SitesBLAST
Comparing PP_3790 FitnessBrowser__Putida:PP_3790 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)
3ejxD Crystal structure of diaminopimelate epimerase from arabidopsis thaliana in complex with ll-azidap (see paper)
33% identity, 93% coverage: 1:250/268 of query aligns to 17:290/301 of 3ejxD
- active site: C89 (≠ S70), H180 (= H147), E235 (= E196), C244 (≠ S205), G247 (≠ S208)
- binding (2s,6s)-2,6-diamino-2-methylheptanedioic acid: N27 (= N11), F29 (≠ Y13), N80 (= N61), P86 (≠ A67), C89 (≠ S70), G90 (= G71), N91 (= N72), N178 (= N145), N217 (= N178), E235 (= E196), R236 (= R197), C244 (≠ S205), G245 (= G206), T246 (= T207)
3ekmA Crystal structure of diaminopimelate epimerase form arabidopsis thaliana in complex with irreversible inhibitor dl-azidap (see paper)
33% identity, 93% coverage: 1:250/268 of query aligns to 3:276/287 of 3ekmA
- active site: C75 (≠ S70), H166 (= H147), E221 (= E196), C230 (≠ S205), G233 (≠ S208)
- binding (2r,6s)-2,6-diamino-2-methylheptanedioic acid: N13 (= N11), N66 (= N61), P72 (≠ A67), C75 (≠ S70), G76 (= G71), N77 (= N72), N164 (= N145), N203 (= N178), E221 (= E196), R222 (= R197), C230 (≠ S205), G231 (= G206), T232 (= T207)
2gkjA Crystal structure of diaminopimelate epimerase in complex with an irreversible inhibitor dl-azidap (see paper)
34% identity, 92% coverage: 1:246/268 of query aligns to 1:258/274 of 2gkjA
- active site: C73 (≠ S70), H159 (= H147), E208 (= E196), C217 (≠ S205), G220 (≠ S208)
- binding (2r,6s)-2,6-diamino-2-methylheptanedioic acid: N11 (= N11), Q44 (≠ G43), N64 (= N61), C73 (≠ S70), G74 (= G71), N75 (= N72), N157 (= N145), N190 (= N178), E208 (= E196), R209 (= R197), C217 (≠ S205), G218 (= G206), S219 (≠ T207)
2gkeA Crystal structure of diaminopimelate epimerase in complex with an irreversible inhibitor ll-azidap (see paper)
34% identity, 92% coverage: 1:246/268 of query aligns to 1:258/274 of 2gkeA
- active site: C73 (≠ S70), H159 (= H147), E208 (= E196), C217 (≠ S205), G220 (≠ S208)
- binding (2s,6s)-2,6-diamino-2-methylheptanedioic acid: N11 (= N11), F13 (≠ Y13), Q44 (≠ G43), N64 (= N61), V70 (≠ A67), C73 (≠ S70), G74 (= G71), N75 (= N72), N157 (= N145), N190 (= N178), E208 (= E196), R209 (= R197), C217 (≠ S205), G218 (= G206), S219 (≠ T207)
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, 92% coverage: 1:246/268 of query aligns to 1:258/274 of P44859
- N11 (= N11) binding
- Q44 (≠ G43) binding
- N64 (= N61) binding
- C73 (≠ S70) 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 71:72) binding
- N157 (= N145) binding
- N190 (= N178) binding
- ER 208:209 (= ER 196:197) binding
- C217 (≠ S205) 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 206:207) binding
P0A6K1 Diaminopimelate epimerase; DAP epimerase; PLP-independent amino acid racemase; EC 5.1.1.7 from Escherichia coli (strain K12) (see paper)
34% identity, 95% coverage: 1:254/268 of query aligns to 1:267/274 of P0A6K1
Sites not aligning to the query:
- 268 Important for dimerization; Y→A: Significantly less active than the wild-type dimer and unable to dimerize.
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, 96% coverage: 1:256/268 of query aligns to 5:272/277 of Q8NP73
5m47A Crystal structure of dapf from corynebacterium glutamicum in complex with d,l-diaminopimelate (see paper)
32% identity, 95% coverage: 3:256/268 of query aligns to 7:272/280 of 5m47A
- active site: C83 (≠ S70), H161 (= H147), E212 (= E196), C221 (≠ S205), G224 (≠ S208)
- binding 2,6-diaminopimelic acid: N15 (= N11), N74 (= N61), C83 (≠ S70), G84 (= G71), N85 (= N72), N159 (= N145), N194 (= N178), E212 (= E196), R213 (= R197), C221 (≠ S205), G222 (= G206), T223 (= T207)
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, 78% coverage: 1:209/268 of query aligns to 1:230/289 of P9WP19
- C87 (≠ S70) active site, Proton donor; mutation to A: Completely abolishes the diaminopimelate epimerase activity.; mutation to S: Strongly reduces the diaminopimelate epimerase activity.
- C226 (≠ S205) 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_3790 FitnessBrowser__Putida:PP_3790
MQFYKYHAAGNDYLVYRDCVPFDCSKPMISRICDRHRGLGSDGILVPVIKEGERLSVRIY
NTDGSQAEKSGNGLRILCRYLWDQNIVAGSPFEISTKGGIVTCQVLDNGQRISIAMGQAA
FANTAAFTVDVDGTPLQLHPVSMGNPHCVVFVDQPTETLARQLGPLIERLSIFPDRTNVQ
FVRVIDRQTLEVQIWERGVGYTLSSGTSSCAAAAVSRRLGLVGPRVAVNMAGGVIMIELD
DDYHVLMQGPVCRVGLYSLDSECLAQAD
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