SitesBLAST
Comparing WP_013451925.1 NCBI__GCF_000183405.1:WP_013451925.1 to proteins with known functional sites using BLASTp with E ≤ 0.001.
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Found 9 hits to proteins with known functional sites (download)
3ekmA Crystal structure of diaminopimelate epimerase form arabidopsis thaliana in complex with irreversible inhibitor dl-azidap (see paper)
34% identity, 96% coverage: 4:264/272 of query aligns to 3:284/287 of 3ekmA
- active site: C75 (= C76), H166 (= H150), E221 (= E200), C230 (= C210), G233 (= G213)
- binding (2r,6s)-2,6-diamino-2-methylheptanedioic acid: N13 (= N14), N66 (= N67), P72 (≠ A73), C75 (= C76), G76 (= G77), N77 (= N78), N164 (≠ V148), N203 (= N182), E221 (= E200), R222 (= R201), C230 (= C210), G231 (= G211), T232 (= T212)
3ejxD Crystal structure of diaminopimelate epimerase from arabidopsis thaliana in complex with ll-azidap (see paper)
34% identity, 96% coverage: 4:264/272 of query aligns to 17:298/301 of 3ejxD
- active site: C89 (= C76), H180 (= H150), E235 (= E200), C244 (= C210), G247 (= G213)
- binding (2s,6s)-2,6-diamino-2-methylheptanedioic acid: N27 (= N14), F29 (= F16), N80 (= N67), P86 (≠ A73), C89 (= C76), G90 (= G77), N91 (= N78), N178 (≠ V148), N217 (= N182), E235 (= E200), R236 (= R201), C244 (= C210), G245 (= G211), T246 (= T212)
2gkjA Crystal structure of diaminopimelate epimerase in complex with an irreversible inhibitor dl-azidap (see paper)
29% identity, 97% coverage: 4:266/272 of query aligns to 1:273/274 of 2gkjA
- active site: C73 (= C76), H159 (= H150), E208 (= E200), C217 (= C210), G220 (= G213)
- binding (2r,6s)-2,6-diamino-2-methylheptanedioic acid: N11 (= N14), Q44 (≠ G49), N64 (= N67), C73 (= C76), G74 (= G77), N75 (= N78), N157 (≠ V148), N190 (= N182), E208 (= E200), R209 (= R201), C217 (= C210), G218 (= G211), S219 (≠ T212)
2gkeA Crystal structure of diaminopimelate epimerase in complex with an irreversible inhibitor ll-azidap (see paper)
29% identity, 97% coverage: 4:266/272 of query aligns to 1:273/274 of 2gkeA
- active site: C73 (= C76), H159 (= H150), E208 (= E200), C217 (= C210), G220 (= G213)
- binding (2s,6s)-2,6-diamino-2-methylheptanedioic acid: N11 (= N14), F13 (= F16), Q44 (≠ G49), N64 (= N67), V70 (≠ A73), C73 (= C76), G74 (= G77), N75 (= N78), N157 (≠ V148), N190 (= N182), E208 (= E200), R209 (= R201), C217 (= C210), G218 (= G211), S219 (≠ T212)
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)
29% identity, 97% coverage: 4:266/272 of query aligns to 1:273/274 of P44859
- N11 (= N14) binding substrate
- Q44 (≠ G49) 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 (≠ V148) binding substrate
- N190 (= N182) binding substrate
- ER 208:209 (= ER 200:201) binding substrate
- C217 (= C210) 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 211:212) binding substrate
P0A6K1 Diaminopimelate epimerase; DAP epimerase; PLP-independent amino acid racemase; EC 5.1.1.7 from Escherichia coli (strain K12) (see paper)
29% identity, 96% coverage: 4:263/272 of query aligns to 1:270/274 of P0A6K1
- Y268 (= Y261) Important for dimerization; mutation to A: Significantly less active than the wild-type dimer and unable to dimerize.
5m47A Crystal structure of dapf from corynebacterium glutamicum in complex with d,l-diaminopimelate (see paper)
30% identity, 78% coverage: 4:214/272 of query aligns to 5:225/280 of 5m47A
- active site: C83 (= C76), H161 (= H150), E212 (= E200), C221 (= C210), G224 (= G213)
- binding 2,6-diaminopimelic acid: N15 (= N14), N74 (= N67), C83 (= C76), G84 (= G77), N85 (= N78), N159 (≠ V148), N194 (= N182), E212 (= E200), R213 (= R201), C221 (= C210), G222 (= G211), T223 (= T212)
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)
29% identity, 96% coverage: 4:263/272 of query aligns to 5:273/277 of Q8NP73
- N15 (= N14) binding substrate
- GN 84:85 (= GN 77:78) binding substrate
- N159 (≠ V148) binding substrate
- N194 (= N182) binding substrate
- ER 212:213 (= ER 200:201) binding substrate
- GT 222:223 (= GT 211:212) 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)
28% identity, 98% coverage: 6:271/272 of query aligns to 3:286/289 of P9WP19
- 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 (= C210) 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_013451925.1 NCBI__GCF_000183405.1:WP_013451925.1
MDGVSFWKMSGSGNDFIIIDNRTLFIDKTDFRNTVAKICKRSMSVGADGVILIEPSNKVD
FKWDFYNSDGSTAEMCGNGSRCAARFCYENGIAGKQMKFESLAGIIEAEITGCSSVKVKL
TRPSDLKLNIDIPLTDLTLNGSFVNTGVPHIAIEVDDIYNFDVKKYGREIRFHKLFSPKG
TNVNFYKILPDKTVKIRTYERGVEDETLACGTGSAAVAFILHKKSILKSPVELITTGGMK
LIIHIDVDDNVYLEGEARLVYKGTLTEESYKY
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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