SitesBLAST
Comparing Ac3H11_1993 FitnessBrowser__acidovorax_3H11:Ac3H11_1993 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)
52% identity, 98% coverage: 1:281/286 of query aligns to 6:274/274 of P0A6K1
- Y268 (≠ F275) 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)
49% identity, 98% coverage: 1:281/286 of query aligns to 6:274/274 of 2gkjA
- active site: C73 (= C68), H159 (= H165), E208 (= E214), C217 (= C223), G220 (= G226)
- binding (2r,6s)-2,6-diamino-2-methylheptanedioic acid: N11 (= N6), Q44 (= Q39), N64 (= N59), C73 (= C68), G74 (= G69), N75 (= N70), N157 (= N163), N190 (= N196), E208 (= E214), R209 (= R215), C217 (= C223), G218 (= G224), S219 (≠ T225)
2gkeA Crystal structure of diaminopimelate epimerase in complex with an irreversible inhibitor ll-azidap (see paper)
49% identity, 98% coverage: 1:281/286 of query aligns to 6:274/274 of 2gkeA
- active site: C73 (= C68), H159 (= H165), E208 (= E214), C217 (= C223), G220 (= G226)
- binding (2s,6s)-2,6-diamino-2-methylheptanedioic acid: N11 (= N6), F13 (= F8), Q44 (= Q39), N64 (= N59), V70 (= V65), C73 (= C68), G74 (= G69), N75 (= N70), N157 (= N163), N190 (= N196), E208 (= E214), R209 (= R215), C217 (= C223), G218 (= G224), S219 (≠ T225)
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)
49% identity, 98% coverage: 1:281/286 of query aligns to 6:274/274 of P44859
- N11 (= N6) binding
- Q44 (= Q39) binding
- N64 (= N59) binding
- C73 (= C68) 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 69:70) binding
- N157 (= N163) binding
- N190 (= N196) binding
- ER 208:209 (= ER 214:215) binding
- C217 (= C223) 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 224:225) binding
3ejxD Crystal structure of diaminopimelate epimerase from arabidopsis thaliana in complex with ll-azidap (see paper)
41% identity, 97% coverage: 2:278/286 of query aligns to 23:298/301 of 3ejxD
- active site: C89 (= C68), H180 (= H165), E235 (= E214), C244 (= C223), G247 (= G226)
- binding (2s,6s)-2,6-diamino-2-methylheptanedioic acid: N27 (= N6), F29 (= F8), N80 (= N59), P86 (≠ V65), C89 (= C68), G90 (= G69), N91 (= N70), N178 (= N163), N217 (= N196), E235 (= E214), R236 (= R215), C244 (= C223), G245 (= G224), T246 (= T225)
3ekmA Crystal structure of diaminopimelate epimerase form arabidopsis thaliana in complex with irreversible inhibitor dl-azidap (see paper)
41% identity, 97% coverage: 2:278/286 of query aligns to 9:284/287 of 3ekmA
- active site: C75 (= C68), H166 (= H165), E221 (= E214), C230 (= C223), G233 (= G226)
- binding (2r,6s)-2,6-diamino-2-methylheptanedioic acid: N13 (= N6), N66 (= N59), P72 (≠ V65), C75 (= C68), G76 (= G69), N77 (= N70), N164 (= N163), N203 (= N196), E221 (= E214), R222 (= R215), C230 (= C223), G231 (= G224), T232 (= T225)
Q8NP73 Diaminopimelate epimerase; DAP epimerase; PLP-independent amino acid racemase; EC 5.1.1.7 from Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / BCRC 11384 / JCM 1318 / LMG 3730 / NCIMB 10025)
32% identity, 97% coverage: 6:281/286 of query aligns to 15:277/277 of Q8NP73
5m47A Crystal structure of dapf from corynebacterium glutamicum in complex with d,l-diaminopimelate (see paper)
32% identity, 97% coverage: 6:281/286 of query aligns to 15:277/280 of 5m47A
- active site: C83 (= C68), H161 (= H165), E212 (= E214), C221 (= C223), G224 (= G226)
- binding 2,6-diaminopimelic acid: N15 (= N6), N74 (= N59), C83 (= C68), G84 (= G69), N85 (= N70), N159 (= N163), N194 (= N196), E212 (= E214), R213 (= R215), C221 (= C223), G222 (= G224), T223 (= T225)
P9WP19 Diaminopimelate epimerase; DAP epimerase; PLP-independent amino acid racemase; EC 5.1.1.7 from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (see paper)
32% identity, 79% coverage: 2:226/286 of query aligns to 7:229/289 of P9WP19
- C87 (= C68) active site, Proton donor; mutation to A: Completely abolishes the diaminopimelate epimerase activity.; mutation to S: Strongly reduces the diaminopimelate epimerase activity.
- C226 (= C223) active site, Proton acceptor; mutation to A: Completely abolishes the diaminopimelate epimerase activity.; mutation to S: Strongly reduces the diaminopimelate epimerase activity.
Query Sequence
>Ac3H11_1993 FitnessBrowser__acidovorax_3H11:Ac3H11_1993
MQGAGNDFVVLDETQGRLGLSAAQYRFLADRHFGVGADQILTVRPSPAEGIDFEYVIHNA
DGGEVEQCGNGARCFARFVHDKGLTGKDQIRVQTQSGVIAPRLTADGRVTVDMGRPEFDP
AKVPFDASGLVPVAQGLGQKWPLPPDGKALSAIVLVAIVSMGNPHAVQLVDNVDTAPVQE
TGPLIESHPRFPQRVNAGYLQIVDRAHVRLRVFERGVGETLACGTGACAAVAAGIRLGLL
DPEVQVDTRGGRLTIAWSGQEADSVFMTGPATTVFEGQIDIPDTLV
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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