SitesBLAST

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)
51% identity, 99% coverage: 3:287/289 of query aligns to 1:274/274 of P44859

query
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P44859

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N11 (= N13) binding substrate
Q44 (= Q47) binding substrate
N64 (= N67) binding substrate
C73 (= C76) 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 77:78) binding substrate
N157 (= N167) binding substrate
N190 (= N200) binding substrate
ER 208:209 (= ER 218:219) binding substrate
C217 (= C227) 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 228:229) binding substrate

P0A6K1 Diaminopimelate epimerase; DAP epimerase; PLP-independent amino acid racemase; EC 5.1.1.7 from Escherichia coli (strain K12) (see paper)
50% identity, 99% coverage: 3:287/289 of query aligns to 1:274/274 of P0A6K1

query
sites
P0A6K1

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Y268 (≠ F281) Important for dimerization; mutation to A: Significantly less active than the wild-type dimer and unable to dimerize.

3ejxD Crystal structure of diaminopimelate epimerase from arabidopsis thaliana in complex with ll-azidap (see paper)
42% identity, 97% coverage: 3:283/289 of query aligns to 17:297/301 of 3ejxD

query
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3ejxD

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active site: C89 (= C76), H180 (= H169), E235 (= E218), C244 (= C227), G247 (= G230)
binding (2s,6s)-2,6-diamino-2-methylheptanedioic acid: N27 (= N13), F29 (= F15), N80 (= N67), P86 (≠ V73), C89 (= C76), G90 (= G77), N91 (= N78), N178 (= N167), N217 (= N200), E235 (= E218), R236 (= R219), C244 (= C227), G245 (= G228), T246 (= T229)

3ekmA Crystal structure of diaminopimelate epimerase form arabidopsis thaliana in complex with irreversible inhibitor dl-azidap (see paper)
42% identity, 97% coverage: 3:283/289 of query aligns to 3:283/287 of 3ekmA

query
sites
3ekmA

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active site: C75 (= C76), H166 (= H169), E221 (= E218), C230 (= C227), G233 (= G230)
binding (2r,6s)-2,6-diamino-2-methylheptanedioic acid: N13 (= N13), N66 (= N67), P72 (≠ V73), C75 (= C76), G76 (= G77), N77 (= N78), N164 (= N167), N203 (= N200), E221 (= E218), R222 (= R219), C230 (= C227), G231 (= G228), T232 (= T229)

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)
32% identity, 99% coverage: 1:287/289 of query aligns to 3:277/277 of Q8NP73

query
sites
Q8NP73

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I

S

P

F

F

T

A

K

K

M

G

H

H

G

A

A

T

G

E

N
|
N

D

D

F

F

V

I

L

I

D

P

G

D

Y

E

S

D

H

A

T

R

L

L

P

D

P

-

L

L

T

T

D

P

V

E

Q

M

V

V

R

V

A

T

L

L

A

C

D

D

R

R

H

R

F

A

G

G

I

I

G

G

A

A

D

D

Q

G

L

I

L

L

V

R

V

V

-

V

-

K

-

A

-

D

-

V

E

E

K

G

P

S

T

T

V

V

D

D

G

P

A

S

D

L

F

W

K

F

Y

M

R

D

I

Y

F

R

N

N

C

A

D

D

G

G

G

S

E

L

V

A

E

E

H

M

C

C

G
|
G

N
|
N

G

G

A

V

R

R

C

L

F

F

V

A

K

H

F

W

V

L

T

Y

D

S

R

R

G

G

L

L

T

V

D

D

K

N

R

T

S

S

V

F

R

D

V

I

Q

G

V

T

M

R

K

A

G

G

L

V

-

R

-

H

-

V

-

D

I

I

T

L

L

Q

T

A

M

D

Q

Q

D

H

N

S

G

A

E

Q

V

V

V

R

V

V

D

D

M

M

G

G

A

I

P

P

V

-

F

-

E

-

P

-

A

-

Q

-

V

-

P

-

F

-

D

D

A

V

S

T

G

G

L

L

D

S

G

-

R

-

T

-

D

-

G

-

N

-

D

-

T

-

L

-

W

-

P

T

L

C

D

D

V

I

G

N

G

G

A

Q

T

V

R

F

W

A

V

G

S

L

T

G

V

V

S

D

M

M

G

G

N
|
N

P

P

H

H

A

L

V

A

Q

C

V

V

D

-

A

-

E

-

A

-

Y

-

P

P

V

G

L

L

A

S

E

A

G

S

P

A

L

L

I

A

E

D

R

M

H

E

A

L

R

R

-

A

-

P

-

T

-

F

-

D

-

Q

-

E

-

F

F

F

P

P

K

H

R

G

V

V

N
|
N

A

V

G

E

F

I

M

V

Q

T

I

E

V

L

S

E

R

D

H

D

E

A

V

V

K

S

L

M

R

R

V

V

Y

W

E
|
E

R
|
R

G

G

A

V

G

G

E

E

T

T

L

R

A

S

C

C

G
|
G

T
|
T

G

G

A

T

C

V

-

A

A

A

V

C

A

A

G

L

I

A

R

D

R

A

G

G

L

L

L

G

D

E

T

G

P

T

V

V

T

K

V

V

H

C

T

V

H

P

G

G

T

E

L

V

T

E

I

V

S

Q

W

-

D

-

G

-

A

I

H

F

D

D

E

D

R

G

A

S

A

T

L

L

T

T

M

-

A

-

G

G

P

P

A

S

T

A

T

I

V

I

F

A

E

L

G

G

E

E

I

V

E

Q

L

I

N15 (= N13) binding substrate
GN 84:85 (= GN 77:78) binding substrate
N159 (= N167) binding substrate
N194 (= N200) binding substrate
ER 212:213 (= ER 218:219) binding substrate
GT 222:223 (= GT 228:229) binding substrate

5m47A Crystal structure of dapf from corynebacterium glutamicum in complex with d,l-diaminopimelate (see paper)
32% identity, 100% coverage: 1:288/289 of query aligns to 3:278/280 of 5m47A

query
sites
5m47A

M

L

K

T

L

I

S

P

F

F

T

A

K

K

M

G

H

H

G

A

A

T

G

E

N
|
N

D

D

F

F

V

I

L

I

D

P

G

D

Y

E

S

D

H

A

T

R

L

L

P

D

P

-

L

L

T

T

D

P

V

E

Q

M

V

V

R

V

A

T

L

L

A

C

D

D

R

R

H

R

F

A

G

G

I

I

G

G

A

A

D

D

Q

G

L

I

L

L

V

R

V

V

-

V

-

K

-

A

-

D

-

V

E

E

K

G

P

S

T

T

V

V

D

D

G

P

A

S

D

L

F

W

K

F

Y

M

R

D

I

Y

F

R

N
|
N

C

A

D

D

G

G

G

S

E

L

V

A

E

E

H

M

C
|
C

G
|
G

N
|
N

G

G

A

V

R

R

C

L

F

F

V

A

K

H

F

W

V

L

T

Y

D

S

R

R

G

G

L

L

T

V

D

D

K

N

R

T

S

S

V

F

R

D

V

I

Q

G

V

T

M

R

K

A

G

G

L

V

-

R

-

H

-

V

-

D

I

I

T

L

L

Q

T

A

M

D

Q

Q

D

H

N

S

G

A

E

Q

V

V

V

R

V

V

D

D

M

M

G

G

A

I

P

P

V

-

F

-

E

-

P

-

A

-

Q

-

V

-

P

-

F

-

D

D

A

V

S

T

G

G

L

L

D

S

G

-

R

-

T

-

D

-

G

-

N

-

D

-

T

-

L

-

W

-

P

T

L

C

D

D

V

I

G

N

G

G

A

Q

T

V

R

F

W

A

V

G

S

L

T

G

V

V

S

D

M

M

G

G

N
|
N

P

P

H
|
H

A

L

V

A

Q

C

V

V

D

-

A

-

E

-

A

-

Y

-

P

P

V

G

L

L

A

S

E

A

G

S

P

A

L

L

I

A

E

D

R

M

H

E

A

L

R

R

-

A

-

P

-

T

-

F

-

D

-

Q

-

E

-

F

F

F

P

P

K

H

R

G

V

V

N
|
N

A

V

G

E

F

I

M

V

Q

T

I

E

V

L

S

E

R

D

H

D

E

A

V

V

K

S

L

M

R

R

V

V

Y

W

E
|
E

R
|
R

G

G

A

V

G

G

E

E

T

T

L

R

A

S

C
|
C

G
|
G

T
|
T

G
|
G

A

T

C

V

-

A

A

A

V

C

A

A

G

L

I

A

R

D

R

A

G

G

L

L

L

G

D

E

T

G

P

T

V

V

T

K

V

V

H

C

T

V

H

P

G

G

T

E

L

V

T

E

I

V

S

Q

W

I

-

F

-

D

D

D

G

G

A

S

H

-

D

-

E

-

R

-

A

-

L

-

T

T

M

L

A

T

G

G

P

P

A

S

T

A

T

I

V

I

F

A

E

L

G

G

E

E

I

V

E

Q

L

I

N

H

active site: C83 (= C76), H161 (= H169), E212 (= E218), C221 (= C227), G224 (= G230)
binding 2,6-diaminopimelic acid: N15 (= N13), N74 (= N67), C83 (= C76), G84 (= G77), N85 (= N78), N159 (= N167), N194 (= N200), E212 (= E218), R213 (= R219), C221 (= C227), G222 (= G228), T223 (= T229)

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, 98% coverage: 3:285/289 of query aligns to 1:280/289 of P9WP19

query
sites
P9WP19

L

M

S

I

F

F

T

A

K

K

M

G

H

H

G

G

A

T

G

Q

N

N

D

D

F

F

V

V

V

L

L

L

D

P

G

D

Y

V

S

D

H

A

T

E

L

L

P

V

P

-

L

L

T

T

D

A

V

A

Q

R

V

V

R

A

A

A

L

L

A

C

D

D

R

R

H

R

F

K

G

G

I

L

G

G

A

A

D

D

Q

G

L

V

L

L

V

R

V

V

E

T

K

T

P

A

T

G

V

A

D

A

G

Q

A

A

-

V

-

G

-

V

-

L

-

D

-

S

-

L

-

P

-

E

-

G

-

V

-

R

-

V

-

T

D

D

F

W

K

Y

Y

M

R

D

I

Y

F

R

N

N

C

A

D

D

G

G

G

S

E

A

V

A

E

Q

H

M

C
|
C

G

G

N

N

G

G

A

V

R

R

C

V

F

F

V

A

K

H

F

Y

V

L

T

R

D

A

R

S

G

G

L

L

T

E

D

V

K

R

R

D

S

E

V

F

R

V

V

V

Q

G

V

S

M

L

K

A

G

G

L

P

I

R

T

P

L

V

T

T

M

C

Q

H

D

H

-

V

-

E

-

A

N

Y

G

A

E

D

V

V

V

S

V

V

D

D

M

M

G

G

A

K

P

A

V

-

F

-

E

-

P

-

A

-

Q

-

V

-

P

-

F

-

D

-

A

-

S

-

G

-

L

-

D

-

G

N

R

R

T

L

D

G

G

A

N

G

D

E

T

A

L

V

W

-

P

-

L

-

D

-

V

V

G

G

A

R

T

R

R

F

W

H

V

G

S

L

T

A

V

V

S

D

M

V

G

G

N

N

P

P

H

H

A

L

V

A

Q

C

V

V

-

D

-

S

-

Q

-

L

-

T

V

V

D

D

D

G

A

L

E

A

A

A

Y

L

P

D

V

V

L

G

A

A

E

-

G

-

P

P

L

V

I

S

E

F

R

D

H

G

A

A

R

Q

F

F

P

P

K

D

R

G

V

V

N

N

A

V

G

E

F

V

M

L

Q

T

I

A

V

P

S

V

R

D

H

G

E

A

V

V

K

W

L

M

R

R

V

V

Y

H

E

E

R

R

G

G

A

V

G

G

E

E

T

T

L

R

A

S

C
|
C

G

G

T

T

G

G

-

T

A

V

C

A

A

A

V

V

A

A

G

L

I

A

R

A

R

V

G

G

L

S

L

P

D

T

T

G

P

T

V

L

T

T

V

V

H

H

T

V

H

P

G

G

T

E

L

V

T

V

I

V

S

T

W

V

D

-

G

-

A

-

H

-

D

-

E

T

R

D

A

A

A

T

L

S

T

F

M

L

A

R

G

G

P

P

A

S

T

V

T

L

V

V

F

A

E

R

G

G

E

D

I

L

C87 (= C76) active site, Proton donor; mutation to A: Completely abolishes the diaminopimelate epimerase activity.; mutation to S: Strongly reduces the diaminopimelate epimerase activity.
C226 (= C227) 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_011886321.1 NCBI__GCF_000016205.1:WP_011886321.1
MKLSFTKMHGAGNDFVVLDGYSHTLPPLTDVQVRALADRHFGIGADQLLVVEKPTVDGAD
FKYRIFNCDGGEVEHCGNGARCFVKFVTDRGLTDKRSVRVQVMKGLITLTMQDNGEVVVD
MGAPVFEPAQVPFDASGLDGRTDGNDTLWPLDVGGATRWVSTVSMGNPHAVQVVDDAEAY
PVLAEGPLIERHARFPKRVNAGFMQIVSRHEVKLRVYERGAGETLACGTGACAAVAAGIR
RGLLDTPVTVHTHGGTLTISWDGAHDERAALTMAGPATTVFEGEIELNV

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