SitesBLAST
Comparing WP_012503123.1 NCBI__GCF_000020505.1:WP_012503123.1 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)
P0A6K1 Diaminopimelate epimerase; DAP epimerase; PLP-independent amino acid racemase; EC 5.1.1.7 from Escherichia coli (strain K12) (see paper)
32% identity, 99% coverage: 3:264/264 of query aligns to 1:274/274 of P0A6K1
- Y268 (= Y258) Important for dimerization; mutation to A: Significantly less active than the wild-type dimer and unable to dimerize.
2gkjA Crystal structure of diaminopimelate epimerase in complex with an irreversible inhibitor dl-azidap (see paper)
30% identity, 99% coverage: 3:264/264 of query aligns to 1:274/274 of 2gkjA
- active site: C73 (= C73), H159 (= H145), E208 (= E195), C217 (= C205), G220 (= G208)
- binding (2r,6s)-2,6-diamino-2-methylheptanedioic acid: N11 (= N13), Q44 (≠ G46), N64 (= N64), C73 (= C73), G74 (= G74), N75 (= N75), N157 (≠ S143), N190 (= N177), E208 (= E195), R209 (= R196), C217 (= C205), G218 (= G206), S219 (≠ T207)
2gkeA Crystal structure of diaminopimelate epimerase in complex with an irreversible inhibitor ll-azidap (see paper)
30% identity, 99% coverage: 3:264/264 of query aligns to 1:274/274 of 2gkeA
- active site: C73 (= C73), H159 (= H145), E208 (= E195), C217 (= C205), G220 (= G208)
- binding (2s,6s)-2,6-diamino-2-methylheptanedioic acid: N11 (= N13), F13 (= F15), Q44 (≠ G46), N64 (= N64), V70 (≠ G70), C73 (= C73), G74 (= G74), N75 (= N75), N157 (≠ S143), N190 (= N177), E208 (= E195), R209 (= R196), C217 (= C205), G218 (= G206), S219 (≠ T207)
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, 99% coverage: 3:264/264 of query aligns to 1:274/274 of P44859
- N11 (= N13) binding substrate
- Q44 (≠ G46) binding substrate
- N64 (= N64) binding substrate
- C73 (= C73) 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 74:75) binding substrate
- N157 (≠ S143) binding substrate
- N190 (= N177) binding substrate
- ER 208:209 (= ER 195:196) binding substrate
- C217 (= C205) 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 206:207) binding substrate
3ejxD Crystal structure of diaminopimelate epimerase from arabidopsis thaliana in complex with ll-azidap (see paper)
29% identity, 99% coverage: 3:264/264 of query aligns to 17:301/301 of 3ejxD
- active site: C89 (= C73), H180 (= H145), E235 (= E195), C244 (= C205), G247 (= G208)
- binding (2s,6s)-2,6-diamino-2-methylheptanedioic acid: N27 (= N13), F29 (= F15), N80 (= N64), P86 (≠ G70), C89 (= C73), G90 (= G74), N91 (= N75), N178 (≠ S143), N217 (= N177), E235 (= E195), R236 (= R196), C244 (= C205), G245 (= G206), T246 (= T207)
3ekmA Crystal structure of diaminopimelate epimerase form arabidopsis thaliana in complex with irreversible inhibitor dl-azidap (see paper)
29% identity, 99% coverage: 3:264/264 of query aligns to 3:287/287 of 3ekmA
- active site: C75 (= C73), H166 (= H145), E221 (= E195), C230 (= C205), G233 (= G208)
- binding (2r,6s)-2,6-diamino-2-methylheptanedioic acid: N13 (= N13), N66 (= N64), P72 (≠ G70), C75 (= C73), G76 (= G74), N77 (= N75), N164 (≠ S143), N203 (= N177), E221 (= E195), R222 (= R196), C230 (= C205), G231 (= G206), T232 (= T207)
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, 100% coverage: 1:264/264 of query aligns to 3:277/277 of Q8NP73
- N15 (= N13) binding substrate
- GN 84:85 (= GN 74:75) binding substrate
- N159 (≠ S143) binding substrate
- N194 (= N177) binding substrate
- ER 212:213 (= ER 195:196) binding substrate
- GT 222:223 (= GT 206:207) binding substrate
5m47A Crystal structure of dapf from corynebacterium glutamicum in complex with d,l-diaminopimelate (see paper)
33% identity, 100% coverage: 1:264/264 of query aligns to 3:277/280 of 5m47A
- active site: C83 (= C73), H161 (= H145), E212 (= E195), C221 (= C205), G224 (= G208)
- binding 2,6-diaminopimelic acid: N15 (= N13), N74 (= N64), C83 (= C73), G84 (= G74), N85 (= N75), N159 (≠ S143), N194 (= N177), E212 (= E195), R213 (= R196), C221 (= C205), G222 (= G206), T223 (= T207)
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: 5:263/264 of query aligns to 3:281/289 of P9WP19
- C87 (= C73) active site, Proton donor; mutation to A: Completely abolishes the diaminopimelate epimerase activity.; mutation to S: Strongly reduces the diaminopimelate epimerase activity.
- C226 (= C205) 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_012503123.1 NCBI__GCF_000020505.1:WP_012503123.1
MQIEFTKMSGAGNDFIVIDNRQSQFNLEPEQVHAMCTRRTGIGADGLILIEASETADFRM
NYHNADGYPGSMCGNGGRCAVYFSYLIGIRPAGNRYRFEAGPGTYEAEITGKESVRLHML
PPKNFRDDLHAGAWSCHFVDTGSPHAIAYVDNLDQMDVFTEGRTIRNNKEVFPEGTNVNF
LEVTAPDALSIRTFERGVEDETLACGTGTVAAALMSYRLGKVASSPVRVTVRSGETLMVG
FNDAMDEIYLEGPARPVYQGTIAL
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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