SitesBLAST
Comparing WP_013553003.1 NCBI__GCF_000186245.1:WP_013553003.1 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)
30% identity, 90% coverage: 1:229/255 of query aligns to 17:280/301 of 3ejxD
- active site: C89 (= C69), H180 (= H139), E235 (= E182), C244 (= C192), G247 (= G195)
- binding (2s,6s)-2,6-diamino-2-methylheptanedioic acid: N27 (= N11), F29 (= F13), N80 (= N60), P86 (≠ A66), C89 (= C69), G90 (= G70), N91 (= N71), N178 (≠ V137), N217 (= N167), E235 (= E182), R236 (= R183), C244 (= C192), G245 (= G193), T246 (= T194)
3ekmA Crystal structure of diaminopimelate epimerase form arabidopsis thaliana in complex with irreversible inhibitor dl-azidap (see paper)
30% identity, 90% coverage: 1:229/255 of query aligns to 3:266/287 of 3ekmA
- active site: C75 (= C69), H166 (= H139), E221 (= E182), C230 (= C192), G233 (= G195)
- binding (2r,6s)-2,6-diamino-2-methylheptanedioic acid: N13 (= N11), N66 (= N60), P72 (≠ A66), C75 (= C69), G76 (= G70), N77 (= N71), N164 (≠ V137), N203 (= N167), E221 (= E182), R222 (= R183), C230 (= C192), G231 (= G193), T232 (= T194)
P0A6K1 Diaminopimelate epimerase; DAP epimerase; PLP-independent amino acid racemase; EC 5.1.1.7 from Escherichia coli (strain K12) (see paper)
31% identity, 81% coverage: 1:207/255 of query aligns to 1:232/274 of P0A6K1
Sites not aligning to the query:
- 268 Important for dimerization; Y→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)
33% identity, 75% coverage: 5:195/255 of query aligns to 9:224/277 of Q8NP73
- N15 (= N11) binding substrate
- GN 84:85 (= GN 70:71) binding substrate
- N159 (≠ V137) binding substrate
- N194 (= N167) binding substrate
- ER 212:213 (= ER 182:183) binding substrate
- GT 222:223 (= GT 193:194) binding substrate
5m47A Crystal structure of dapf from corynebacterium glutamicum in complex with d,l-diaminopimelate (see paper)
33% identity, 75% coverage: 5:195/255 of query aligns to 9:224/280 of 5m47A
- active site: C83 (= C69), H161 (= H139), E212 (= E182), C221 (= C192), G224 (= G195)
- binding 2,6-diaminopimelic acid: N15 (= N11), N74 (= N60), C83 (= C69), G84 (= G70), N85 (= N71), N159 (≠ V137), N194 (= N167), E212 (= E182), R213 (= R183), C221 (= C192), G222 (= G193), T223 (= T194)
2gkjA Crystal structure of diaminopimelate epimerase in complex with an irreversible inhibitor dl-azidap (see paper)
30% identity, 78% coverage: 1:198/255 of query aligns to 1:223/274 of 2gkjA
- active site: C73 (= C69), H159 (= H139), E208 (= E182), C217 (= C192), G220 (= G195)
- binding (2r,6s)-2,6-diamino-2-methylheptanedioic acid: N11 (= N11), Q44 (≠ G42), N64 (= N60), C73 (= C69), G74 (= G70), N75 (= N71), N157 (≠ V137), N190 (= N167), E208 (= E182), R209 (= R183), C217 (= C192), G218 (= G193), S219 (≠ T194)
2gkeA Crystal structure of diaminopimelate epimerase in complex with an irreversible inhibitor ll-azidap (see paper)
30% identity, 78% coverage: 1:198/255 of query aligns to 1:223/274 of 2gkeA
- active site: C73 (= C69), H159 (= H139), E208 (= E182), C217 (= C192), G220 (= G195)
- binding (2s,6s)-2,6-diamino-2-methylheptanedioic acid: N11 (= N11), F13 (= F13), Q44 (≠ G42), N64 (= N60), V70 (≠ A66), C73 (= C69), G74 (= G70), N75 (= N71), N157 (≠ V137), N190 (= N167), E208 (= E182), R209 (= R183), C217 (= C192), G218 (= G193), S219 (≠ T194)
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, 78% coverage: 1:198/255 of query aligns to 1:223/274 of P44859
- N11 (= N11) binding substrate
- Q44 (≠ G42) binding substrate
- N64 (= N60) binding substrate
- C73 (= C69) 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 70:71) binding substrate
- N157 (≠ V137) binding substrate
- N190 (= N167) binding substrate
- ER 208:209 (= ER 182:183) binding substrate
- C217 (= C192) 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 193:194) 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)
31% identity, 76% coverage: 1:195/255 of query aligns to 1:229/289 of P9WP19
- C87 (= C69) active site, Proton donor; mutation to A: Completely abolishes the diaminopimelate epimerase activity.; mutation to S: Strongly reduces the diaminopimelate epimerase activity.
- C226 (= C192) 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_013553003.1 NCBI__GCF_000186245.1:WP_013553003.1
MFVTKYNANGNDFVIFHDNQKRDRHELAKLLCDRHKGVGADGMVVLIPHAEYDFEWEFYN
SDGSEATMCGNATRAVAHYAVEKGISVNDRAEFLTGAGVITAEVNGLYVVTDMLEPKILR
RDIEEEGLQWWLIDTGVPHLVAEVEDLENFDLEMARRLREKYDANVNIYTVAEDELRLRT
YERGVEGETLACGTGMTACYVRAREEGKARDLCIVFPRSGDELYLEYKEGRYRFGGKVDK
TFVAELTLDIPHYML
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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