SitesBLAST
Comparing GFF3342 FitnessBrowser__Phaeo:GFF3342 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)
38% identity, 92% coverage: 12:269/281 of query aligns to 1:270/274 of P0A6K1
- Y268 (≠ A267) 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)
40% identity, 92% coverage: 12:269/281 of query aligns to 17:297/301 of 3ejxD
- active site: C89 (= C81), H180 (= H160), E235 (= E209), C244 (≠ S218), G247 (≠ S221)
- binding (2s,6s)-2,6-diamino-2-methylheptanedioic acid: N27 (= N22), F29 (= F24), N80 (= N72), P86 (≠ S78), C89 (= C81), G90 (= G82), N91 (= N83), N178 (= N158), N217 (= N191), E235 (= E209), R236 (= R210), C244 (≠ S218), G245 (= G219), T246 (≠ S220)
3ekmA Crystal structure of diaminopimelate epimerase form arabidopsis thaliana in complex with irreversible inhibitor dl-azidap (see paper)
40% identity, 92% coverage: 12:269/281 of query aligns to 3:283/287 of 3ekmA
- active site: C75 (= C81), H166 (= H160), E221 (= E209), C230 (≠ S218), G233 (≠ S221)
- binding (2r,6s)-2,6-diamino-2-methylheptanedioic acid: N13 (= N22), N66 (= N72), P72 (≠ S78), C75 (= C81), G76 (= G82), N77 (= N83), N164 (= N158), N203 (= N191), E221 (= E209), R222 (= R210), C230 (≠ S218), G231 (= G219), T232 (≠ S220)
2gkjA Crystal structure of diaminopimelate epimerase in complex with an irreversible inhibitor dl-azidap (see paper)
38% identity, 93% coverage: 12:272/281 of query aligns to 1:273/274 of 2gkjA
- active site: C73 (= C81), H159 (= H160), E208 (= E209), C217 (≠ S218), G220 (≠ S221)
- binding (2r,6s)-2,6-diamino-2-methylheptanedioic acid: N11 (= N22), Q44 (= Q55), N64 (= N72), C73 (= C81), G74 (= G82), N75 (= N83), N157 (= N158), N190 (= N191), E208 (= E209), R209 (= R210), C217 (≠ S218), G218 (= G219), S219 (= S220)
2gkeA Crystal structure of diaminopimelate epimerase in complex with an irreversible inhibitor ll-azidap (see paper)
38% identity, 93% coverage: 12:272/281 of query aligns to 1:273/274 of 2gkeA
- active site: C73 (= C81), H159 (= H160), E208 (= E209), C217 (≠ S218), G220 (≠ S221)
- binding (2s,6s)-2,6-diamino-2-methylheptanedioic acid: N11 (= N22), F13 (= F24), Q44 (= Q55), N64 (= N72), V70 (≠ S78), C73 (= C81), G74 (= G82), N75 (= N83), N157 (= N158), N190 (= N191), E208 (= E209), R209 (= R210), C217 (≠ S218), G218 (= G219), S219 (= S220)
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)
38% identity, 93% coverage: 12:272/281 of query aligns to 1:273/274 of P44859
- N11 (= N22) binding
- Q44 (= Q55) binding
- N64 (= N72) binding
- C73 (= C81) 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 82:83) binding
- N157 (= N158) binding
- N190 (= N191) binding
- ER 208:209 (= ER 209:210) binding
- C217 (≠ S218) 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 219:220) binding
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, 92% coverage: 12:270/281 of query aligns to 5:274/277 of Q8NP73
5m47A Crystal structure of dapf from corynebacterium glutamicum in complex with d,l-diaminopimelate (see paper)
30% identity, 92% coverage: 12:270/281 of query aligns to 5:274/280 of 5m47A
- active site: C83 (= C81), H161 (= H160), E212 (= E209), C221 (≠ S218), G224 (≠ S221)
- binding 2,6-diaminopimelic acid: N15 (= N22), N74 (= N72), C83 (= C81), G84 (= G82), N85 (= N83), N159 (= N158), N194 (= N191), E212 (= E209), R213 (= R210), C221 (≠ S218), G222 (= G219), T223 (≠ S220)
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, 91% coverage: 14:269/281 of query aligns to 3:278/289 of P9WP19
- C87 (= C81) active site, Proton donor; mutation to A: Completely abolishes the diaminopimelate epimerase activity.; mutation to S: Strongly reduces the diaminopimelate epimerase activity.
- C226 (≠ S218) active site, Proton acceptor; mutation to A: Completely abolishes the diaminopimelate epimerase activity.; mutation to S: Strongly reduces the diaminopimelate epimerase activity.
Query Sequence
>GFF3342 FitnessBrowser__Phaeo:GFF3342
MPEMTIGSDTRLPFMKMHGLGNDFVVVDARDQTWDITPAMAEGIAHRQMGIGFDQLTVIT
KGDEDAHLTFYNADGSTSAACGNATRCIARHLLDESGKTHLRLTTDRGLLLAEDAGNGLT
SVNMGEPQLDWQDIPLAEDVDTLELPIEGAPTATGMGNPHCTFFVDNAEVIPLAEFGARY
EHHPLYPERTNVQVAHVVAPDHLRMRVWERGVGITLASGSSSCATAVAAARRGLTSRKVQ
IDLDGGTLWIDWRKDGVWMTGPTMHVADGHFTRQFLESLSK
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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