SitesBLAST
Comparing WP_012399501.1 NCBI__GCF_000020045.1:WP_012399501.1 to proteins with known functional sites using BLASTp with E ≤ 0.001.
Or try Sites on a Tree, PaperBLAST, Conserved Domains, or compare to all protein structures
Found 9 hits to proteins with known functional sites (download)
2gkjA Crystal structure of diaminopimelate epimerase in complex with an irreversible inhibitor dl-azidap (see paper)
52% identity, 99% coverage: 3:284/286 of query aligns to 1:274/274 of 2gkjA
- active site: C73 (= C75), H159 (= H168), E208 (= E217), C217 (= C226), G220 (= G229)
- binding (2r,6s)-2,6-diamino-2-methylheptanedioic acid: N11 (= N13), Q44 (= Q46), N64 (= N66), C73 (= C75), G74 (= G76), N75 (= N77), N157 (= N166), N190 (= N199), E208 (= E217), R209 (= R218), C217 (= C226), G218 (= G227), S219 (≠ T228)
2gkeA Crystal structure of diaminopimelate epimerase in complex with an irreversible inhibitor ll-azidap (see paper)
52% identity, 99% coverage: 3:284/286 of query aligns to 1:274/274 of 2gkeA
- active site: C73 (= C75), H159 (= H168), E208 (= E217), C217 (= C226), G220 (= G229)
- binding (2s,6s)-2,6-diamino-2-methylheptanedioic acid: N11 (= N13), F13 (= F15), Q44 (= Q46), N64 (= N66), V70 (= V72), C73 (= C75), G74 (= G76), N75 (= N77), N157 (= N166), N190 (= N199), E208 (= E217), R209 (= R218), C217 (= C226), G218 (= G227), S219 (≠ T228)
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)
52% identity, 99% coverage: 3:284/286 of query aligns to 1:274/274 of P44859
- N11 (= N13) binding substrate
- Q44 (= Q46) binding substrate
- N64 (= N66) binding substrate
- C73 (= C75) 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 76:77) binding substrate
- N157 (= N166) binding substrate
- N190 (= N199) binding substrate
- ER 208:209 (= ER 217:218) binding substrate
- C217 (= C226) 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 227:228) binding substrate
P0A6K1 Diaminopimelate epimerase; DAP epimerase; PLP-independent amino acid racemase; EC 5.1.1.7 from Escherichia coli (strain K12) (see paper)
53% identity, 99% coverage: 3:284/286 of query aligns to 1:274/274 of P0A6K1
- Y268 (≠ F278) 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, 99% coverage: 3:284/286 of query aligns to 17:301/301 of 3ejxD
- active site: C89 (= C75), H180 (= H168), E235 (= E217), C244 (= C226), G247 (= G229)
- binding (2s,6s)-2,6-diamino-2-methylheptanedioic acid: N27 (= N13), F29 (= F15), N80 (= N66), P86 (≠ V72), C89 (= C75), G90 (= G76), N91 (= N77), N178 (= N166), N217 (= N199), E235 (= E217), R236 (= R218), C244 (= C226), G245 (= G227), T246 (= T228)
3ekmA Crystal structure of diaminopimelate epimerase form arabidopsis thaliana in complex with irreversible inhibitor dl-azidap (see paper)
42% identity, 99% coverage: 3:284/286 of query aligns to 3:287/287 of 3ekmA
- active site: C75 (= C75), H166 (= H168), E221 (= E217), C230 (= C226), G233 (= G229)
- binding (2r,6s)-2,6-diamino-2-methylheptanedioic acid: N13 (= N13), N66 (= N66), P72 (≠ V72), C75 (= C75), G76 (= G76), N77 (= N77), N164 (= N166), N203 (= N199), E221 (= E217), R222 (= R218), C230 (= C226), G231 (= G227), T232 (= T228)
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: 1:284/286 of query aligns to 3:277/277 of Q8NP73
- N15 (= N13) binding substrate
- GN 84:85 (= GN 76:77) binding substrate
- N159 (= N166) binding substrate
- N194 (= N199) binding substrate
- ER 212:213 (= ER 217:218) binding substrate
- GT 222:223 (= GT 227:228) binding substrate
5m47A Crystal structure of dapf from corynebacterium glutamicum in complex with d,l-diaminopimelate (see paper)
32% identity, 99% coverage: 1:284/286 of query aligns to 3:277/280 of 5m47A
- active site: C83 (= C75), H161 (= H168), E212 (= E217), C221 (= C226), G224 (= G229)
- binding 2,6-diaminopimelic acid: N15 (= N13), N74 (= N66), C83 (= C75), G84 (= G76), N85 (= N77), N159 (= N166), N194 (= N199), E212 (= E217), R213 (= R218), C221 (= C226), G222 (= G227), T223 (= T228)
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: 3:282/286 of query aligns to 1:280/289 of P9WP19
- C87 (= C75) active site, Proton donor; mutation to A: Completely abolishes the diaminopimelate epimerase activity.; mutation to S: Strongly reduces the diaminopimelate epimerase activity.
- C226 (= C226) 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_012399501.1 NCBI__GCF_000020045.1:WP_012399501.1
MKLKFTKMHGAGNDFVVLDGYTQPLNLTETQVRALANRHFGVGADQLLVVEKPTVDGVDF
RYRIFNCDGGEVEHCGNGARCFVKFVRDSRLTDKRSVRVQVQKGVITLTMQDNGEVVVDM
GAPVFEPVQVPFDASGVEARREGNDTLYALEVNGETRWVSVVSMGNPHAVQVVDDVEAFP
VLVDGPVIETHPRFPQRVNAGFMQIVGRSEVKLRVYERGAGETLACGTGACAAVAAGIRR
GLLDAPVKVHTHGGTLTITWNGESASSLMMAGPAATVFEGEIELAD
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