SitesBLAST

SitesBLAST – Find functional sites

SitesBLAST

Comparing Ac3H11_2083 4-Hydroxy-2-oxoglutarate aldolase (EC 4.1.3.16) @ 2-dehydro-3-deoxyphosphogluconate aldolase (EC 4.1.2.14) 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)

3vcrA Crystal structure of a putative kdpg (2-keto-3-deoxy-6- phosphogluconate) aldolase from oleispira antarctica (see paper)
51% identity, 99% coverage: 1:206/209 of query aligns to 1:212/216 of 3vcrA

query
sites
3vcrA

M

M

N

T

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Q

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L

D

D

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active site: E42 (= E40), R46 (= R44), K136 (= K128)
binding pyruvic acid: R46 (= R44), T70 (= T68), V89 (= V87), S90 (= S88), P91 (= P89)

6oviA Crystal structure of kdpg aldolase from legionella pneumophila with pyruvate captured at low ph as a covalent carbinolamine intermediate
51% identity, 94% coverage: 11:206/209 of query aligns to 13:208/210 of 6oviA

query
sites
6oviA

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binding 2,2-bis(oxidanyl)propanoic acid: E42 (= E40), R46 (= R44), T70 (= T68), P91 (= P89), K130 (= K128), F132 (= F130)

1euaA Schiff base intermediate in kdpg aldolase from escherichia coli (see paper)
54% identity, 86% coverage: 21:200/209 of query aligns to 26:205/213 of 1euaA

query
sites
1euaA

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active site: E45 (= E40), R49 (= R44), K133 (= K128)
binding pyruvic acid: E45 (= E40), T73 (= T68), I92 (≠ V87), K133 (= K128)

P0A955 KHG/KDPG aldolase; EC 4.1.3.16; EC 4.1.2.14 from Escherichia coli (strain K12) (see 3 papers)
54% identity, 86% coverage: 21:200/209 of query aligns to 26:205/213 of P0A955

query
sites
P0A955

V

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E45 (= E40) mutation to N: 50-fold decrease in catalytic efficiency and 6-fold decrease of binding affinity.
R49 (= R44) binding
T73 (= T68) binding
K133 (= K128) 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 (= T156) 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 (= G158) binding
N168 (≠ T163) mutation to S: Shows activity significantly greater than wild-type.
S184 (= S179) binding

1wauA Structure of kdpg aldolase e45n mutant (see paper)
54% identity, 86% coverage: 21:200/209 of query aligns to 26:205/213 of 1wauA

query
sites
1wauA

V

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active site: N45 (≠ E40), R49 (= R44), K133 (= K128)
binding sulfate ion: G162 (= G157), G163 (= G158), S184 (= S179)

2c0aB Mechanism of the class i kdpg aldolase (see paper)
54% identity, 86% coverage: 21:200/209 of query aligns to 27:206/214 of 2c0aB

query
sites
2c0aB

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active site: N46 (≠ E40), R50 (= R44), K134 (= K128)
binding phosphate ion: E132 (≠ F126)

Sites not aligning to the query:

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

5xsfA Crystal structure of the 2-keto-3-deoxy-6-phosphogluconate aldolase of zymomonas mobilis zm4 with 3-phosphoglycerate
52% identity, 95% coverage: 11:208/209 of query aligns to 13:206/209 of 5xsfA

query
sites
5xsfA

P

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E

A

A

I

I

E

K

A

-

I

I

A

M

R

K

H

E

L

V

P

P

E

G

A

A

V

V

G

G

V

A

G

G

T

T

V

V

L

L

N

N

A

A

D

K

D

M

A

L

R

D

R

Q

A

A

S

Q

E

E

A

A

G

G

A

C

R

E

F

F

A

F

V

V

S

S

P

P

G

G

Y

L

T

T

S

A

E

D

V

L

G

G

S

K

A

H

C

A

K

V

G

A

L

Q

N

K

L

A

P

A

L

L

P

P

G

G

V

V

A

A

T

N

S

A

E

D

I

V

M

M

T

L

A

G

L

L

A

D

D

L

G

G

F

L

S

D

F

R

L

F

K

K

L

F

F

F

P

P

A

A

E

E

A

N

V

I

G

G

I

L

P

P

L

A

L

L

K

K

S

S

W

M

A

A

S

S

P

V

F

F

G

R

Q

Q

V

V

S

R

F

F

C

C

P

P

T

T

G

G

I

I

T

T

N

P

A

T

T

S

A

A

P

P

N

K

Y

Y

L

L

A

E

L

N

P

P

N

S

V

I

R

L

C

C

V

V

G

G

S

S

W

W

L

V

T

V

P

P

T

A

D

G

A

-

V

-

R

-

A

K

G

P

D

D

W

V

A

A

R

K

I

I

T

T

E

A

L

L

A

A

R

K

A

E

T

A

Q

S

A

A

L

F

R

K

N

R

A

A

binding 3-hydroxypyruvic acid: V19 (= V17), E21 (≠ D19), D22 (≠ R20), D25 (= D23)

1mxsA Crystal structure of 2-keto-3-deoxy-6-phosphogluconate (kdpg) aldolase from pseudomonas putida. (see paper)
47% identity, 97% coverage: 6:208/209 of query aligns to 13:215/216 of 1mxsA

query
sites
1mxsA

I

I

A

C

S

E

H

K

G

A

P

R

V

I

I

L

P

P

V

V

I

I

V

T

I

I

D

A

R

R

V

E

E

E

D

D

A

I

L

L

P

P

L

L

A

A

E

D

A

A

L

L

L

A

A

A

G

G

V

I

K

R

V

T

L

L

E
|
E

V

V

T

T

L

L

R
|
R

T

S

A

Q

A

H

G

G

L

L

P

K

A

A

I

I

E

Q

A

V

I

L

A

R

R

E

H

Q

L

R

P

P

E

E

A

L

V

C

V

V

G

G

V

A

G

G

T
|
T

V

V

L

L

N

D

A

R

D

S

D

M

A

F

R

A

A

V

S

E

E

A

A

A

G

G

A

A

R

Q

F

F

A

V

V
|
V

S
x
T

P
|
P

G

G

Y

I

T

T

S

E

E

D

V

I

G

L

S

E

A

A

C

G

K

V

G

D

L

S

N

E

L

I

P

P

L

L

P

P

G

G

V

I

A

S

T

T

S

P

S

S

E

E

I

I

M

M

T

M

A

G

L

Y

A

A

D

L

G

G

F

Y

S

R

F

R

L

F

K
|
K

L

L

F

F

P

P

A

A

E

E

A

I

V

S

G

G

I

V

P

A

L

A

L

I

K

K

S

A

W

F

A

G

S

G

P

P

F

F

G

G

Q

D

V

I

S

R

F

F

C

C

P

P

T

T

G

G

I

V

T

N

N

P

A

A

T

N

A

V

P

R

N

N

Y

Y

L

M

A

A

L

L

P

P

N

N

V

V

R

M

C

C

V

V

G

G

G

T

S

T

W

W

L

M

T

L

P

D

T

S

D

S

A

W

V

I

R

K

A

N

G

G

D

D

W

W

A

A

R

R

I

I

T

E

E

A

L

C

A

S

R

A

A

E

T

A

Q

I

A

A

L

L

R

L

N

D

A

A

active site: E47 (= E40), R51 (= R44), K135 (= K128)
binding sulfate ion: E47 (= E40), R51 (= R44), T75 (= T68), V94 (= V87), T95 (≠ S88), P96 (= P89), K135 (= K128)

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)
47% identity, 97% coverage: 6:208/209 of query aligns to 23:225/226 of P00885

query
sites
P00885

I

I

A

C

S

E

H

K

G

A

P

R

V

I

I

L

P

P

V

V

I

I

V

T

I

I

D

A

R

R

V

E

E

E

D

D

A

I

L

L

P

P

L

L

A

A

E

D

A

A

L

L

L

A

A

A

G

G

V

I

K

R

V

T

L

L

E

E

V

V

T

T

L

L

R

R

T

S

A

Q

A

H

G

G

L

L

P

K

A

A

I

I

E

Q

A

V

I

L

A

R

R

E

H

Q

L

R

P

P

E

E

A

L

V

C

V

V

G

G

V

A

G

G

T

T

V

V

L

L

N

D

A

R

D

S

D

M

A

F

R

A

A

V

S

E

E

A

A

A

G

G

A

A

R

Q

F

F

A

V

V

V

S

T

P

P

G

G

Y

I

T

T

S

E

E

D

V

I

G

L

S

E

A

A

C

G

K

V

G

D

L

S

N

E

L

I

P

P

L

L

P

P

G

G

V

I

A

S

T

T

S

P

S

S

E

E

I

I

M

M

T

M

A

G

L

Y

A

A

D

L

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G

F

Y

S

R

F

R

L

F

K
|
K

L

L

F

F

P

P

A

A

E

E

A

I

V

S

G

G

I

V

P

A

L

A

L

I

K

K

S

A

W

F

A

G

S

G

P

P

F

F

G

G

Q

D

V

I

S

R

F

F

C

C

P

P

T

T

G

G

I

V

T

N

N

P

A

A

T

N

A

V

P

R

N

N

Y

Y

L

M

A

A

L

L

P

P

N

N

V

V

R

M

C

C

V

V

G

G

G

T

S

G

W

W

L

M

T

L

P

D

T

S

D

S

A

W

V

I

R

K

A

N

G

G

D

D

W

W

A

A

R

R

I

I

T

E

E

A

L

C

A

S

R

A

A

E

T

A

Q

I

A

A

L

L

R

L

N

D

A

A

K145 (= K128) active site, Schiff-base intermediate with substrate

Sites not aligning to the query:

1 modified: Initiator methionine, Removed

1wa3D Mechanism of the class i kdpg aldolase (see paper)
35% identity, 75% coverage: 5:160/209 of query aligns to 4:159/203 of 1wa3D

query
sites
1wa3D

D

E

I

L

A

F

S

K

H

K

G

H

P

K

V

I

I

V

P

A

V

V

I

L

V

R

I

A

D

N

R

S

V

V

E

E

D

E

A

A

L

K

P

E

L

K

A

A

E

L

A

A

L

V

L

F

A

E

G

G

V

V

K

H

V

L

L

I

E
|
E

V

I

T

T

L

F

R
x
T

T

V

A

P

A

D

G

A

L

D

P

T

A

V

I

I

E

K

A

E

I

L

A

S

R

-

H

F

L

L

P

K

E

E

-

K

-

G

A

A

V

I

G

G

V

A

G

G

T
|
T

V

V

L

T

N

S

A

V

D

E

D

Q

A

C

R

R

R

K

A

A

S

V

E

E

A

S

G

G

A

A

R

E

F

F

A

I

V

V

S
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S

P
|
P

G

H

Y

L

T

D

S

E

E

E

V

I

G

S

S

Q

A

F

C

C

K

K

G

E

L

K

N

G

L

V

P

F

L

Y

L

M

P

P

G

G

V

V

A

M

T

T

S

P

S

T

E

E

I

L

M

V

T

K

A

A

L

M

A

K

D

L

G

G

F

H

S

T

F

I

L

L

K
|
K

L

L

F
|
F

P

P

A

G

E

E

A

V

V

V

G

G

G

P

I

-

P

Q

L

F

L

V

K

K

S

A

W

M

A

K

S

G

P

P

F

F

G

P

Q

N

V

V

S

K

F

F

C

V

P

P

T

T

G

G

G
|
G

I

V

T

N

active site: E39 (= E40), T43 (≠ R44), K128 (= K128)
binding pyruvic acid: T68 (= T68), S88 (= S88), P89 (= P89), K128 (= K128), F130 (= F130)
binding sulfate ion: G157 (= G158)

Sites not aligning to the query:

binding sulfate ion: 177, 178

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)
32% identity, 59% coverage: 13:136/209 of query aligns to 7:134/205 of Q6BF16

query
sites
Q6BF16

I

L

P

P

V

L

I

I

V

A

I

I

D

L

R
|
R

-

G

-

I

-

T

V

P

E

D

D

E

A

A

L

L

P

A

L

H

A

V

E

G

A

A

L

V

L

I

A

D

G

A

G

G

V

F

K

D

V

A

L

V

E
|
E

V

I

T

P

L

L

R

N

T

S

A

P

A

Q

G

W

L

E

P

Q

A

S

I

I

E

P

A

A

I

I

A

V

R

D

-

A

H

Y

L

G

P

D

E

K

A

A

V

L

V

I

G

G

V

A

G

G

T
|
T

V

V

L

L

N

K

A

P

D

E

D

Q

A

V

R

D

R

A

A

L

S

A

E

R

A

M

G

G

A

C

R

Q

F

L

A

I

V

V

S

T

P

P

G

N

Y

I

T

H

S

S

E

E

V

V

G

I

S

R

A

R

C

A

K

V

G

G

L

Y

N

G

L

M

P

T

L

V

L

C

P

P

G

G

V

C

A

A

T

T

S

A

S

T

E

E

I

A

M

F

T

T

A

A

L

L

A

E

D

A

G

G

F

A

S

Q

F

A

L

L

K
|
K

L

I

F

F

P

P

A

S

E

S

A

A

V

F

G

G

R14 (= R20) binding
E37 (= E40) mutation to N: 50-fold decrease in catalytic efficiency and 6-fold decrease of binding affinity.
T66 (= T68) binding
K126 (= K128) active site, Schiff-base intermediate with substrate; binding covalent

Sites not aligning to the query:

154 V→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.

2v82A Kdpgal complexed to kdpgal (see paper)
32% identity, 59% coverage: 13:136/209 of query aligns to 6:133/205 of 2v82A

query
sites
2v82A

I

L

P

P

V

L

I

I

V

A

I

I

D

L

R
|
R

-

G

-

I

-

T

V

P

E

D

D

E

A

A

L

L

P

A

L

H

A

V

E

G

A

A

L

V

L

I

A

D

G

A

G

G

V

F

K

D

V

A

L

V

E
|
E

V

I

T

P

L

L

R
x
N

T

S

A

P

A

Q

G

W

L

E

P

Q

A

S

I

I

E

P

A

A

I

I

A

V

R

D

-

A

H

Y

L

G

P

D

E

K

A

A

V

L

V

I

G

G

V

A

G

G

T
|
T

V

V

L

L

N

K

A

P

D

E

D

Q

A

V

R

D

R

A

A

L

S

A

E

R

A

M

G

G

A

C

R

Q

F

L

A

I

V
|
V

S
x
T

P

P

G

N

Y

I

T

H

S

S

E

E

V

V

G

I

S

R

A

R

C

A

K

V

G

G

L

Y

N

G

L

M

P

T

L

V

L

C

P

P

G

G

V

C

A

A

T

T

S

A

S

T

E

E

I

A

M

F

T

T

A

A

L

L

A

E

D

A

G

G

F

A

S

Q

F

A

L

L

K
|
K

L

I

F
|
F

P

P

A

S

E

S

A

A

V

F

G

G

active site: E36 (= E40), N40 (≠ R44), K125 (= K128)
binding 2-keto-deoxy-galactose: R13 (= R20), T65 (= T68), V84 (= V87), T85 (≠ S88), K125 (= K128), F127 (= F130)

Sites not aligning to the query:

binding 2-keto-deoxy-galactose: 153, 175, 176, 205

Query Sequence

>Ac3H11_2083 4-Hydroxy-2-oxoglutarate aldolase (EC 4.1.3.16) @ 2-dehydro-3-deoxyphosphogluconate aldolase (EC 4.1.2.14)
MNPLDIASHGPVIPVIVIDRVEDALPLAEALLAGGVKVLEVTLRTAAGLPAIEAIARHLP
EAVVGVGTVLNADDARRASEAGARFAVSPGYTSEVGSACKGLNLPLLPGVATSSEIMTAL
ADGFSFLKLFPAEAVGGIPLLKSWASPFGQVSFCPTGGITNATAPNYLALPNVRCVGGSW
LTPTDAVRAGDWARITELARATQALRNAG

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