SitesBLAST
Comparing WP_043745759.1 NCBI__GCF_000009985.1:WP_043745759.1 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)
39% identity, 95% coverage: 8:278/284 of query aligns to 3:272/274 of 2gkjA
- active site: C73 (= C78), H159 (= H161), E208 (= E215), C217 (= C224), G220 (= G227)
- binding (2r,6s)-2,6-diamino-2-methylheptanedioic acid: N11 (= N16), Q44 (= Q49), N64 (= N69), C73 (= C78), G74 (= G79), N75 (= N80), N157 (= N159), N190 (= N192), E208 (= E215), R209 (= R216), C217 (= C224), G218 (= G225), S219 (≠ T226)
2gkeA Crystal structure of diaminopimelate epimerase in complex with an irreversible inhibitor ll-azidap (see paper)
39% identity, 95% coverage: 8:278/284 of query aligns to 3:272/274 of 2gkeA
- active site: C73 (= C78), H159 (= H161), E208 (= E215), C217 (= C224), G220 (= G227)
- binding (2s,6s)-2,6-diamino-2-methylheptanedioic acid: N11 (= N16), F13 (= F18), Q44 (= Q49), N64 (= N69), V70 (= V75), C73 (= C78), G74 (= G79), N75 (= N80), N157 (= N159), N190 (= N192), E208 (= E215), R209 (= R216), C217 (= C224), G218 (= G225), S219 (≠ T226)
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)
39% identity, 95% coverage: 8:278/284 of query aligns to 3:272/274 of P44859
- N11 (= N16) binding
- Q44 (= Q49) binding
- N64 (= N69) binding
- C73 (= C78) 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 79:80) binding
- N157 (= N159) binding
- N190 (= N192) binding
- ER 208:209 (= ER 215:216) binding
- C217 (= C224) 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 225:226) binding
3ejxD Crystal structure of diaminopimelate epimerase from arabidopsis thaliana in complex with ll-azidap (see paper)
39% identity, 95% coverage: 8:277/284 of query aligns to 19:298/301 of 3ejxD
- active site: C89 (= C78), H180 (= H161), E235 (= E215), C244 (= C224), G247 (= G227)
- binding (2s,6s)-2,6-diamino-2-methylheptanedioic acid: N27 (= N16), F29 (= F18), N80 (= N69), P86 (≠ V75), C89 (= C78), G90 (= G79), N91 (= N80), N178 (= N159), N217 (= N192), E235 (= E215), R236 (= R216), C244 (= C224), G245 (= G225), T246 (= T226)
3ekmA Crystal structure of diaminopimelate epimerase form arabidopsis thaliana in complex with irreversible inhibitor dl-azidap (see paper)
39% identity, 95% coverage: 8:277/284 of query aligns to 5:284/287 of 3ekmA
- active site: C75 (= C78), H166 (= H161), E221 (= E215), C230 (= C224), G233 (= G227)
- binding (2r,6s)-2,6-diamino-2-methylheptanedioic acid: N13 (= N16), N66 (= N69), P72 (≠ V75), C75 (= C78), G76 (= G79), N77 (= N80), N164 (= N159), N203 (= N192), E221 (= E215), R222 (= R216), C230 (= C224), G231 (= G225), T232 (= T226)
P0A6K1 Diaminopimelate epimerase; DAP epimerase; PLP-independent amino acid racemase; EC 5.1.1.7 from Escherichia coli (strain K12) (see paper)
40% identity, 95% coverage: 8:278/284 of query aligns to 3:272/274 of P0A6K1
- Y268 (≠ F274) Important for dimerization; mutation to 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)
33% identity, 96% coverage: 7:278/284 of query aligns to 6:275/277 of Q8NP73
5m47A Crystal structure of dapf from corynebacterium glutamicum in complex with d,l-diaminopimelate (see paper)
33% identity, 96% coverage: 7:278/284 of query aligns to 6:275/280 of 5m47A
- active site: C83 (= C78), H161 (= H161), E212 (= E215), C221 (= C224), G224 (= G227)
- binding 2,6-diaminopimelic acid: N15 (= N16), N74 (= N69), C83 (= C78), G84 (= G79), N85 (= N80), N159 (= N159), N194 (= N192), E212 (= E215), R213 (= R216), C221 (= C224), G222 (= G225), T223 (= T226)
P9WP19 Diaminopimelate epimerase; DAP epimerase; PLP-independent amino acid racemase; EC 5.1.1.7 from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (see paper)
33% identity, 94% coverage: 8:274/284 of query aligns to 3:267/289 of P9WP19
- C87 (= C78) active site, Proton donor; mutation to A: Completely abolishes the diaminopimelate epimerase activity.; mutation to S: Strongly reduces the diaminopimelate epimerase activity.
- C226 (= C224) active site, Proton acceptor; mutation to A: Completely abolishes the diaminopimelate epimerase activity.; mutation to S: Strongly reduces the diaminopimelate epimerase activity.
Query Sequence
>WP_043745759.1 NCBI__GCF_000009985.1:WP_043745759.1
MSDRAWPFLKMHGLGNDFVVLDARARALDLTPERVRAIASRGTGVGCDQLVVMTQATDPC
ADATMLIYNADGSEVAACGNASRCVAWLLMKEIAADKVVFQTKAGLLDAESRGPHQVAVD
MGPARLDWREIPLAEAVDTLHLGISAGPLADPVGVSMGNPHAVFFVDDAEAVNLAQLGRG
LEHHALFPERANIEVAQVLTPPDAEMGRIRMRVWERGAGITMACGTGACATLVAAARRGL
SPRKAEIILDGGTLTIEWLKDGHVLMTGPVAVAFTGTLDSSLLP
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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