SitesBLAST
Comparing WP_011427146.1 NCBI__GCF_000092045.1:WP_011427146.1 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)
3ejxD Crystal structure of diaminopimelate epimerase from arabidopsis thaliana in complex with ll-azidap (see paper)
34% identity, 93% coverage: 2:281/301 of query aligns to 14:297/301 of 3ejxD
- active site: C89 (= C76), H180 (= H165), E235 (= E215), C244 (= C224), G247 (≠ A227)
- binding (2s,6s)-2,6-diamino-2-methylheptanedioic acid: N27 (= N15), F29 (≠ I17), N80 (= N67), P86 (≠ A73), C89 (= C76), G90 (= G77), N91 (= N78), N178 (= N163), N217 (= N197), E235 (= E215), R236 (= R216), C244 (= C224), G245 (= G225), T246 (≠ S226)
3ekmA Crystal structure of diaminopimelate epimerase form arabidopsis thaliana in complex with irreversible inhibitor dl-azidap (see paper)
35% identity, 93% coverage: 3:281/301 of query aligns to 1:283/287 of 3ekmA
- active site: C75 (= C76), H166 (= H165), E221 (= E215), C230 (= C224), G233 (≠ A227)
- binding (2r,6s)-2,6-diamino-2-methylheptanedioic acid: N13 (= N15), N66 (= N67), P72 (≠ A73), C75 (= C76), G76 (= G77), N77 (= N78), N164 (= N163), N203 (= N197), E221 (= E215), R222 (= R216), C230 (= C224), G231 (= G225), T232 (≠ S226)
2gkjA Crystal structure of diaminopimelate epimerase in complex with an irreversible inhibitor dl-azidap (see paper)
33% identity, 92% coverage: 5:281/301 of query aligns to 1:270/274 of 2gkjA
- active site: C73 (= C76), H159 (= H165), E208 (= E215), C217 (= C224), G220 (≠ A227)
- binding (2r,6s)-2,6-diamino-2-methylheptanedioic acid: N11 (= N15), Q44 (= Q47), N64 (= N67), C73 (= C76), G74 (= G77), N75 (= N78), N157 (= N163), N190 (= N197), E208 (= E215), R209 (= R216), C217 (= C224), G218 (= G225), S219 (= S226)
2gkeA Crystal structure of diaminopimelate epimerase in complex with an irreversible inhibitor ll-azidap (see paper)
33% identity, 92% coverage: 5:281/301 of query aligns to 1:270/274 of 2gkeA
- active site: C73 (= C76), H159 (= H165), E208 (= E215), C217 (= C224), G220 (≠ A227)
- binding (2s,6s)-2,6-diamino-2-methylheptanedioic acid: N11 (= N15), F13 (≠ I17), Q44 (= Q47), N64 (= N67), V70 (≠ A73), C73 (= C76), G74 (= G77), N75 (= N78), N157 (= N163), N190 (= N197), E208 (= E215), R209 (= R216), C217 (= C224), G218 (= G225), S219 (= S226)
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)
33% identity, 92% coverage: 5:281/301 of query aligns to 1:270/274 of P44859
- N11 (= N15) 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 (= N163) binding substrate
- N190 (= N197) binding substrate
- ER 208:209 (= ER 215:216) binding substrate
- C217 (= C224) 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 (= GS 225:226) binding substrate
P0A6K1 Diaminopimelate epimerase; DAP epimerase; PLP-independent amino acid racemase; EC 5.1.1.7 from Escherichia coli (strain K12) (see paper)
33% identity, 92% coverage: 5:281/301 of query aligns to 1:270/274 of P0A6K1
- Y268 (≠ W279) Important for dimerization; mutation to A: Significantly less active than the wild-type dimer and unable to dimerize.
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)
27% identity, 91% coverage: 1:275/301 of query aligns to 1:267/277 of Q8NP73
- N15 (= N15) binding substrate
- GN 84:85 (= GN 77:78) binding substrate
- N159 (= N163) binding substrate
- N194 (= N197) binding substrate
- ER 212:213 (= ER 215:216) binding substrate
- GT 222:223 (≠ GS 225:226) binding substrate
5m47A Crystal structure of dapf from corynebacterium glutamicum in complex with d,l-diaminopimelate (see paper)
27% identity, 91% coverage: 1:275/301 of query aligns to 1:267/280 of 5m47A
- active site: C83 (= C76), H161 (= H165), E212 (= E215), C221 (= C224), G224 (≠ A227)
- binding 2,6-diaminopimelic acid: N15 (= N15), N74 (= N67), C83 (= C76), G84 (= G77), N85 (= N78), N159 (= N163), N194 (= N197), E212 (= E215), R213 (= R216), C221 (= C224), G222 (= G225), T223 (≠ S226)
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, 60% coverage: 47:227/301 of query aligns to 55:229/289 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 (= C224) 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_011427146.1 NCBI__GCF_000092045.1:WP_011427146.1
MSATVEFARMNGLGNKILVVDMRGRSDKVTPAAAVALNADPQTEFDQIMAIHDPKADGTD
AFIDILNSDGSKAQACGNGTRCVVQALAAETGRKAFTFQTVAGILNAIEHEDGTISVDMG
KPVFDWDRIPLAEEFHDTSRIELQIGPIDNPLLHSPSAMSMGNPHAIFWVDKDVMSYDLA
RFGPLLENHPMFPERANITLAQVTSPTTMTTRTWERGAGLTLACGSAACSAAVSAARTGR
TGRKVKINVASAKPPAMLSIEWRERDDHVIMTGPAEWEWSGRLDPATGCWSRDDAREVEA
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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