SitesBLAST
Comparing PP_5228 FitnessBrowser__Putida:PP_5228 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)
2gkjA Crystal structure of diaminopimelate epimerase in complex with an irreversible inhibitor dl-azidap (see paper)
58% identity, 95% coverage: 14:287/287 of query aligns to 1:274/274 of 2gkjA
- active site: C73 (= C86), H159 (= H172), E208 (= E221), C217 (= C230), G220 (= G233)
- binding (2r,6s)-2,6-diamino-2-methylheptanedioic acid: N11 (= N24), Q44 (= Q57), N64 (= N77), C73 (= C86), G74 (= G87), N75 (= N88), N157 (= N170), N190 (= N203), E208 (= E221), R209 (= R222), C217 (= C230), G218 (= G231), S219 (≠ T232)
2gkeA Crystal structure of diaminopimelate epimerase in complex with an irreversible inhibitor ll-azidap (see paper)
58% identity, 95% coverage: 14:287/287 of query aligns to 1:274/274 of 2gkeA
- active site: C73 (= C86), H159 (= H172), E208 (= E221), C217 (= C230), G220 (= G233)
- binding (2s,6s)-2,6-diamino-2-methylheptanedioic acid: N11 (= N24), F13 (= F26), Q44 (= Q57), N64 (= N77), V70 (= V83), C73 (= C86), G74 (= G87), N75 (= N88), N157 (= N170), N190 (= N203), E208 (= E221), R209 (= R222), C217 (= C230), G218 (= G231), S219 (≠ T232)
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)
58% identity, 95% coverage: 14:287/287 of query aligns to 1:274/274 of P44859
- N11 (= N24) binding
- Q44 (= Q57) binding
- N64 (= N77) binding
- C73 (= C86) 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 87:88) binding
- N157 (= N170) binding
- N190 (= N203) binding
- ER 208:209 (= ER 221:222) binding
- C217 (= C230) 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 231:232) binding
P0A6K1 Diaminopimelate epimerase; DAP epimerase; PLP-independent amino acid racemase; EC 5.1.1.7 from Escherichia coli (strain K12) (see paper)
58% identity, 95% coverage: 14:287/287 of query aligns to 1:274/274 of P0A6K1
- Y268 (= Y281) 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)
43% identity, 98% coverage: 8:287/287 of query aligns to 11:301/301 of 3ejxD
- active site: C89 (= C86), H180 (= H172), E235 (= E221), C244 (= C230), G247 (= G233)
- binding (2s,6s)-2,6-diamino-2-methylheptanedioic acid: N27 (= N24), F29 (= F26), N80 (= N77), P86 (≠ V83), C89 (= C86), G90 (= G87), N91 (= N88), N178 (= N170), N217 (= N203), E235 (= E221), R236 (= R222), C244 (= C230), G245 (= G231), T246 (= T232)
3ekmA Crystal structure of diaminopimelate epimerase form arabidopsis thaliana in complex with irreversible inhibitor dl-azidap (see paper)
43% identity, 96% coverage: 13:287/287 of query aligns to 2:287/287 of 3ekmA
- active site: C75 (= C86), H166 (= H172), E221 (= E221), C230 (= C230), G233 (= G233)
- binding (2r,6s)-2,6-diamino-2-methylheptanedioic acid: N13 (= N24), N66 (= N77), P72 (≠ V83), C75 (= C86), G76 (= G87), N77 (= N88), N164 (= N170), N203 (= N203), E221 (= E221), R222 (= R222), C230 (= C230), G231 (= G231), T232 (= T232)
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, 96% coverage: 12:287/287 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)
30% identity, 96% coverage: 12:287/287 of query aligns to 3:277/280 of 5m47A
- active site: C83 (= C86), H161 (= H172), E212 (= E221), C221 (= C230), G224 (= G233)
- binding 2,6-diaminopimelic acid: N15 (= N24), N74 (= N77), C83 (= C86), G84 (= G87), N85 (= N88), N159 (= N170), N194 (= N203), E212 (= E221), R213 (= R222), C221 (= C230), G222 (= G231), T223 (= T232)
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, 94% coverage: 16:285/287 of query aligns to 3:280/289 of P9WP19
- C87 (= C86) active site, Proton donor; mutation to A: Completely abolishes the diaminopimelate epimerase activity.; mutation to S: Strongly reduces the diaminopimelate epimerase activity.
- C226 (= C230) active site, Proton acceptor; mutation to A: Completely abolishes the diaminopimelate epimerase activity.; mutation to S: Strongly reduces the diaminopimelate epimerase activity.
Query Sequence
>PP_5228 FitnessBrowser__Putida:PP_5228
MLAKACCRSKPMLLRFTKMHGLGNDFMVLDLVSQHAHIQPKHAKQWGDRHTGVGFDQLLI
VEAPNNPEVDFRYRIFNADGSEVEQCGNGARCFARFVLDKRLTAKKRIRVETKSGIIVLD
VQNDGQVSVDMGPPRFIPAEIPFVADAQALNYPLEVDGQLHSIAAVSMGNPHAVLRVDDV
QTAPVHELGPKIENHPRFPQRVNAGFIQVIDRHRANLRVWERGAGETQACGTGACAAAVA
AISQGWMDSPVSLDLPGGRLHIEWAGPGKPVMMTGPAVRVYEGQVRL
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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