SitesBLAST
Comparing WP_013554474.1 NCBI__GCF_000186245.1:WP_013554474.1 to proteins with known functional sites using BLASTp with E ≤ 0.001.
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Found 20 (the maximum) hits to proteins with known functional sites (download)
7kh2D Structure of n-citrylornithine decarboxylase bound with plp (see paper)
30% identity, 92% coverage: 16:426/447 of query aligns to 2:409/415 of 7kh2D
Q58497 Diaminopimelate decarboxylase; DAP decarboxylase; DAPDC; EC 4.1.1.20 from Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) (Methanococcus jannaschii) (see paper)
31% identity, 92% coverage: 32:444/447 of query aligns to 20:437/438 of Q58497
- K73 (= K81) modified: N6-(pyridoxal phosphate)lysine
- S217 (≠ T216) binding pyridoxal 5'-phosphate
- G254 (= G254) binding pyridoxal 5'-phosphate
- EPGR 294:297 (≠ ETGR 301:304) binding pyridoxal 5'-phosphate
- Y391 (= Y398) binding pyridoxal 5'-phosphate
1tufA Crystal structure of diaminopimelate decarboxylase from m. Jannaschi (see paper)
31% identity, 92% coverage: 32:444/447 of query aligns to 16:433/434 of 1tufA
1twiA Crystal structure of diaminopimelate decarboxylase from m. Jannaschii in co-complex with l-lysine (see paper)
31% identity, 92% coverage: 32:444/447 of query aligns to 16:433/434 of 1twiA
- active site: K69 (= K81), H210 (= H213), E290 (= E301)
- binding lysine: S213 (≠ T216), R293 (= R304), R329 (≠ Y340), Y333 (≠ W344), Y387 (= Y398)
- binding pyridoxal-5'-phosphate: A67 (≠ S79), K69 (= K81), D88 (≠ E100), N111 (= N123), H210 (= H213), S213 (≠ T216), G250 (= G254), E290 (= E301), G292 (= G303), R293 (= R304), Y387 (= Y398)
8d5rA Structure of y430f d-ornithine/d-lysine decarboxylase complex with d- ornithine (see paper)
26% identity, 90% coverage: 34:434/447 of query aligns to 34:451/461 of 8d5rA
- binding n~2~-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)-d-ornithine: A78 (≠ S79), K80 (= K81), H210 (= H213), D213 (≠ T216), G251 (= G254), E299 (= E301), G301 (= G303), R302 (= R304), Y414 (= Y398)
- binding 1,4-diaminobutane: Q350 (≠ T343), H351 (vs. gap), D353 (vs. gap)
8d88A Structure of y430f d-ornithine/d-lysine decarboxylase complex with d- lysine (see paper)
26% identity, 90% coverage: 34:434/447 of query aligns to 34:453/461 of 8d88A
- binding pentane-1,5-diamine: Q352 (≠ T343), H353 (vs. gap), D355 (vs. gap)
- binding N~2~-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)-D-lysine: A78 (≠ S79), K80 (= K81), H212 (= H213), D215 (≠ T216), G253 (= G254), E301 (= E301), G303 (= G303), R304 (= R304), Y416 (= Y398)
8d4iA Structure of y430f d-ornithine/d-lysine decarboxylase complex with putrescine (see paper)
26% identity, 90% coverage: 34:434/447 of query aligns to 34:453/462 of 8d4iA
8d5dA Structure of y430f d-ornithine/d-lysine decarboxylase complex with d- arginine (see paper)
26% identity, 90% coverage: 34:434/447 of query aligns to 33:449/458 of 8d5dA
- binding (E)-N~2~-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)-D-arginine: K79 (= K81), H208 (= H213), D211 (≠ T216), G249 (= G254), E297 (= E301), G299 (= G303), R300 (= R304), D346 (≠ T341), F350 (vs. gap), C377 (= C369), D378 (vs. gap), Y412 (= Y398)
3c5qA Crystal structure of diaminopimelate decarboxylase (i148l mutant) from helicobacter pylori complexed with l-lysine
26% identity, 89% coverage: 39:434/447 of query aligns to 4:386/394 of 3c5qA
- active site: K44 (≠ S79), H183 (= H213), E257 (= E301)
- binding lysine: L146 (≠ W180), R260 (= R304), R294 (≠ T341), Y298 (= Y345), Y351 (= Y398)
- binding pyridoxal-5'-phosphate: K44 (≠ S79), D63 (≠ E100), H183 (= H213), S186 (≠ T216), G223 (= G254), E257 (= E301), P258 (≠ T302), G259 (= G303), R260 (= R304), Y351 (= Y398)
4xg1B Psychromonas ingrahamii diaminopimelate decarboxylase with llp
27% identity, 91% coverage: 32:440/447 of query aligns to 13:415/418 of 4xg1B
- active site: K60 (= K81), H199 (= H213), E273 (= E301)
- binding (2S)-2-amino-6-[[3-hydroxy-2-methyl-5-(phosphonooxymethyl)pyridin-4-yl]methylideneamino]hexanoic acid: K60 (= K81), D79 (≠ E100), H199 (= H213), S202 (≠ T216), G239 (= G254), E273 (= E301), G275 (= G303), R276 (= R304), R310 (vs. gap), Y314 (= Y340), C345 (= C369), E346 (≠ M370), Y373 (= Y398)
- binding propane: A35 (≠ Q54), E38 (= E57), E206 (≠ D220), I207 (≠ A221), A208 (≠ S222)
B4XMC6 Diaminopimelate decarboxylase; DAP decarboxylase; DAPDC; EC 4.1.1.20 from Helicobacter pylori (Campylobacter pylori) (see paper)
25% identity, 89% coverage: 39:434/447 of query aligns to 6:394/405 of B4XMC6
- K46 (≠ S79) modified: N6-(pyridoxal phosphate)lysine
- I148 (≠ W180) mutation to A: Nearly no change in substrate affinity and 47-fold decrease in catalytic activity.; mutation to D: 2-fold decrease in substrate affinity and 235-fold decrease in catalytic activity.; mutation to F: 4-fold increase in substrate affinity and 23-fold decrease in catalytic activity.; mutation to G: Nearly no change in substrate affinity and 235-fold decrease in catalytic activity.; mutation to K: Nearly no change in substrate affinity and 55-fold decrease in catalytic activity.; mutation to L: 13-fold increase in substrate affinity and 40-fold decrease in catalytic activity.
- G225 (= G254) binding pyridoxal 5'-phosphate
- EPGR 259:262 (≠ ETGR 301:304) binding pyridoxal 5'-phosphate
- Y358 (= Y398) binding pyridoxal 5'-phosphate
4xg1A Psychromonas ingrahamii diaminopimelate decarboxylase with llp
27% identity, 91% coverage: 32:440/447 of query aligns to 11:390/393 of 4xg1A
- active site: K55 (= K81), H178 (= H213), E246 (= E301)
- binding (2S)-2-amino-6-[[3-hydroxy-2-methyl-5-(phosphonooxymethyl)pyridin-4-yl]methylideneamino]hexanoic acid: K55 (= K81), D74 (≠ E100), S97 (≠ N123), H178 (= H213), S181 (≠ T216), G216 (= G254), E246 (= E301), G248 (= G303), R249 (= R304), R285 (vs. gap), Y289 (= Y340), C320 (= C369), E321 (≠ M370), Y348 (= Y398)
- binding propane: S121 (≠ H146), I122 (≠ L147)
7ru7A Crystal structure of btrk, a decarboxylase involved in butirosin biosynthesis
26% identity, 82% coverage: 36:403/447 of query aligns to 7:374/412 of 7ru7A
O50657 Lysine/ornithine decarboxylase; LDC; EC 4.1.1.17; EC 4.1.1.18 from Selenomonas ruminantium (see paper)
25% identity, 89% coverage: 36:432/447 of query aligns to 10:388/393 of O50657
- AGV 44:46 (≠ VVF 74:76) mutation to VTP: 2-fold increase in substrate specificity towards ornithine. 5-fold increase in substrate specificity towards ornithine; when associated with D-54. 70-fold increase in substrate specificity towards ornithine; when associated with D-54 and A-322. 16-fold increase in substrate specificity towards ornithine; when associated with D-54; T-322 and L-326.
- P54 (≠ Y84) mutation to D: 3-fold increase in substrate specificity towards ornithine. 5-fold increase in substrate specificity towards ornithine; when associated with 44-V--P-46. 70-fold increase in substrate specificity towards ornithine; when associated with 44-V--P-46 and A-322. 16-fold increase in substrate specificity towards ornithine; when associated with 44-V--P-46; T-322 and L-326.
- G319 (≠ N365) mutation to W: 7-fold increase in substrate specificity towards ornithine.
- S322 (≠ L368) mutation to A: 29-fold increase in substrate specificity towards ornithine. 70-fold increase in substrate specificity towards ornithine; when associated with 44-V--P-46 and D-54.; mutation to T: 16-fold increase in substrate specificity towards ornithine; when associated with L-326. 16-fold increase in substrate specificity towards ornithine; when associated with 44-V--P-46; D-54 and L-326.
- I326 (= I372) mutation to L: 16-fold increase in substrate specificity towards ornithine; when associated with T-322. 16-fold increase in substrate specificity towards ornithine; when associated with 44-V--P-46; D-54 and T-322.
- G350 (= G396) mutation to D: Loss of dimer formation and decarboxylase activity.
5gjpA Crystal structure of srldc in complex with plp and cadaverine (see paper)
25% identity, 89% coverage: 36:432/447 of query aligns to 10:380/381 of 5gjpA
- active site: K51 (= K81), H171 (= H213), E247 (vs. gap)
- binding pentane-1,5-diamine: Y290 (= Y345), D291 (≠ N346), Y344 (= Y398)
- binding pyridoxal-5'-phosphate: A49 (≠ S79), K51 (= K81), H171 (= H213), S174 (≠ T216), G211 (= G254), E247 (vs. gap), G249 (= G303), R250 (= R304), Y344 (= Y398)
5gjoA Crystal structure of srldc mutant (a225c/t302c) in complex with plp (see paper)
26% identity, 85% coverage: 36:416/447 of query aligns to 11:371/385 of 5gjoA
- active site: K52 (= K81), H180 (= H213), E256 (vs. gap)
- binding pyridoxal-5'-phosphate: A50 (≠ S79), K52 (= K81), D71 (≠ E100), H180 (= H213), S183 (≠ T216), G219 (= G253), G220 (= G254), E256 (vs. gap), G258 (= G303), R259 (= R304), Y353 (= Y398)
6n2aA Meso-diaminopimelate decarboxylase from arabidopsis thaliana (isoform 1)
25% identity, 89% coverage: 36:432/447 of query aligns to 22:413/422 of 6n2aA
- binding lysine: K63 (= K81), R281 (= R304), R317 (≠ T341), Y321 (= Y345), C349 (= C369), E350 (≠ M370), Y378 (= Y398)
- binding pyridoxal-5'-phosphate: K63 (= K81), H202 (= H213), S205 (≠ T216), G242 (= G254), E278 (= E301), G280 (= G303), R281 (= R304), Y378 (= Y398)
5gjnA Crystal structure of lysine decarboxylase from selenomonas ruminantium in p43212 space group (see paper)
26% identity, 85% coverage: 36:416/447 of query aligns to 10:359/369 of 5gjnA
Q9X1K5 Diaminopimelate decarboxylase; DAP decarboxylase; DAPDC; EC 4.1.1.20 from Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)
25% identity, 87% coverage: 37:426/447 of query aligns to 4:372/386 of Q9X1K5
- G214 (= G254) binding pyridoxal 5'-phosphate
- EIGR 246:249 (≠ ETGR 301:304) binding pyridoxal 5'-phosphate
- Y343 (= Y398) binding pyridoxal 5'-phosphate
P9WIU7 Diaminopimelate decarboxylase; DAP decarboxylase; DAPDC; EC 4.1.1.20 from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (see 2 papers)
24% identity, 86% coverage: 32:416/447 of query aligns to 26:424/447 of P9WIU7
- K72 (= K81) modified: N6-(pyridoxal phosphate)lysine
- C93 (≠ V102) modified: Interchain (with C-375)
- G258 (= G254) binding pyridoxal 5'-phosphate
- EPGR 300:303 (≠ ETGR 301:304) binding pyridoxal 5'-phosphate
- C375 (= C369) modified: Interchain (with C-72)
- Y405 (= Y398) binding pyridoxal 5'-phosphate
Query Sequence
>WP_013554474.1 NCBI__GCF_000186245.1:WP_013554474.1
MSYQKPTINKVDFAMMSKYGSPLKSQKIRSEIAGVDVRELVQNYGSPLFVFSQQEIEEKY
HRLHEAFSSRYPDVVFGWSYKTNYLNAICNLYHKLGSIAEVVSEFEYQKARALGIEGKDI
IFNGPYKPKEALKVAVEEGAKIHIDHLFEINDLEEIARELGVKIPVAIRVNMDTGIYPQW
SRFGFNYESGEAIDAIERIHSGGLLELTGLHSHIGTFMLDASAYGKETAKLMDLKHQAEE
RFGYRIEYIDIGGGFASKNRLKGVYQSPDVIVPTPDDYAQQITEAIYTHNKSDTLPRLYL
ETGRHLIDEAGYLLTTVQAYKRFPDGMKGYILDAGVNLLYTATWYNFNFELDRRYEGLNE
PSMLNGPLCMNIDILSENIMLPPLDRGTVITIGPVGAYNYTQSMQFIRYRPAAVLIDKER
NVHLIKEPDDLETINYKERIPDYLKRS
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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