SitesBLAST

SitesBLAST – Find functional sites

SitesBLAST

Comparing CCNA_01562 CCNA_01562 4-hydroxy-2-oxoglutarate aldolase/2-dehydro-3-deoxyphosphogluconate aldolase 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 12 hits to proteins with known functional sites (download)

1wa3D Mechanism of the class i kdpg aldolase (see paper)
33% identity, 92% coverage: 17:222/224 of query aligns to 11:201/203 of 1wa3D

query
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1wa3D

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active site: E39 (= E45), T43 (≠ R49), K128 (= K137)
binding pyruvic acid: R16 (≠ Y22), E39 (= E45), G67 (= G76), T68 (≠ S77), V87 (= V96), S88 (≠ G97), P89 (= P98), K128 (= K137), F130 (= F139)
binding sulfate ion: G156 (= G166), G157 (= G167), G177 (= G189), S178 (= S190)

1euaA Schiff base intermediate in kdpg aldolase from escherichia coli (see paper)
30% identity, 81% coverage: 34:215/224 of query aligns to 34:209/213 of 1euaA

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1euaA

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active site: E45 (= E45), R49 (= R49), K133 (= K137)
binding pyruvic acid: E45 (= E45), R49 (= R49), G72 (= G76), T73 (≠ S77), I92 (≠ V96), S93 (≠ G97), P94 (= P98), K133 (= K137), F135 (= F139)

Sites not aligning to the query:

binding pyruvic acid: 20

P0A955 KHG/KDPG aldolase; EC 4.1.3.16; EC 4.1.2.14 from Escherichia coli (strain K12) (see 3 papers)
30% identity, 81% coverage: 34:215/224 of query aligns to 34:209/213 of P0A955

query
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P0A955

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E45 (= E45) mutation to N: 50-fold decrease in catalytic efficiency and 6-fold decrease of binding affinity.
R49 (= R49) binding
T73 (≠ S77) binding
K133 (= K137) binding covalent; mutation to Q: Absence of aldolase activity. Shows a markedly altered substrate specificity relative to the wild-type, with an enhanced activity against pyridine carboxaldehyde, benzaldehyde, and alpha-ketobutyrate; when associated with k-161.
T161 (= T165) binding ; mutation to K: Shows activity significantly greater than wild-type. Shows a markedly altered substrate specificity relative to the wild-type, with an enhanced activity against pyridine carboxaldehyde, benzaldehyde, and alpha-ketobutyrate; when associated with Q-133.; mutation to V: Little stereoselectivity, accepting KDPG and KDPGal as substrate with roughly equal efficacy. It strongly diminishes the activity against KDPG and slightly increases activity against KDPGal.
G163 (= G167) binding
N168 (≠ S174) mutation to S: Shows activity significantly greater than wild-type.
S184 (= S190) binding

1wauA Structure of kdpg aldolase e45n mutant (see paper)
29% identity, 81% coverage: 34:215/224 of query aligns to 34:209/213 of 1wauA

query
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1wauA

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active site: N45 (≠ E45), R49 (= R49), K133 (= K137)
binding sulfate ion: G162 (= G166), G163 (= G167), I164 (≠ V168), S184 (= S190)

2c0aB Mechanism of the class i kdpg aldolase (see paper)
29% identity, 81% coverage: 34:215/224 of query aligns to 35:210/214 of 2c0aB

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active site: N46 (≠ E45), R50 (= R49), K134 (= K137)
binding phosphate ion: K131 (≠ E134), E132 (≠ I135), G163 (= G166), G164 (= G167), G184 (= G189), S185 (= S190)

Sites not aligning to the query:

binding phosphate ion: 1, 5, 8, 9, 10

3vcrA Crystal structure of a putative kdpg (2-keto-3-deoxy-6- phosphogluconate) aldolase from oleispira antarctica (see paper)
28% identity, 89% coverage: 17:216/224 of query aligns to 14:213/216 of 3vcrA

query
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3vcrA

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active site: E42 (= E45), R46 (= R49), K136 (= K137)
binding pyruvic acid: E42 (= E45), R46 (= R49), G69 (= G76), T70 (≠ S77), V89 (= V96), S90 (≠ G97), P91 (= P98), F138 (= F139)

1mxsA Crystal structure of 2-keto-3-deoxy-6-phosphogluconate (kdpg) aldolase from pseudomonas putida. (see paper)
28% identity, 96% coverage: 2:217/224 of query aligns to 3:213/216 of 1mxsA

query
sites
1mxsA

V

M

K

A

D

D

R

K

M

A

A

A

V

R

L

I

T

D

A

A

L

I

M

C

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E

Q

K

G

A

-

R

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I

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V

F

I

Y

T

H

I

P

A

D

R

V

E

E

E

V

D

C

I

K

L

N

P

V

L

I

A

Q

D

A

A

C

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A

A

D

A

G

G

A

I

P

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C

T

I

L

E
|
E

F

V

T

T

N

L

R
|
R

G

-

D

-

F

-

A

-

S

S

H

Q

V

H

F

G

Y

L

E

K

V

A

T

I

R

Q

Y

V

F

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A

R

E

E

A

Q

D

R

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P

R

E

V

L

I

C

M

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A

G
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G

S
x
T

I

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V

L

D

D

A

R

P

S

T

M

A

F

G

A

I

A

Y

V

I

E

A

A

N

A

G

G

A

A

K

Q

F

F

V

V

V
|
V

G
x
T

P
|
P

I

G

L

I

N

T

A

E

D

D

V

I

A

L

K

E

V

A

C

G

N

V

R

D

R

S

K

E

I

I

P

P

Y

L

S

L

P

P

G

G

C

I

G

S

S

T

A

P

S

S

E

E

I

I

S

M

Y

M

A

G

E

Y

E

A

L

L

G

G

C

Y

E

R

I

R

V

F

K
|
K

V

L

F

F

P

P

G

A

S

E

S

I

V

S

G

G

P

V

D

A

F

A

V

I

K

K

A

A

V

F

L

G

G

G

P

P

M

F

P

G

W

D

T

I

R

R

I

F

M

C

P

P

T

T

G
|
G

V

V

D

N

P

P

D

-

E

-

A

A

S

N

V

V

K

R

K

N

W

Y

F

M

G

A

A

L

G

P

I

N

V

V

A

M

A

C

G

V

M

G

G
x
T

S
x
T

K

W

L

M

I

L

T

D

Q

S

E

S

M

W

L

I

D

K

A

N

K

G

D

D

Y

W

A

A

G

R

I

I

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E

K

A

K

C

V

S

R

A

E

E

T

A

V

I

D

A

L

L

I

L

active site: E47 (= E45), R51 (= R49), K135 (= K137)
binding sulfate ion: E47 (= E45), R51 (= R49), G74 (= G76), T75 (≠ S77), V94 (= V96), T95 (≠ G97), P96 (= P98), K135 (= K137), G164 (= G166), G165 (= G167), T185 (≠ G189), T186 (≠ S190)

P00885 2-dehydro-3-deoxy-phosphogluconate aldolase; KDPG-aldolase; Phospho-2-dehydro-3-deoxygluconate aldolase; Phospho-2-keto-3-deoxygluconate aldolase; EC 4.1.2.14 from Pseudomonas putida (Arthrobacter siderocapsulatus) (see paper)
28% identity, 96% coverage: 2:217/224 of query aligns to 13:223/226 of P00885

query
sites
P00885

V

M

K

A

D

D

R

K

M

A

A

A

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R

L

I

T

D

A

A

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K

G

A

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E

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A

A

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A

A

D

A

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G

A

I

P

R

C

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I

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E

E

F

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T

T

N

L

R

R

G

-

D

-

F

-

A

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S

H

Q

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H

F

G

Y

L

E

K

V

A

T

I

R

Q

Y

V

F

L

A

R

E

E

A

Q

D

R

P

P

R

E

V

L

I

C

M

V

G

G

V

A

G

G

S

T

I

V

V

L

D

D

A

R

P

S

T

M

A

F

G

A

I

A

Y

V

I

E

A

A

N

A

G

G

A

A

K

Q

F

F

V

V

G

T

P

P

I

G

L

I

N

T

A

E

D

D

V

I

A

L

K

E

V

A

C

G

N

V

R

D

R

S

K

E

I

I

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Y

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L

P

P

G

G

C

I

G

S

S

T

A

P

S

S

E

E

I

I

S

M

Y

M

A

G

E

Y

E

A

L

L

G

G

C

Y

E

R

I

R

V

F

K
|
K

V

L

F

F

P

P

G

A

S

E

S

I

V

S

G

G

P

V

D

A

F

A

V

I

K

K

A

A

V

F

L

G

G

G

P

P

M

F

P

G

W

D

T

I

R

R

I

F

M

C

P

P

T

T

G

G

V

V

D

N

P

P

D

-

E

-

A

A

S

N

V

V

K

R

K

N

W

Y

F

M

G

A

A

L

-

P

G

N

I

V

V

M

A

C

A

V

G

G

M

T

G

G

S

-

K

W

L

M

I

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T

D

Q

S

E

S

M

W

L

I

D

K

A

N

K

G

D

D

Y

W

A

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R

I

I

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E

K

A

K

C

V

S

R

A

E

E

T

A

V

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D

A

L

L

I

L

K145 (= K137) active site, Schiff-base intermediate with substrate

Sites not aligning to the query:

1 modified: Initiator methionine, Removed

5xsfA Crystal structure of the 2-keto-3-deoxy-6-phosphogluconate aldolase of zymomonas mobilis zm4 with 3-phosphoglycerate
29% identity, 70% coverage: 17:173/224 of query aligns to 14:165/209 of 5xsfA

query
sites
5xsfA

V

V

I

M

P

P

V

V

F

L

Y
x
V

H
x
I

P
x
E

D
|
D

V

I

E

A

V
x
D

C

A

K

K

N

P

V
x
I

I

A

Q

E

A

A

C

L

A

V

D

A

G

G

A

L

P

N

C

V

I

L

E

E

F

V

T

T

N

L

R

R

G

T

D

P

F

C

A

A

S

-

H

-

V

-

F

-

Y

L

E

E

V

A

T

I

R

K

Y

I

F

M

A

K

E

E

A

V

D

-

P

P

R

G

V

A

I

V

M

V

G

G

V

A

G

G

S

T

I

V

V

L

D

N

A

A

P

K

T

M

A

L

G

D

I

Q

Y

A

I

Q

A

E

N

A

G

G

A

C

K

E

F

F

V

F

V

V

G

S

P

P

I

G

L

L

N

T

A

A

D

D

V

L

A

G

K

K

V

H

C

A

N

V

R

A

R

Q

K

K

I

A

P

A

Y

L

S

L

P

P

G

G

C

V

G

A

S

N

A

A

S

A

E

D

I

V

S

M

Y

L

A

G

E

L

E

D

L

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G

G

C

L

E

D

I

R

V

F

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K

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F

F

F

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P

G

A

S

E

S

N

V

I

G

G

P

L

D

P

F

A

V

L

K

K

A

S

V

M

L

A

G

S

P

V

M

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W

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T

V

R

R

I

F

M

C

P

P

T

T

G

G

V

I

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T

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P

D

T

E

S

A

A

binding 3-hydroxypyruvic acid: V19 (≠ Y22), I20 (≠ H23), E21 (≠ P24), D22 (= D25), D25 (≠ V28), I29 (≠ V32)

Sites not aligning to the query:

binding 3-hydroxypyruvic acid: 183, 186

6oviA Crystal structure of kdpg aldolase from legionella pneumophila with pyruvate captured at low ph as a covalent carbinolamine intermediate
25% identity, 86% coverage: 17:208/224 of query aligns to 14:199/210 of 6oviA

query
sites
6oviA

V

V

I

I

P

P

V

V

F

I

Y

V

H

I

P

K

D

E

V

L

E

E

V

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C

A

K

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N

P

V

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I

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Q

E

A

A

C

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A

F

D

A

G

G

A

I

P

H

C

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L

E
|
E

F

V

T

T

N

L

R
|
R

G

T

D

P

F

V

A

A

S

I

H

K

V

A

F

L

Y

E

E

L

V

L

T

I

R

N

Y

T

F

F

A

-

E

-

A

-

D

-

P

P

R

D

V

E

I

L

M

I

G

G

V

A

G
|
G

S
x
T

I

V

V

I

D

T

A

P

P

G

T

Q

A

F

G

H

I

D

Y

V

I

V

A

A

N

A

G

G

A

A

K

R

F

F

V

A

V
x
I

G
x
S

P
|
P

I

G

L

Q

N

T

A

R

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E

V

L

A

L

K

I

V

A

C

G

N

Q

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K

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K

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I

I

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P

Y

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S

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P

G

G

C

V

G

A

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S

A

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E

I

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S

M

Y

E

A

G

E

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E

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M

G

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E

N

I

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K
|
K

V

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F
|
F

P

P

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A

S

A

V

A

G

G

P

I

D

P

F

M

V

L

K

K

A

A

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I

L

S

G

G

P

V

M

F

P

P

W

Q

T

V

R

K

I

F

M

C

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P

T
|
T

G

G

V

I

D

-

P

-

D

N

E

S

A

K

S

N

V

Y

K

E

W

Y

F

L

G

C

A

L

G

P

I

N

V

V

A

A

A

C

G

V

M

G

G

G

S

S

K

W

L

I

I

V

T

P

Q

E

E

E

M

A

L

I

D

K

A

N

K

H

D

N

Y

W

A

S

G

L

I

I

S

T

K

E

binding 2,2-bis(oxidanyl)propanoic acid: E42 (= E45), R46 (= R49), G69 (= G76), T70 (≠ S77), I89 (≠ V96), S90 (≠ G97), P91 (= P98), K130 (= K137), F132 (= F139), T158 (= T165)

2v82A Kdpgal complexed to kdpgal (see paper)
28% identity, 66% coverage: 70:216/224 of query aligns to 58:205/205 of 2v82A

query
sites
2v82A

R

K

V

A

I

L

M

I

G

G

V

A

G
|
G

S
x
T

I

V

V

L

D

K

A

P

P

E

T

Q

A

V

G

D

I

A

Y

L

I

A

A

R

N

M

G

G

A

C

K

Q

F

L

V

I

V
|
V

G
x
T

P
|
P

I

N

L

I

N

H

A

S

D

E

V

V

A

I

K

R

V

R

C

A

N

V

R

G

R

Y

K

G

I

M

P

T

Y

V

S

C

P

P

G

G

C

C

G

A

S

T

A

A

S

T

E

E

I

A

S

F

Y

T

A

A

E

L

E

E

L

A

G

G

C

A

E

Q

I

A

V

L

K
|
K

V

I

F
|
F

P

P

G

-

S

S

V

A

G

F

G

G

P

P

D

Q

F

Y

V

I

K

K

A

A

V

L

L

K

G

A

P

V

M

L

P

P

W

S

-

D

T

I

R

A

I

V

M

F

P

A

T
x
V

G
|
G

V

V

D

T

P

P

D

E

E

-

A

-

S

N

V

L

K

A

K

Q

W

W

F

I

G

D

A

A

G

G

I

C

V

A

A

G

A

A

G

G

M

L

G
|
G

S
|
S

K

D

L

L

I

Y

T

R

Q

A

E

G

M

Q

-

S

-

V

-

E

L

R

D

T

A

A

K

Q

D

Q

Y

A

A

A

G

A

I

F

S

V

K

K

K

A

V

Y

R

R

E

E

T
x
A

V

V

D

Q

L
|
L

active site: K125 (= K137)
binding 2-keto-deoxy-galactose: G64 (= G76), T65 (≠ S77), V84 (= V96), T85 (≠ G97), P86 (= P98), K125 (= K137), F127 (= F139), V153 (≠ T165), G154 (= G166), G155 (= G167), G175 (= G189), S176 (= S190), A202 (≠ T213), L205 (= L216)

Sites not aligning to the query:

active site: 36, 40
binding 2-keto-deoxy-galactose: 11, 13, 36

Q6BF16 2-dehydro-3-deoxy-6-phosphogalactonate aldolase; 2-oxo-3-deoxygalactonate 6-phosphate aldolase; 6-phospho-2-dehydro-3-deoxygalactonate aldolase; 6-phospho-2-keto-3-deoxygalactonate aldolase; KDPGal; EC 4.1.2.21 from Escherichia coli (strain K12) (see paper)
28% identity, 65% coverage: 70:215/224 of query aligns to 59:205/205 of Q6BF16

query
sites
Q6BF16

R

K

V

A

I

L

M

I

G

G

V

A

G

G

S
x
T

I

V

V

L

D

K

A

P

P

E

T

Q

A

V

G

D

I

A

Y

L

I

A

A

R

N

M

G

G

A

C

K

Q

F

L

V

I

V

V

G

T

P

P

I

N

L

I

N

H

A

S

D

E

V

V

A

I

K

R

V

R

C

A

N

V

R

G

R

Y

K

G

I

M

P

T

Y

V

S

C

P

P

G

G

C

C

G

A

S

T

A

A

S

T

E

E

I

A

S

F

Y

T

A

A

E

L

E

E

L

A

G

G

C

A

E

Q

I

A

V

L

K
|
K

V

I

F

F

P

P

G

-

S

S

V

A

G

F

G

G

P

P

D

Q

F

Y

V

I

K

K

A

A

V

L

L

K

G

A

P

V

M

L

P

P

W

S

-

D

T

I

R

A

I

V

M

F

P

A

T
x
V

G

G

V

V

D

T

P

P

D

E

E

-

A

-

S

N

V

L

K

A

K

Q

W

W

F

I

G

D

A

A

G

G

I

C

V

A

A

G

A

A

G

G

M

L

G

G

S

S

K

D

L

L

I

Y

T

R

Q

A

E

G

M

Q

-

S

-

V

-

E

L

R

D

T

A

A

K

Q

D

Q

Y

A

A

A

G

A

I

F

S

V

K

K

K

A

V

Y

R

R

E

E

T

A

V

V

D

Q

T66 (≠ S77) binding
K126 (= K137) active site, Schiff-base intermediate with substrate; binding covalent
V154 (≠ T165) mutation to T: Little stereoselectivity, accepting KDPG and KDPGal as substrate with roughly equal efficacy. Reduced the preference for KDPGal. It diminishes the activity against KDPGal and increases activity against KDPG.

Sites not aligning to the query:

14 binding
37 E→N: 50-fold decrease in catalytic efficiency and 6-fold decrease of binding affinity.

Query Sequence

>CCNA_01562 CCNA_01562 4-hydroxy-2-oxoglutarate aldolase/2-dehydro-3-deoxyphosphogluconate aldolase
MVKDRMAVLTALMDQGVIPVFYHPDVEVCKNVIQACADGGAPCIEFTNRGDFASHVFYEV
TRYFAEADPRVIMGVGSIVDAPTAGIYIANGAKFVVGPILNADVAKVCNRRKIPYSPGCG
SASEISYAEELGCEIVKVFPGSSVGGPDFVKAVLGPMPWTRIMPTGGVDPDEASVKKWFG
AGIVAAGMGSKLITQEMLDAKDYAGISKKVRETVDLIKKVRGKA

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