SitesBLAST
Comparing GFF249 FitnessBrowser__Marino:GFF249 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)
61% identity, 90% coverage: 12:285/304 of query aligns to 1:274/274 of P0A6K1
- Y268 (≠ F279) 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)
57% identity, 90% coverage: 12:285/304 of query aligns to 1:274/274 of 2gkjA
- active site: C73 (= C84), H159 (= H170), E208 (= E219), C217 (= C228), G220 (= G231)
- binding (2r,6s)-2,6-diamino-2-methylheptanedioic acid: N11 (= N22), Q44 (= Q55), N64 (= N75), C73 (= C84), G74 (= G85), N75 (= N86), N157 (= N168), N190 (= N201), E208 (= E219), R209 (= R220), C217 (= C228), G218 (= G229), S219 (= S230)
2gkeA Crystal structure of diaminopimelate epimerase in complex with an irreversible inhibitor ll-azidap (see paper)
57% identity, 90% coverage: 12:285/304 of query aligns to 1:274/274 of 2gkeA
- active site: C73 (= C84), H159 (= H170), E208 (= E219), C217 (= C228), G220 (= G231)
- binding (2s,6s)-2,6-diamino-2-methylheptanedioic acid: N11 (= N22), F13 (= F24), Q44 (= Q55), N64 (= N75), V70 (= V81), C73 (= C84), G74 (= G85), N75 (= N86), N157 (= N168), N190 (= N201), E208 (= E219), R209 (= R220), C217 (= C228), G218 (= G229), S219 (= S230)
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)
57% identity, 90% coverage: 12:285/304 of query aligns to 1:274/274 of P44859
- N11 (= N22) binding
- Q44 (= Q55) binding
- N64 (= N75) binding
- C73 (= C84) 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 85:86) binding
- N157 (= N168) binding
- N190 (= N201) binding
- ER 208:209 (= ER 219:220) binding
- C217 (= C228) 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 229:230) binding
3ejxD Crystal structure of diaminopimelate epimerase from arabidopsis thaliana in complex with ll-azidap (see paper)
42% identity, 90% coverage: 11:285/304 of query aligns to 16:301/301 of 3ejxD
- active site: C89 (= C84), H180 (= H170), E235 (= E219), C244 (= C228), G247 (= G231)
- binding (2s,6s)-2,6-diamino-2-methylheptanedioic acid: N27 (= N22), F29 (= F24), N80 (= N75), P86 (≠ V81), C89 (= C84), G90 (= G85), N91 (= N86), N178 (= N168), N217 (= N201), E235 (= E219), R236 (= R220), C244 (= C228), G245 (= G229), T246 (≠ S230)
3ekmA Crystal structure of diaminopimelate epimerase form arabidopsis thaliana in complex with irreversible inhibitor dl-azidap (see paper)
42% identity, 90% coverage: 11:285/304 of query aligns to 2:287/287 of 3ekmA
- active site: C75 (= C84), H166 (= H170), E221 (= E219), C230 (= C228), G233 (= G231)
- binding (2r,6s)-2,6-diamino-2-methylheptanedioic acid: N13 (= N22), N66 (= N75), P72 (≠ V81), C75 (= C84), G76 (= G85), N77 (= N86), N164 (= N168), N203 (= N201), E221 (= E219), R222 (= R220), C230 (= C228), G231 (= G229), T232 (≠ S230)
5m47A Crystal structure of dapf from corynebacterium glutamicum in complex with d,l-diaminopimelate (see paper)
30% identity, 89% coverage: 14:285/304 of query aligns to 7:277/280 of 5m47A
- active site: C83 (= C84), H161 (= H170), E212 (= E219), C221 (= C228), G224 (= G231)
- binding 2,6-diaminopimelic acid: N15 (= N22), N74 (= N75), C83 (= C84), G84 (= G85), N85 (= N86), N159 (= N168), N194 (= N201), E212 (= E219), R213 (= R220), C221 (= C228), G222 (= G229), T223 (≠ S230)
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)
30% identity, 89% coverage: 14:285/304 of query aligns to 7:277/277 of Q8NP73
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, 72% coverage: 14:231/304 of query aligns to 3:229/289 of P9WP19
- C87 (= C84) active site, Proton donor; mutation to A: Completely abolishes the diaminopimelate epimerase activity.; mutation to S: Strongly reduces the diaminopimelate epimerase activity.
- C226 (= C228) active site, Proton acceptor; mutation to A: Completely abolishes the diaminopimelate epimerase activity.; mutation to S: Strongly reduces the diaminopimelate epimerase activity.
Query Sequence
>GFF249 FitnessBrowser__Marino:GFF249
MTQQRRTQGPMLRFTKMHGLGNDFMVVDAISQPFRLRPEMIRELANRNFGIGFDQLLVVE
PPGLPDVDFRYRIFNADGSEVEQCGNGARCFARFVRDQRLTNKKVIRVQTAKGVIELRVG
REGMVMVNMGVPEFNPPAIPFAADRRKDVYTVDVDGQTVELSALSMGNPHGVLLVEDVDQ
APVETLGPKLERHPRFPARANIGFLQILDRTHVRLRVFERGSGETLACGSGACAAVVAGC
LRGLLDARVEVELRGGPLVIEWQGEGTPVMMEGPATSVFEGQLRLPGDSGGRRRRSARPH
KQRS
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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