SitesBLAST

Q8NP73 Diaminopimelate epimerase; DAP epimerase; PLP-independent amino acid racemase; EC 5.1.1.7 from Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / JCM 1318 / BCRC 11384 / CCUG 27702 / LMG 3730 / NBRC 12168 / NCIMB 10025 / NRRL B-2784 / 534)
33% identity, 75% coverage: 5:195/255 of query aligns to 9:224/277 of Q8NP73

query
sites
Q8NP73

K

K

Y

G

N

H

A

A

N

T

G

E

N
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N

D

D

F

F

V

I

I

I

F

I

H

P

D

D

N

E

Q

D

K

A

R

R

D

L

-

D

-

L

R

T

H

P

E

E

L

M

A

V

K

V

L

T

L

L

C

C

D

D

R

R

H

R

K

A

G

G

V

I

G

G

A

A

D

D

G

G

M

I

V

L

V

R

L

V

I

V

P

K

H

A

A

A

E

D

Y

V

D

E

F

G

E

S

-

T

-

V

-

D

-

P

-

S

-

L

W

W

-

F

-

M

E

D

F

Y

Y

R

N

N

S

A

D

D

G

G

S

S

E

L

A

A

T

E

M

M

C

C

G
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G

N
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N

A

G

T

V

R

R

A

L

V

F

A

A

H

H

Y

W

A

L

V

Y

E

S

K

R

G

G

I

L

S

V

V

D

N

N

D

T

R

S

A

F

E

D

F

I

L

G

T

T

G

R

A

A

G

G

V

V

-

R

-

H

-

V

-

D

-

I

I

L

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Q

A

A

E

D

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Q

N

H

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S

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Y

Q

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V

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R

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D

M

M

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E

I

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P

K

D

I

V

L

T

-

G

-

L

-

S

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C

D

D

I

I

E

N

E

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E

Q

G

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L

F

Q

A

W

G

W

L

L

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I

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D

D

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M

G

G

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x
N

P

P

H

H

L

L

V

A

A

C

E

V

V

V

E

P

D

G

L

L

E

S

-

A

-

S

-

A

-

L

-

A

N

D

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M

D

E

L

L

E

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M

A

A

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R

F

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D

R

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E

E

K

F

Y

F

D

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A

H

N

G

V

V

N
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N

I

V

Y

E

T

I

V

V

A

T

E

E

-

L

-

E

-

D

D

D

E

A

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L

M

R

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Y

W

E
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E

R
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R

G

G

V

V

E

-

G

G

E

E

T

T

L

R

A

S

C

C

G
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G

T
|
T

G

G

N15 (= N11) binding substrate
GN 84:85 (= GN 70:71) binding substrate
N159 (≠ V137) binding substrate
N194 (= N167) binding substrate
ER 212:213 (= ER 182:183) binding substrate
GT 222:223 (= GT 193:194) binding substrate

5m47A Crystal structure of dapf from corynebacterium glutamicum in complex with d,l-diaminopimelate (see paper)
33% identity, 75% coverage: 5:195/255 of query aligns to 9:224/280 of 5m47A

query
sites
5m47A

K

K

Y

G

N

H

A

A

N

T

G

E

N
|
N

D

D

F

F

V

I

I

I

F

I

H

P

D

D

N

E

Q

D

K

A

R

R

D

L

-

D

-

L

R

T

H

P

E

E

L

M

A

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K

V

L

T

L

L

C

C

D

D

R

R

H

R

K

A

G

G

V

I

G

G

A

A

D

D

G

G

M

I

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L

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L

V

I

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K

H

A

A

A

E

D

Y

V

D

E

F

G

E

S

-

T

-

V

-

D

-

P

-

S

-

L

W

W

-

F

-

M

E

D

F

Y

Y

R

N
|
N

S

A

D

D

G

G

S

S

E

L

A

A

T

E

M

M

C
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C

G
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G

N
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N

A

G

T

V

R

R

A

L

V

F

A

A

H

H

Y

W

A

L

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Y

E

S

K

R

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G

I

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S

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V

D

N

N

D

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S

A

F

E

D

F

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L

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T

T

G

R

A

A

G

G

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V

-

R

-

H

-

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-

D

-

I

I

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A

A

E

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N

H

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Y

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D

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M

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E

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K

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E

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x
N

P

P

H
|
H

L

L

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A

A

C

E

V

V

V

E

P

D

G

L

L

E

S

-

A

-

S

-

A

-

L

-

A

N

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M

D

E

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L

E

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M

A

A

P

R

T

R

F

L

D

R

Q

E

E

K

F

Y

F

D

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N

G

V

V

N
|
N

I

V

Y

E

T

I

V

V

A

T

E

E

-

L

-

E

-

D

D

D

E

A

L

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S

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M

R

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Y

W

E
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E

R
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R

G

G

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V

E

-

G

G

E

E

T

T

L

R

A

S

C
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C

G
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G

T
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T

G
|
G

active site: C83 (= C69), H161 (= H139), E212 (= E182), C221 (= C192), G224 (= G195)
binding 2,6-diaminopimelic acid: N15 (= N11), N74 (= N60), C83 (= C69), G84 (= G70), N85 (= N71), N159 (≠ V137), N194 (= N167), E212 (= E182), R213 (= R183), C221 (= C192), G222 (= G193), T223 (= T194)

2gkjA Crystal structure of diaminopimelate epimerase in complex with an irreversible inhibitor dl-azidap (see paper)
30% identity, 78% coverage: 1:198/255 of query aligns to 1:223/274 of 2gkjA

query
sites
2gkjA

M

M

F

Q

V

F

T

S

K

K

Y

M

N

H

A

G

N

L

G

G

N
|
N

D

D

F

F

V

V

I

V

F

V

H

-

D

D

N

G

Q

V

K

T

R

Q

D

N

-

V

-

F

R

T

H

P

E

E

L

T

A

I

K

R

L

R

L

L

C

A

D

N

R

R

H

H

K

C

G

G

V

I

G

G

A

F

D

D

G
x
Q

M

L

V

L

V

I

L

V

-

E

I

A

P

P

H

Y

-

D

A

P

E

E

Y

L

D

D

F

F

E

H

W

Y

E

R

F

I

Y

F

N
|
N

S

A

D

D

G

G

S

S

E

E

A

V

T

S

M

Q

C
|
C

G
|
G

N
|
N

A

G

T

A

R

R

A

C

V

F

A

A

H

R

Y

F

A

V

V

T

E

L

K

K

G

G

I

L

S

T

V

N

N

K

D

K

R

D

A

I

E

S

F

V

L

S

T

T

G

Q

A

K

G

G

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N

I

M

T

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A

L

E

T

V

V

-

K

N

D

G

D

L

N

Y

Q

V

I

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R

T

V

D

N

M

M

L

G

E

E

P

P

-

I

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W

-

E

-

P

-

A

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K

-

I

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P

-

F

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T

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A

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N

-

K

-

F

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E

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K

-

N

K

Y

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I

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L

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R

T

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D

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T

E

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-

L

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C

W

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L

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x
N

P

P

H
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H

L

C

V

V

A

V

E

Q

V

V

E

D

D

D

L

I

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N

T

F

A

D

N

L

V

E

E

M

Q

A

L

R

G

R

P

L

L

-

L

-

E

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S

R

H

E

E

K

R

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F

D

P

A

E

N

R

V

V

N
|
N

-

A

-

G

-

F

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Y

Q

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I

A

N

E

K

D

E

E

H

L

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K

L

L

R

R

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Y

E
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E

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R

G

G

V

A

E

-

G

G

E

E

T

T

L

Q

A

A

C
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C

G
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G

T
x
S

G
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G

M

A

T

C

A

A

active site: C73 (= C69), H159 (= H139), E208 (= E182), C217 (= C192), G220 (= G195)
binding (2r,6s)-2,6-diamino-2-methylheptanedioic acid: N11 (= N11), Q44 (≠ G42), N64 (= N60), C73 (= C69), G74 (= G70), N75 (= N71), N157 (≠ V137), N190 (= N167), E208 (= E182), R209 (= R183), C217 (= C192), G218 (= G193), S219 (≠ T194)

2gkeA Crystal structure of diaminopimelate epimerase in complex with an irreversible inhibitor ll-azidap (see paper)
30% identity, 78% coverage: 1:198/255 of query aligns to 1:223/274 of 2gkeA

query
sites
2gkeA

M

M

F

Q

V

F

T

S

K

K

Y

M

N

H

A

G

N

L

G

G

N
|
N

D

D

F
|
F

V

V

I

V

F

V

H

-

D

D

N

G

Q

V

K

T

R

Q

D

N

-

V

-

F

R

T

H

P

E

E

L

T

A

I

K

R

L

R

L

L

C

A

D

N

R

R

H

H

K

C

G

G

V

I

G

G

A

F

D

D

G
x
Q

M

L

V

L

V

I

L

V

-

E

I

A

P

P

H

Y

-

D

A

P

E

E

Y

L

D

D

F

F

E

H

W

Y

E

R

F

I

Y

F

N
|
N

S

A

D

D

G

G

S

S

E

E

A
x
V

T

S

M

Q

C
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C

G
|
G

N
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N

A

G

T

A

R

R

A

C

V

F

A

A

H

R

Y

F

A

V

V

T

E

L

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K

G

G

I

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N

N

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D

K

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D

A

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T

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A

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G

G

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I

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V

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D

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N

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M

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I

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F

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-

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Y

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I

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L

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R

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D

D

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E

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E

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C

W

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x
N

P

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H
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H

L

C

V

V

A

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E

Q

V

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E

D

D

D

L

I

E

Q

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T

F

A

D

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E

E

M

Q

A

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G

R

P

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L

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L

-

E

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S

R

H

E

E

K

R

Y

F

D

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A

E

N

R

V

V

N
|
N

-

A

-

G

-

F

I

M

Y

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T

I

V

I

A

N

E

K

D

E

E

H

L

I

R

K

L

L

R

R

T

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Y

Y

E
|
E

R
|
R

G

G

V

A

E

-

G

G

E

E

T

T

L

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A

A

C
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C

G
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G

T
x
S

G
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G

M

A

T

C

A

A

active site: C73 (= C69), H159 (= H139), E208 (= E182), C217 (= C192), G220 (= G195)
binding (2s,6s)-2,6-diamino-2-methylheptanedioic acid: N11 (= N11), F13 (= F13), Q44 (≠ G42), N64 (= N60), V70 (≠ A66), C73 (= C69), G74 (= G70), N75 (= N71), N157 (≠ V137), N190 (= N167), E208 (= E182), R209 (= R183), C217 (= C192), G218 (= G193), S219 (≠ T194)

P44859 Diaminopimelate epimerase; DAP epimerase; PLP-independent amino acid racemase; EC 5.1.1.7 from Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd) (see 2 papers)
30% identity, 78% coverage: 1:198/255 of query aligns to 1:223/274 of P44859

query
sites
P44859

M

M

F

Q

V

F

T

S

K

K

Y

M

N

H

A

G

N

L

G

G

N
|
N

D

D

F

F

V

V

I

V

F

V

H

-

D

D

N

G

Q

V

K

T

R

Q

D

N

-

V

-

F

R

T

H

P

E

E

L

T

A

I

K

R

L

R

L

L

C

A

D

N

R

R

H

H

K

C

G

G

V

I

G

G

A

F

D

D

G
x
Q

M

L

V

L

V

I

L

V

-

E

I

A

P

P

H

Y

-

D

A

P

E

E

Y

L

D

D

F

F

E

H

W

Y

E

R

F

I

Y

F

N
|
N

S

A

D

D

G

G

S

S

E

E

A

V

T

S

M

Q

C
|
C

G
|
G

N
|
N

A

G

T

A

R

R

A

C

V

F

A

A

H

R

Y

F

A

V

V

T

E

L

K

K

G

G

I

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S

T

V

N

N

K

D

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R

D

A

I

E

S

F

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S

T

T

G

Q

A

K

G

G

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T

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A

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T

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V

-

K

N

D

G

D

L

N

Y

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I

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R

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D

N

M

M

L

G

E

E

P

P

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W

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E

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P

-

A

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K

-

I

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P

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F

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T

-

A

-

N

-

K

-

F

-

E

-

K

-

N

K

Y

I

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L

L

R

R

R

T

D

D

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T

E

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L

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L

W

C

W

G

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G

G

V
x
N

P

P

H

H

L

C

V

V

A

V

E

Q

V

V

E

D

D

D

L

I

E

Q

N

T

F

A

D

N

L

V

E

E

M

Q

A

L

R

G

R

P

L

L

-

L

-

E

-

S

R

H

E

E

K

R

Y

F

D

P

A

E

N

R

V

V

N
|
N

-

A

-

G

-

F

I

M

Y

Q

T

I

V

I

A

N

E

K

D

E

E

H

L

I

R

K

L

L

R

R

T

V

Y

Y

E
|
E

R
|
R

G

G

V

A

E

-

G

G

E

E

T

T

L

Q

A

A

C
|
C

G
|
G

T
x
S

G

G

M

A

T

C

A

A

N11 (= N11) binding substrate
Q44 (≠ G42) binding substrate
N64 (= N60) binding substrate
C73 (= C69) mutation to A: Inactive as epimerase, but it is able to rapidly catalyze the HF elimination via abstraction of the C-2 hydrogen of the D,L-3-fluoro-DAP analog and is essentially unable to catalyze the same elimination with the L,L-3-fluoro-DAP analog.; mutation to S: Enzymatically active, but it adopts a more open conformation. It is able to catalyze both epimerization of DAP and HF elimination of L,L-3-fluoro-DAP and D,L-3-fluoro-DAP. Able to slowly eliminate HF but does not catalyze epimerization; when associated with S-217.
GN 74:75 (= GN 70:71) binding substrate
N157 (≠ V137) binding substrate
N190 (= N167) binding substrate
ER 208:209 (= ER 182:183) binding substrate
C217 (= C192) mutation to A: Inactive as epimerase. It is able to rapidly catalyze the HF elimination via abstraction of the C-2 hydrogen of the L,L-3-fluoro-DAP analog and is essentially unable to catalyze the same elimination with the D,L-3-fluoro-DAP analog.; mutation to S: Enzymatically active, but it adopts a more open conformation. It is able to catalyze both epimerization of DAP and HF elimination of L,L-3-fluoro-DAP and D,L-3-fluoro-DAP. Able to slowly eliminate HF but does not catalyze epimerization; when associated with S-73.
GS 218:219 (≠ GT 193:194) binding substrate

P9WP19 Diaminopimelate epimerase; DAP epimerase; PLP-independent amino acid racemase; EC 5.1.1.7 from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (see paper)
31% identity, 76% coverage: 1:195/255 of query aligns to 1:229/289 of P9WP19

query
sites
P9WP19

M

M

F

I

V

F

T

A

K

K

Y

G

N

H

A

G

N

T

G

Q

N

N

D

D

F

F

V

V

I

L

F

L

H

P

D

D

N

V

Q

D

K

A

R

E

D

L

R

V

H

L

E

T

L

A

A

A

K

R

L

V

-

A

L

L

C

C

D

D

R

R

H

R

K

K

G

G

V

L

G

G

A

A

D

D

G

G

M

V

V

L

V

R

L

V

-

T

-

A

-

G

-

A

-

Q

-

A

-

V

-

G

-

V

-

L

-

D

-

S

I

L

P

P

H

E

A

G

E

V

Y

R

D

V

F

T

E

D

W

W

-

Y

-

M

E

D

F

Y

Y

R

N

N

S

A

D

D

G

G

S

S

E

A

A

A

T

Q

M

M

C
|
C

G

G

N

N

A

G

T

V

R

R

A

V

V

F

A

A

H

H

Y

Y

A

L

V

R

E

A

K

S

G

G

I

L

S

E

V

V

N

R

D

D

R

-

A

-

E

E

F

F

L

V

T

V

G

G

A

S

-

L

-

A

-

G

-

P

-

R

G

P

V

V

I

T

T

C

A

H

E

H

V

V

N

E

G

A

L

A

Y

Y

-

A

-

D

V

V

V

S

T

V

D

D

M

M

L

G

E

K

P

A

K

N

I

R

L

L

R

G

R

A

D

G

I

E

E

A

E

V

G

G

-

G

-

R

L

F

Q

H

W

G

W

L

L

A

I

V

D

D

T

V

G

G

V

N

P

P

H

H

L

L

V

A

A

C

-

V

-

D

-

S

-

Q

-

L

E

T

V

V

E

D

D

G

L

L

E

A

N

A

F

L

D

D

L

V

E

G

M

A

A

P

R

V

R

S

L

F

R

D

E

G

K

A

Y

Q

-

F

-

P

-

D

D

G

A

V

N

N

V

V

N

E

I

V

Y

L

T

T

V

A

A

P

E

V

D

D

-

G

E

A

L

V

R

W

L

M

R

R

T

V

Y

H

E

E

R

R

G

G

V

V

E

-

G

G

E

E

T

T

L

R

A

S

C
|
C

G

G

T

T

G

G

C87 (= C69) active site, Proton donor; mutation to A: Completely abolishes the diaminopimelate epimerase activity.; mutation to S: Strongly reduces the diaminopimelate epimerase activity.
C226 (= C192) active site, Proton acceptor; mutation to A: Completely abolishes the diaminopimelate epimerase activity.; mutation to S: Strongly reduces the diaminopimelate epimerase activity.

Query Sequence

>WP_013553003.1 NCBI__GCF_000186245.1:WP_013553003.1
MFVTKYNANGNDFVIFHDNQKRDRHELAKLLCDRHKGVGADGMVVLIPHAEYDFEWEFYN
SDGSEATMCGNATRAVAHYAVEKGISVNDRAEFLTGAGVITAEVNGLYVVTDMLEPKILR
RDIEEEGLQWWLIDTGVPHLVAEVEDLENFDLEMARRLREKYDANVNIYTVAEDELRLRT
YERGVEGETLACGTGMTACYVRAREEGKARDLCIVFPRSGDELYLEYKEGRYRFGGKVDK
TFVAELTLDIPHYML

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