

I

Q

N

N

D

G

G

V

L

S

A

V

I

R

R

G

G

Y

Y

V

V

S

S

C

C

V

V

L

V

G

E

C

C

P

P

Y

Y

E

D

G

G

Q

P

I

V

A

T

P

P

E

Q

Q

A

V

V

A

A

A

S

V

V

A

T

R

E

E

Q

L

L

Y

F

A

S

M

L

G

G

C

C

Y

H

E

E

V

V

S

S

L

L

G

G

D

D

T

T

I

I

G

G

T

R

G

G

T

T

A

P

G

D

A

T

T

V

R

A

L

M

F

L

E

D

V

A

V

V

G

L

A

A

Q

I

V

A

P

P

R

A

D

H

K

S

L

L

A

A

G

G

H
|
H

F

Y

H
|
H

D

D

T

T

Y

G

G

G

Q

R

A

A

I

L

A

D

N

N

I

I

Y

R

A

V

S

S

L

L

L

E

E

K

G

G

I

L

S

R

V

V

F

F

D

D

S

A

S

S

I

V

A

G

G

G

L

L

G

G

C

C

P

P

Y

F

A

A

K

P

G

G

A

A

S

K

G

G

N
|
N

V

V

A

D

T

T

E

V

D

A

V

V

Y

E

L

M

L

L

N

H

G

E

L

M

G

G

I

F

E

E

T

T

G

G

I

L

D

D

L

L

E

D

A

R

L

L

I

R

G

S

A

A

G

G

binding calcium ion: D13 (= D16), H204 (= H207), H206 (= H209), N246 (= N249)

6ndsA Structure of an hmg-coa lyase from acenitobacter baumannii in complex with coenzyme a and 3-methylmalate
37% identity, 96% coverage: 11:298/299 of query aligns to 12:299/305 of 6ndsA

query
sites
6ndsA

E

E

V

V

G

S

P

P

R

R

D
|
D

G

G

L

L

Q
|
Q

N

I

E

E

A

P

Q

T

P

W

I

V

S

P

V

T

S

D

D

K

K

K

V

I

R

D

L

L

V

I

D

N

A

Q

L

L

S

S

A

T

A

M

G

G

L

F

S

S

Y

R

I

I

E

E

V

A

G

G

S

S

F
|
F

V
|
V

S
|
S

P
|
P

K

K

W
x
A

V
x
I

P

P

Q

N

M

L

A

R

G

D

S

G

A

E

E

E

V

V

F

F

A

T

Q

G

I

I

Q

T

R

R

K

H

P

K

G

D

V

I

T

I

Y

Y

G

V

A

G

L
|
L

A

I

P
|
P

N
|
N

L

L

R
x
K

G
|
G

F

A

E

L

D
x
R

A

A

V

V

S

E

A

A

G

N

V

A

K

N

E

E

V

L

A

N

V

L

F

V

A

L

A

S

A

A

S

S

E

Q

A

T

F

H

S

N

Q

L

R

A

N
|
N

I
x
M

N
x
R

C

M

S

T

I

K

S

A

E

Q

S

S

L

F

E

A

R

G

F

F

A

T

P

E

I

I

M

V

A

E

A

Q

A

L

K

-

Q

Q

N

G

G

K

V

T

S

Q

V

F

R

N

G

G

Y

T

V

V

S

A

C

T

V

T

L

F

G

G

C

C

P

P

Y

F

E

E

G

G

Q

K

I

I

A

S

P

E

E

R

Q

E

V

V

A

F

A

S

V

L

A

V

R

E

E

H

L

Y

Y

L

A

K

M

L

G

G

C

I

Y

H

E

N

V

I

S

T

L

L

G

A

D

D

T

T

I

T

G

G

T

M

G

A

T

N

A

P

G

V

A

Q

T

V

R

K

R

R

L

I

F

V

E

S

V

H

V

V

G

L

A

S

Q

L

V

I

P

S

R

P

D

E

K

Q

L

L

A

T

G

L

H
|
H

F

F

H
|
H

D

N

T

T

Y

R

G

G

Q

L

A

G

I

L

A

T

N

N

I

V

Y

L

A

A

S

A

L

Y

L

E

E

V

G

G

I

A

S

R

V

R

F

F

D

D

S

A

I

L

A

G

G

G

L

L

G

G

C
|
C

P

P

Y

F

A

A

K

P

G

G

A

A

S

S

G

G

N

N

V

I

A

C

T

T

E

E

D

D

V

L

V

V

Y

N

L

M

L

C

N

E

G

E

L

I

G

G

I

I

E

P

T

T

G

T

I

I

D

D

L

L

E

D

A

A

L

L

I

I

G

Q

A

L

G

S

Q

R

Q

T

I

L

S

P

S

A

V

L

L

L

G

G

R

H

P

D

T

T

G

P

S

S

R

Q

V

L

A

A

K

K

A

A

-

G

R

R

N

N

A

T

binding coenzyme a: Q20 (= Q19), F51 (= F50), V52 (= V51), S53 (= S52), P54 (= P53), A56 (≠ W55), I57 (≠ V56), L81 (= L80), P83 (= P82), N84 (= N83), K86 (≠ R85), G87 (= G86), R90 (≠ D89), N113 (= N112), M114 (≠ I113), R115 (≠ N114), C240 (= C240)
binding zinc ion: D17 (= D16), H207 (= H207), H209 (= H209)

6ktqA Crystal structure of catalytic domain of homocitrate synthase from sulfolobus acidocaldarius (sahcs(dram)) in complex with alpha- ketoglutarate/zn2+/coa (see paper)
24% identity, 79% coverage: 2:238/299 of query aligns to 17:247/399 of 6ktqA

query
sites
6ktqA

S

S

L

L

P

H

S

M

H

K

V

V

R

G

L

I

V

L

E

D

V

S

G

T

P

L

R
|
R

D
x
E

G

G

L

E

Q

Q

N

T

E

P

A

G

Q

V

P

V

I

F

S

T

V

T

S

D

D

Q

K

R

V

V

R

E

L

I

V

A

D

K

A

A

L

L

S

S

A

D

A

I

G

G

L

V

S

Q

Y

M

I

I

E

E

V

A

G

G

S
x
H

F

-

V

-

S

-

P

P

K

A

W
x
V

V

S

P

P

Q

D

M

I

A

Y

G

E

S

G

A

I

E

R

V

R

F

I

A

I

Q

K

I

L

Q

K

R

R

K

E

P

-

G

G

V

V

T

I

Y

K

G

S

A

E

L

I

A

V

P

A

N
x
H

L

S

R
|
R

G
x
A

F
x
V

E

K

D

R

A

D

V

I

S

E

A

V

G

G

V

A

K

E

-

I

-

E

-

A

-

D

E

R

V

I

A

A

V

I

F
|
F

A
x
Y

A

G

A

I

S

S

E

D

A

T

F

H

S

L

Q

K

R

A

N
x
K

I
x
H

N

H

C

T

S

T

I

R

S

D

E

E

S

A

L

L

E

R

R

S

F

I

A

A

P

E

I

T

M

V

A

S

A

Y

A

A

K

K

Q

S

N

H

G

G

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S

K

V

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R
|
R

G

F

Y
x
T

V

A

S
x
E

C

D

V

A

L

T

G

R

C

A

P

D

Y

Y

E

Q

G

-

Q

-

I

-

A

-

P

-

E

-

Q

Y

V

L

A

L

A

E

V

V

A

I

R

K

E

T

L

V

Y

R

A

D

M

A

G

G

C

A

Y

D

E

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|
S

L

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x
A

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|
T

I

V

G

G

T

V

G

L

T

Y

A

P

G

S

A

R

T

T

R

R

R

E

L

L

F

F

E

K

V

D

V

L

G

T

A

S

Q

R

V

F

P

P

R

D

D

I

K

E

L

F

A

D

G

I

H
|
H

F

A

H
|
H

D

N

T

D

Y

L

G

G

Q

M

A

A

I

V

A

A

N

N

I

V

Y

L

A

A

S

A

L

A

L

E

E

G

G

G

I

A

S

T

V

I

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I

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x
H

S

T

I

L

A

N

G

G

L

L

G

G

binding 2-oxoglutaric acid: R30 (= R15), E31 (≠ D16), H94 (≠ N83), R154 (= R139), T156 (≠ Y141), E158 (≠ S143), S184 (= S175), A186 (≠ G177), T188 (= T179), H216 (= H207), H218 (= H209), H240 (≠ D231)
binding coenzyme a: H64 (≠ S49), V67 (≠ W55), R96 (= R85), A97 (≠ G86), V98 (≠ F87), F116 (= F101), Y117 (≠ A102), K127 (≠ N112), H128 (≠ I113), E158 (≠ S143)
binding zinc ion: E31 (≠ D16), H216 (= H207), H218 (= H209)

2zyfA Crystal structure of homocitrate synthase from thermus thermophilus complexed with magnesuim ion and alpha-ketoglutarate (see paper)
30% identity, 77% coverage: 8:238/299 of query aligns to 5:220/314 of 2zyfA

query
sites
2zyfA

R

K

L

I

V

I

E

D

V

S

G

T

P

L

R
|
R

D
x
E

G

G

L

E

Q
|
Q

N

F

E

E

A

K

Q

A

P

N

I

F

S

S

V

T

S

Q

D

D

K

K

V

V

R

E

L

I

V

A

D

K

A

A

L

L

S

D

A

E

A

F

G

G

L

I

S

E

Y

Y

I

I

E

E

V

V

G

-

S

-

F

-

V

T

S

T

P

P

K

V

W

A

V

S

P

P

Q

Q

M

S

A

R

G

K

S

D

A

A

E

E

V

V

F

L

A

A

Q

S

I

L

Q

G

R

L

K

K

P

A

G

K

V

V

T

V

Y

-

G

T

A
x
H

L

I

A

Q

P

C

N

R

L

L

R

D

G

A

F

A

E

K

D

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A

A

V

V

S

E

A

T

G

G

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V

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Q

E

G

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I

A

D

V

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F
x
L

A

F

A

G

A

T

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S

E

K

A

G

F

-

S

-

Q

-

R

R

N

D

I

I

N

P

C

R

S

I

I

I

S

E

E

E

S

A

L

K

E

E

R

V

F

I

A

A

P

Y

I

I

M

R

A

E

A

A

K

P

Q

H

N

-

G

-

V

V

S

E

V

V

R
|
R

G

F

Y
x
S

V

A

S

E

C

D

V

T

L

F

G

R

C

-

P

-

Y

-

E

-

G

-

Q

-

I

-

A

S

P

E

E

E

Q

Q

V

D

A

L

V

A

A

V

R

Y

E

E

L

A

Y

V

A

A

M

P

G

Y

C

V

Y

D

E

R

V

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G

L

L

G
x
A

D

D

T
|
T

I

V

G

G

T

V

G

A

T

T

A

P

-

R

-

Q

-

V

-

Y

G

A

A

L

T

V

R

R

R

E

L

V

F

R

E

R

V

V

G

G

A

-

Q

-

V

-

P

P

R

R

D

V

K

D

L

I

A

E

G

F

H
|
H

F

G

H
|
H

D

N

T

D

Y

T

G

G

Q

C

A

A

I

I

A

A

N

N

I

A

Y

Y

A

E

S

A

L

I

L

E

E

A

G

G

I

A

S

T

V

H

F

V

D

D

S

T

I

I

A

L

G

G

L

I

G

G

active site: Q16 (= Q19)
binding 2-oxoglutaric acid: R12 (= R15), H72 (≠ A79), L94 (≠ F101), R127 (= R139), S129 (≠ Y141), A158 (≠ G177), T160 (= T179), H189 (= H207), H191 (= H209)
binding magnesium ion: E13 (≠ D16), H189 (= H207), H191 (= H209)

O87198 Homocitrate synthase; HCS; EC 2.3.3.14 from Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27) (see paper)
30% identity, 77% coverage: 8:238/299 of query aligns to 5:226/376 of O87198

query
sites
O87198

R

K

L

I

V

I

E

D

V

S

G

T

P

L

R
|
R

D
x
E

G

G

L

E

Q

Q

N

F

E

E

A

K

Q

A

P

N

I

F

S

S

V

T

S

Q

D

D

K

K

V

V

R

E

L

I

V

A

D

K

A

A

L

L

S

D

A

E

A

F

G

G

L

I

S

E

Y

Y

I

I

E

E

V

V

G

-

S

-

F

-

V

T

S

T

P

P

K

V

W

A

V

S

P

P

Q

Q

M

S

A

R

G

K

S

D

A

A

E

E

V

V

F

L

A

A

Q

S

I

L

Q

G

R

L

K

K

P

A

G

K

V

V

T

V

Y

-

G

T

A
x
H

L

I

A

Q

P

C

N

R

L

L

R

D

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A

F

A

E

K

D

V

A

A

V

V

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E

A

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G

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Q

E

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A
x
D

V

L

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L

A

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A

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S

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K

-

Y

-

L

-

R

A

A

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Q

G

R

R

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I

I

N

P

C

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I

I

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E

E

S

A

L

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V

F

I

A

A

P

Y

I

I

M

R

A

E

A

A

K

P

Q

H

N

-

G

-

V

V

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E

V

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R

G

F

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x
S

V

A

S

E

C

D

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T

L

F

G

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C

-

P

-

Y

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E

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I

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A

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A

A

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Y

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A

M

P

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C

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D

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L

L

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I

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G

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G

A

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A

P

-

R

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Y

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A

A

L

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L

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F

R

E

R

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V

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G

A

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-

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D

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K

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I

A

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H

F

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H
|
H

D

N

T

D

Y

T

G

G

Q

C

A

A

I

I

A

A

N

N

I

A

Y

Y

A

E

S

A

L

I

L

E

E

A

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G

I

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H

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I

A

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G

L

I

G

G

R12 (= R15) binding
E13 (≠ D16) binding
H72 (≠ A79) 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 (≠ A99) binding
R133 (= R139) binding
S135 (≠ Y141) binding
T166 (= T179) binding ; binding
H195 (= H207) binding
H197 (= H209) binding

3a9iA Crystal structure of homocitrate synthase from thermus thermophilus complexed with lys (see paper)
30% identity, 77% coverage: 8:238/299 of query aligns to 4:219/347 of 3a9iA

query
sites
3a9iA

R

K

L

I

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I

E

D

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L

R
|
R

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x
E

G

G

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E

Q

Q

N

F

E

E

A

K

Q

A

P

N

I

F

S

S

V

T

S

Q

D

D

K

K

V

V

R

E

L

I

V

A

D

K

A

A

L

L

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D

A

E

A

F

G

G

L

I

S

E

Y

Y

I

I

E

E

V

V

G

-

S

-

F

-

V

T

S

T

P

P

K

V

W

A

V

S

P

P

Q

Q

M

S

A

R

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K

S

D

A

A

E

E

V

V

F

L

A

A

Q

S

I

L

Q

G

R

L

K

K

P

A

G

K

V

V

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V

Y

-

G

T

A

H

L

I

A

Q

P

C

N

R

L

L

R

D

G

A

F

A

E

K

D

V

A

A

V

V

S

E

A

T

G

G

V

V

K

Q

E

G

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I

A
x
D

V

L

F
x
L

A

F

A

G

A

T

S

S

E

K

A

Y

F

L

S

-

Q

-

R

-

N

D

I

I

N

P

C

R

S

I

I

I

S

E

E

E

S

A

L

K

E

E

R

V

F

I

A

A

P

Y

I

I

M

R

A

E

A

A

K

P

Q

H

N

-

G

-

V

V

S

E

V

V

R

R

G

F

Y
x
S

V

A

S

E

C

D

V

T

L

F

G

R

C

-

P

-

Y

-

E

-

G

-

Q

-

I

-

A

S

P

E

E

E

Q

Q

V

D

A

L

V

A

A

V

R

Y

E

E

L

A

Y

V

A

A

M

P

G

Y

C

V

Y

D

E

R

V

V

S

G

L

L

G
x
A

D

D

T
|
T

I

V

G

G

T

V

G

A

T

T

A

P

-

R

-

Q

-

V

-

Y

G

A

A

L

T

V

R

R

R

E

L

V

F

R

E

R

V

V

G

G

A

-

Q

-

V

-

P

P

R

R

D

V

K

D

L

I

A

E

G

F

H
|
H

F

G

H
|
H

D

N

T

D

Y

T

G

G

Q

C

A

A

I

I

A

A

N

N

I

A

Y

Y

A

E

S

A

L

I

L

E

E

A

G

G

I

A

S

T

V

H

F

V

D

D

S

T

I

I

A

L

G

G

L

I

G

G

binding cobalt (ii) ion: E12 (≠ D16), H188 (= H207), H190 (= H209)
binding lysine: R11 (= R15), E12 (≠ D16), D91 (≠ A99), L93 (≠ F101), S128 (≠ Y141), A157 (≠ G177), T159 (= T179), H188 (= H207), H190 (= H209)

2ztjA Crystal structure of homocitrate synthase from thermus thermophilus complexed with alpha-ketoglutarate (see paper)
30% identity, 77% coverage: 8:238/299 of query aligns to 5:218/312 of 2ztjA

query
sites
2ztjA

R

K

L

I

V

I

E

D

V

S

G

T

P

L

R
|
R

D
x
E

G

G

L

E

Q
|
Q

N

F

E

E

A

K

Q

A

P

N

I

F

S

S

V

T

S

Q

D

D

K

K

V

V

R

E

L

I

V

A

D

K

A

A

L

L

S

D

A

E

A

F

G

G

L

I

S

E

Y

Y

I

I

E

E

V

V

G

-

S

-

F

-

V

T

S

T

P

P

K

V

W

A

V

S

P

P

Q

Q

M

S

A

R

G

K

S

D

A

A

E

E

V

V

F

L

A

A

Q

S

I

L

Q

G

R

L

K

K

P

A

G

K

V

V

T

V

Y

-

G

T

A
x
H

L

I

A

Q

P

C

N

R

L

L

R

D

G

A

F

A

E

K

D

V

A

A

V

V

S

E

A

T

G

G

V

V

K

Q

E

G

V

I

A

D

V

L

F
x
L

A

F

A

G

A

T

S

G

E

-

A

-

F

-

S

-

Q

-

R

R

N

D

I

I

N

P

C

R

S

I

I

I

S

E

E

E

S

A

L

K

E

E

R

V

F

I

A

A

P

Y

I

I

M

R

A

E

A

A

K

P

Q

H

N

-

G

-

V

V

S

E

V

V

R
|
R

G

F

Y
x
S

V

A

S

E

C

D

V

T

L

F

G

R

C

-

P

-

Y

-

E

-

G

-

Q

-

I

-

A

S

P

E

E

E

Q

Q

V

D

A

L

V

A

A

V

R

Y

E

E

L

A

Y

V

A

A

M

P

G

Y

C

V

Y

D

E

R

V

V

S

G

L

L

G
x
A

D

D

T
|
T

I

V

G

G

T

V

G

A

T

T

A

P

-

R

-

Q

-

V

-

Y

G

A

A

L

T

V

R

R

R

E

L

V

F

R

E

R

V

V

G

G

A

-

Q

-

V

-

P

P

R

R

D

V

K

D

L

I

A

E

G

F

H
|
H

F

G

H
|
H

D

N

T

D

Y

T

G

G

Q

C

A

A

I

I

A

A

N

N

I

A

Y

Y

A

E

S

A

L

I

L

E

E

A

G

G

I

A

S

T

V

H

F

V

D

D

S

T

I

I

A

L

G

G

L

I

G

G

active site: Q16 (= Q19)
binding 2-oxoglutaric acid: R12 (= R15), E13 (≠ D16), H72 (≠ A79), L94 (≠ F101), R125 (= R139), S127 (≠ Y141), A156 (≠ G177), T158 (= T179), H187 (= H207), H189 (= H209)
binding copper (ii) ion: E13 (≠ D16), H187 (= H207), H189 (= H209)

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)
24% identity, 96% coverage: 1:287/299 of query aligns to 1:282/517 of Q9JZG1

query
sites
Q9JZG1

M

M

S

T

L

Q

P

T

S

N

H

R

V

V

R

I

L

I

V

F

E

D

V

T

G

T

P

L

R

R

D
|
D

G

G

L

E

Q

Q

N

S

E

P

A

G

Q

A

P

A

I

M

S

T

V

K

S

E

D

E

K

K

V

I

R

R

L

V

V

A

D

R

A

Q

L

L

S

E

A

K

A

L

G

G

L

V

S

D

Y

I

I

I

E

E

V

A

G

G

S

-

F

F

V

A

S

A

P

A

K

S

W

-

V

-

P

P

Q

G

M

D

A

F

G

E

S

A

A

V

E

N

V

A

F

I

A

A

Q

K

I

T

Q

I

R

T

K

K

P

S

G

T

V

V

T

C

Y

S

-

L

-

S

G

R

A

A

L

I

A

E

P

R

N

D

L

I

R

R

G

Q

F

A

E

G

D

E

A

A

V

V

S

A

-

P

A

A

G

P

V

K

K

K

E

R

V

I

A

H

V

T

F

F

A

I

A

A

A

T

S

S

E

P

A

I

F

H

S

M

Q

E

R

Y

N

K

I

L

N

K

C

M

S

K

I

P

S

K

E

Q

S

V

L

I

E

E

R

A

F

A

A

V

P

K

I

A

M

V

A

K

A

I

A

A

K

R

Q

E

N

Y

G

T

V

D

S

D

V

V

R

E

G

-

Y

-

V

F

S

S

C

C

V

E

L

D

G

A

C

L

P

R

Y

S

E

E

G

I

Q

D

I

F

A

L

P

A

E

E

Q

I

V

C

A

G

A

A

V

V

A

I

R

E

E

-

L

-

Y

-

A

-

M

A

G

G

C

A

Y

T

E

T

V

I

S

N

L

I

G

P

D

D

T

T

I

V

G

G

T

Y

G

S

T

I

A

P

G

Y

A

K

T

T

R

E

L

F

F

F

E

R

V

E

V

L

G

I

A

A

Q

K

V

T

P

P

-

N

-

G

R

K

D

V

K

V

L

W

A

S

G

A

H
|
H

F

C

H
|
H

D

N

T

D

Y

L

G

G

Q

L

A

A

I

V

A

A

N

N

I

S

Y

L

A

A

S

A

L

L

L

K

E

G

G

G

I

A

S

R

V

Q

F

V

D

E

S

C

S

T

I

V

A

N

G

G

L

L

G

G

G

-

C

-

P

-

Y

-

A

-

K

-

G

E

A

R

S

A

G

G

N
|
N

V

A

A

S

T

V

E

E

D

E

V

I

V

V

Y

M

L

A

L

L

-

K

-

V

-

R

-

H

N

D

G

L

L

F

G

G

I

L

E

E

T

T

G

G

I

I

D

D

L

T

E

T

A

Q

L

I

I

V

G

P

A

S

G

S

Q

K

Q

L

I

V

S

S

S

T

V

I

L

T

G

G

R

Y

P

P

D16 (= D16) binding
H204 (= H207) binding
H206 (= H209) binding
N240 (= N249) binding

Sites not aligning to the query:

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

3rmjB Crystal structure of truncated alpha-isopropylmalate synthase from neisseria meningitidis (see paper)
23% identity, 95% coverage: 5:287/299 of query aligns to 2:279/308 of 3rmjB

query
sites
3rmjB

S

N

H

R

V

V

R

I

L

I

V

F

E

D

V

T

G

T

P

L

R

R

D
|
D

G

G

L

E

Q
|
Q

N

S

E

P

A

G

Q

A

P

A

I

M

S

T

V

K

S

E

D

E

K

K

V

I

R

R

L

V

V

A

D

R

A

Q

L

L

S

E

A

K

A

L

G

G

L

V

S

D

Y

I

I

I

E

E

V

A

G

G

S

-

F

F

V

A

S

A

P

A

K

S

W

-

V

-

P

P

Q

G

M

D

A

F

G

E

S

A

A

V

E

N

V

A

F

I

A

A

Q

K

I

T

Q

I

R

T

K

K

P

S

G

T

V

V

T

C

Y

S

-

L

-

S

G

R

A

A

L

I

A

E

P

R

N

D

L

I

R

R

G

Q

F

A

E

G

D

E

A

A

V

V

S

A

-

P

A

A

G

P

V

K

K

K

E

R

V

I

A

H

V

T

F

F

A

I

A

A

A

T

S

S

E

P

A

I

F

H

S

M

Q

E

R

Y

N

K

I

L

N

K

C

M

S

K

I

P

S

K

E

Q

S

V

L

I

E

E

R

-

F

-

A

-

P

-

I

-

M

-

A

A

A

V

K

K

Q

A

N

V

G

K

V

I

S

A

V

-

R

R

G

E

Y

Y

V

T

S

D

C

D

V

V

-

E

L

F

G

S

C

C

P

E

Y

D

E

A

G

L

Q

R

I

S

A

E

P

I

E

D

Q

F

V

L

A

A

A

E

V

I

A

C

R

G

E

A

L

V

Y

I

A

E

M

A

G

G

C

A

Y

T

E

T

V

I

S

N

L

I

G

P

D

D

T

T

I

V

G

G

T

Y

G

S

T

I

A

P

G

Y

A

K

T

T

R

E

L

F

F

F

E

R

V

E

V

L

G

I

A

A

Q

K

V

T

P

P

-

N

-

G

R

K

D

V

K

V

L

W

A

S

G

A

H
|
H

F

C

H
|
H

D

N

T

D

Y

L

G

G

Q

L

A

A

I

V

A

A

N

N

I

S

Y

L

A

A

S

A

L

L

L

K

E

G

G

G

I

A

S

R

V

Q

F

V

D

E

S

C

S

T

I

V

A

N

G

G

L

L

G

G

G

-

C

-

P

-

Y

-

A

-

K

-

G

E

A

R

S

A

G

G

N
|
N

V

A

A

S

T

V

E

E

D

E

V

I

V

V

Y

M

L

A

L

L

-

K

-

V

-

R

-

H

N

D

G

L

L

F

G

G

I

L

E

E

T

T

G

G

I

I

D

D

L

T

E

T

A

Q

L

I

I

V

G

P

A

S

G

S

Q

K

Q

L

I

V

S

S

S

T

V

I

L

T

G

G

R

Y

P

P

active site: Q16 (= Q19)
binding manganese (ii) ion: D13 (= D16), H201 (= H207), H203 (= H209), N237 (= N249)

3ivtB Homocitrate synthase lys4 bound to 2-og (see paper)
23% identity, 80% coverage: 1:238/299 of query aligns to 24:250/400 of 3ivtB

query
sites
3ivtB

M

L

S

S

L

R

P

V

S

N

H

N

V

F

R

S

L

I

V

I

E

E

V

S

G

T

P

L

R
|
R

D
x
E

G

G

L

E

Q
|
Q

N

F

E

A

A

N

Q

A

P

F

I

F

S

D

V

T

S

E

D

K

K

K

V

I

R

Q

L

I

V

A

D

K

A

A

L

L

S

D

A

N

A

F

G

G

L

V

S

D

Y

Y

I

I

E

E

V

L

G

-

S

-

F

-

V

T

S

S

P

P

K

V

W

A

V

S

P

E

Q

Q

M

S

A

R

G

Q

S

D

A

C

E

E

V

A

F

I

A

C

Q

K

I

L

Q

G

R

L

K

K

P

C

G

K

V

I

T

-

Y

-

G

-

A

-

L

-

A

L

P

T

N
x
H

L

I

R

R

G

C

F

H

E

M

D

D

-

D

-

A

-

R

-

V

A

A

V

V

S

E

A

T

G

G

V

V

K

D

E

G

V

V

A

D

V

V

F
x
V

A

I

A

G

A

T

S

S

E

Q

A

Y

F

L

S

R

Q

K

R

Y

N

S

I

H

N

G

C

K

S

D

I

M

S

T

E

Y

S

I

L

I

E

D

R

S

F

A

A

T

P

E

I

V

M

I

A

N

A

F

A

V

K

K

Q

S

N

K

G

G

V

I

S

E

V

V

R
|
R

G

-

Y

-

V

-

S

-

C

-

V

-

L

-

G

-

C

F

P
x
S

Y

S

E

E

G

D

Q

S

I

F

A

R

P

S

E

D

Q

L

V

V

A

D

A

L

V

L

A

S

-

L

-

Y

R

K

E

A

L

V

Y

D

A

K

M

I

G

G

C

V

Y

N

E

R

V

V

S

G

L

I

G
x
A

D

D

T
|
T

I

V

G

G

T

C

G

A

T

T

A

P

G

R

A

Q

T

V

R

Y

R

D

L

L

F

I

E

R

V

T

V

L

G

R

A

G

Q

V

V

V

P

S

R

C

D

D

K

-

L

I

A

E

G

C

H
|
H

F

F

H
|
H

D

N

T

D

Y

T

G

G

Q

M

A

A

I

I

A

A

N

N

I

A

Y

Y

A

C

S

A

L

L

L

E

E

A

G

G

I

A

S

T

V

H

F

I

D

D

S

T

S

S

I

I

A

L

G

G

L

I

G

G

active site: Q42 (= Q19)
binding 2-oxoglutaric acid: R38 (= R15), E39 (≠ D16), H98 (≠ N83), V120 (≠ F101), R158 (= R139), S160 (≠ P149), A190 (≠ G177), T192 (= T179), H219 (= H207), H221 (= H209)
binding zinc ion: E39 (≠ D16), H219 (= H207), H221 (= H209)

2nx9B Crystal structure of the carboxyltransferase domain of the oxaloacetate decarboxylase na+ pump from vibrio cholerae (see paper)
26% identity, 62% coverage: 88:273/299 of query aligns to 106:266/453 of 2nx9B

query
sites
2nx9B

E

E

D

R

A

A

V

V

S

K

A

N

G

G

V

M

K

D

E

V

V

F

A

R

V

V

F

F

A
x
D

A

A

A

M

S

N

E

D

A

V

F

-

S

-

Q

-

R

R