SitesBLAST
Comparing GFF3002 FitnessBrowser__WCS417:GFF3002 to proteins with known functional sites using BLASTp with E ≤ 0.001.
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Found 8 hits to proteins with known functional sites (download)
2gkjA Crystal structure of diaminopimelate epimerase in complex with an irreversible inhibitor dl-azidap (see paper)
34% identity, 97% coverage: 3:262/267 of query aligns to 1:270/274 of 2gkjA
- active site: C73 (= C73), H159 (= H152), E208 (= E201), C217 (≠ S210), G220 (≠ C213)
- binding (2r,6s)-2,6-diamino-2-methylheptanedioic acid: N11 (≠ D13), Q44 (= Q46), N64 (= N64), C73 (= C73), G74 (= G74), N75 (≠ S75), N157 (= N150), N190 (= N183), E208 (= E201), R209 (= R202), C217 (≠ S210), G218 (= G211), S219 (= S212)
2gkeA Crystal structure of diaminopimelate epimerase in complex with an irreversible inhibitor ll-azidap (see paper)
34% identity, 97% coverage: 3:262/267 of query aligns to 1:270/274 of 2gkeA
- active site: C73 (= C73), H159 (= H152), E208 (= E201), C217 (≠ S210), G220 (≠ C213)
- binding (2s,6s)-2,6-diamino-2-methylheptanedioic acid: N11 (≠ D13), F13 (= F15), Q44 (= Q46), N64 (= N64), V70 (≠ L70), C73 (= C73), G74 (= G74), N75 (≠ S75), N157 (= N150), N190 (= N183), E208 (= E201), R209 (= R202), C217 (≠ S210), G218 (= G211), S219 (= S212)
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)
34% identity, 97% coverage: 3:262/267 of query aligns to 1:270/274 of P44859
- N11 (≠ D13) binding
- Q44 (= Q46) binding
- N64 (= N64) binding
- 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 (≠ GS 74:75) binding
- N157 (= N150) binding
- N190 (= N183) binding
- ER 208:209 (= ER 201:202) binding
- C217 (≠ S210) 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 211:212) binding
P0A6K1 Diaminopimelate epimerase; DAP epimerase; PLP-independent amino acid racemase; EC 5.1.1.7 from Escherichia coli (strain K12) (see paper)
36% identity, 97% coverage: 3:262/267 of query aligns to 1:270/274 of P0A6K1
- Y268 (≠ M260) 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)
34% identity, 99% coverage: 3:266/267 of query aligns to 17:301/301 of 3ejxD
- active site: C89 (= C73), H180 (= H152), E235 (= E201), C244 (≠ S210), G247 (≠ C213)
- binding (2s,6s)-2,6-diamino-2-methylheptanedioic acid: N27 (≠ D13), F29 (= F15), N80 (= N64), P86 (≠ L70), C89 (= C73), G90 (= G74), N91 (≠ S75), N178 (= N150), N217 (= N183), E235 (= E201), R236 (= R202), C244 (≠ S210), G245 (= G211), T246 (≠ S212)
3ekmA Crystal structure of diaminopimelate epimerase form arabidopsis thaliana in complex with irreversible inhibitor dl-azidap (see paper)
34% identity, 99% coverage: 3:266/267 of query aligns to 3:287/287 of 3ekmA
- active site: C75 (= C73), H166 (= H152), E221 (= E201), C230 (≠ S210), G233 (≠ C213)
- binding (2r,6s)-2,6-diamino-2-methylheptanedioic acid: N13 (≠ D13), N66 (= N64), P72 (≠ L70), C75 (= C73), G76 (= G74), N77 (≠ S75), N164 (= N150), N203 (= N183), E221 (= E201), R222 (= R202), C230 (≠ S210), G231 (= G211), T232 (≠ S212)
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)
27% identity, 100% coverage: 1:266/267 of query aligns to 3:277/277 of Q8NP73
5m47A Crystal structure of dapf from corynebacterium glutamicum in complex with d,l-diaminopimelate (see paper)
27% identity, 100% coverage: 1:266/267 of query aligns to 3:277/280 of 5m47A
- active site: C83 (= C73), H161 (= H152), E212 (= E201), C221 (= C213), G224 (= G216)
- binding 2,6-diaminopimelic acid: N15 (≠ D13), N74 (= N64), C83 (= C73), G84 (= G74), N85 (≠ S75), N159 (= N150), N194 (= N183), E212 (= E201), R213 (= R202), C221 (= C213), G222 (≠ C214), T223 (≠ C215)
Query Sequence
>GFF3002 FitnessBrowser__WCS417:GFF3002
MPLPFVKMHAHGDDFIIIDRRGLHDPITAKVARQLGNRHTGIGFNQLAVLLDCDDAAARI
KFWNPNGTLLATCGSATRGVADRLMHEAGTDSVVLRTDRGLLTCARAAGRQISVNMGEPS
LDWSAVPLAEAMDTLTLPIDGNPAACSMGNPHCTFFVEDLTAVDVATVGPALEIHPLFPA
KTNVHFVQVLDRGHIRLRIWERGGGVPLGSGSCCCGAVVNGIRRGLLDATVQVHCDGGTV
TVHWAGEGAVVLTGSVEPVMQGSAYVG
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