SitesBLAST
Comparing 3609317 Dshi_2702 Pyridoxal-5'-phosphate-dependent protein beta subunit (RefSeq) 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)
A4F2N8 L-threo-3-hydroxyaspartate ammonia-lyase; L-threo-3-hydroxyaspartate dehydratase; L-THA DH; EC 4.3.1.16 from Pseudomonas sp. (see paper)
43% identity, 96% coverage: 8:324/330 of query aligns to 8:318/319 of A4F2N8
- K53 (= K54) mutation to A: Loss of enzymatic activity.
Q7XSN8 Serine racemase; D-serine dehydratase; D-serine ammonia-lyase; L-serine dehydratase; L-serine ammonia-lyase; EC 5.1.1.18; EC 4.3.1.18; EC 4.3.1.17 from Oryza sativa subsp. japonica (Rice) (see paper)
34% identity, 97% coverage: 4:323/330 of query aligns to 18:336/339 of Q7XSN8
- E219 (= E209) mutation to A: Reduces catalytic activity and abolishes the regulatory effect of Mg(2+) addition; when associated with A-225.
- D225 (= D215) mutation to A: Reduces catalytic activity and abolishes the regulatory effect of Mg(2+) addition; when associated with A-219.
5cvcA Structure of maize serine racemase (see paper)
36% identity, 94% coverage: 4:314/330 of query aligns to 2:311/329 of 5cvcA
- active site: K52 (= K54), S77 (= S79), E203 (= E209), A207 (≠ F213), D209 (= D215), G231 (≠ A238), V306 (≠ A309), S307 (≠ T310)
- binding magnesium ion: E203 (= E209), A207 (≠ F213), D209 (= D215)
- binding pyridoxal-5'-phosphate: F51 (= F53), K52 (= K54), N79 (= N81), S178 (≠ G184), G179 (= G185), G180 (= G186), G181 (= G187), L232 (= L240), E275 (= E283), S307 (≠ T310), G308 (= G311)
1wtcA Crystal structure of s.Pombe serine racemase complex with amppcp (see paper)
35% identity, 97% coverage: 5:325/330 of query aligns to 3:318/318 of 1wtcA
- active site: K52 (= K54), S77 (= S79), E203 (= E209), G207 (≠ F213), D209 (= D215), G231 (≠ A238), I302 (≠ A309), S303 (≠ T310)
- binding phosphomethylphosphonic acid adenylate ester: N20 (≠ R22), K47 (≠ H49), M48 (≠ T50), A109 (≠ E111), A110 (≠ N112), Y114 (≠ L116)
- binding magnesium ion: E203 (= E209), G207 (≠ F213), D209 (= D215)
- binding pyridoxal-5'-phosphate: F51 (= F53), K52 (= K54), N79 (= N81), G178 (= G184), G179 (= G185), G180 (= G186), G181 (= G187), G231 (≠ A238), E276 (= E283), T278 (≠ G285), S303 (≠ T310)
1v71A Crystal structure of s.Pombe serine racemase
35% identity, 97% coverage: 5:325/330 of query aligns to 3:318/318 of 1v71A
- active site: K52 (= K54), S77 (= S79), E203 (= E209), G207 (≠ F213), D209 (= D215), G231 (≠ A238), I302 (≠ A309), S303 (≠ T310)
- binding magnesium ion: E203 (= E209), G207 (≠ F213), D209 (= D215)
- binding pyridoxal-5'-phosphate: F51 (= F53), K52 (= K54), N79 (= N81), G178 (= G184), G179 (= G185), G180 (= G186), G181 (= G187), G231 (≠ A238), E276 (= E283), T278 (≠ G285), S303 (≠ T310), G304 (= G311)
2zr8A Crystal structure of modified serine racemase complexed with serine (see paper)
35% identity, 97% coverage: 5:325/330 of query aligns to 4:319/319 of 2zr8A
- active site: K53 (= K54), S78 (= S79), E204 (= E209), G208 (≠ F213), D210 (= D215), G232 (≠ A238), I303 (≠ A309), S304 (≠ T310)
- binding magnesium ion: E204 (= E209), G208 (≠ F213), D210 (= D215)
- binding n-(5'-phosphopyridoxyl)-d-alanine: F52 (= F53), K53 (= K54), S77 (= S78), S78 (= S79), N80 (= N81), H81 (= H82), P147 (= P148), G179 (= G184), G180 (= G185), G181 (= G186), G182 (= G187), G232 (≠ A238), E277 (= E283), T279 (≠ G285), S304 (≠ T310)
- binding serine: S78 (= S79), R129 (= R130), D231 (= D237), G232 (≠ A238), A233 (≠ I239), Q234 (≠ L240), T235 (= T241)
2zpuA Crystal structure of modified serine racemase from s.Pombe. (see paper)
35% identity, 97% coverage: 5:325/330 of query aligns to 4:319/319 of 2zpuA
- active site: K53 (= K54), S78 (= S79), E204 (= E209), G208 (≠ F213), D210 (= D215), G232 (≠ A238), I303 (≠ A309), S304 (≠ T310)
- binding magnesium ion: E204 (= E209), G208 (≠ F213), D210 (= D215)
- binding n-(5'-phosphopyridoxyl)-d-alanine: F52 (= F53), K53 (= K54), S77 (= S78), S78 (= S79), N80 (= N81), H81 (= H82), P147 (= P148), G179 (= G184), G180 (= G185), G181 (= G186), G182 (= G187), G232 (≠ A238), E277 (= E283), T279 (≠ G285), S304 (≠ T310)
O59791 Serine racemase; D-serine ammonia-lyase; D-serine dehydratase; L-serine ammonia-lyase; L-serine dehydratase; EC 4.3.1.17; EC 4.3.1.18; EC 5.1.1.18 from Schizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast) (see paper)
35% identity, 97% coverage: 5:324/330 of query aligns to 8:322/323 of O59791
- S82 (= S79) mutation to A: Loss of racemase activity. Reduces D-serine dehydratase activity by 99%. Slightly reduced L-serine dehydratase activity.
1ve5A Crystal structure of t.Th. Hb8 threonine deaminase
46% identity, 88% coverage: 5:294/330 of query aligns to 1:285/308 of 1ve5A
- active site: K50 (= K54), S56 (≠ A60), S72 (= S79), E200 (= E209), A204 (≠ F213), D206 (= D215), G229 (≠ A238)
- binding calcium ion: E200 (= E209), A204 (≠ F213), D206 (= D215)
- binding pyridoxal-5'-phosphate: F49 (= F53), K50 (= K54), N74 (= N81), G175 (= G184), G176 (= G185), G177 (= G186), G178 (= G187), E274 (= E283), T276 (≠ G285)
Sites not aligning to the query:
6zspAAA serine racemase bound to atp and malonate. (see paper)
32% identity, 93% coverage: 7:314/330 of query aligns to 6:307/320 of 6zspAAA
- active site: K53 (= K54), S74 (= S79), E200 (= E209), A204 (≠ F213), D206 (= D215), G229 (≠ A238), L302 (≠ A309), S303 (≠ T310)
- binding adenosine-5'-triphosphate: S28 (≠ A29), S29 (≠ P30), I30 (≠ A31), K48 (≠ H49), T49 (= T50), Q79 (= Q84), Y111 (≠ L116), E266 (≠ Q276), R267 (≠ H277), K269 (= K279), N306 (= N313)
- binding magnesium ion: E200 (= E209), A204 (≠ F213), D206 (= D215)
- binding malonate ion: K53 (= K54), S73 (= S78), S74 (= S79), N76 (= N81), H77 (= H82), R125 (= R130), G229 (≠ A238), S232 (≠ T241)
7nbfAAA structure of human serine racemase in complex with DSiP fragment Z126932614, XChem fragment screen (see paper)
32% identity, 93% coverage: 7:314/330 of query aligns to 6:314/323 of 7nbfAAA
- active site: K53 (= K54), S81 (= S79), E207 (= E209), A211 (≠ F213), D213 (= D215), G236 (≠ A238), L309 (≠ A309), S310 (≠ T310)
- binding calcium ion: E207 (= E209), A211 (≠ F213), D213 (= D215)
- binding magnesium ion: N244 (≠ I247)
- binding pyridoxal-5'-phosphate: F52 (= F53), K53 (= K54), N83 (= N81), G182 (= G184), G183 (= G185), G184 (= G186), G185 (= G187), M186 (≠ L188), G236 (≠ A238), V237 (≠ I239), T282 (≠ G285), S310 (≠ T310), G311 (= G311)
- binding 2-[(methylsulfonyl)methyl]-1H-benzimidazole: H21 (≠ R22), L22 (≠ R23), T23 (= T24), P24 (= P25), L26 (= L27), T27 (≠ S28), F46 (≠ L47)
Sites not aligning to the query:
7nbdAAA structure of human serine racemase in complex with DSiP fragment Z235449082, XChem fragment screen (see paper)
32% identity, 93% coverage: 7:314/330 of query aligns to 6:314/323 of 7nbdAAA
- active site: K53 (= K54), S81 (= S79), E207 (= E209), A211 (≠ F213), D213 (= D215), G236 (≠ A238), L309 (≠ A309), S310 (≠ T310)
- binding calcium ion: E207 (= E209), A211 (≠ F213), D213 (= D215)
- binding [4-(1H-benzimidazol-1-yl)phenyl]methanol: W272 (≠ F275), L278 (≠ V281), V314 (= V314)
- binding magnesium ion: N244 (≠ I247)
- binding pyridoxal-5'-phosphate: F52 (= F53), K53 (= K54), N83 (= N81), G182 (= G184), G183 (= G185), G184 (= G186), G185 (= G187), M186 (≠ L188), G236 (≠ A238), V237 (≠ I239), E280 (= E283), T282 (≠ G285), S310 (≠ T310), G311 (= G311)
Sites not aligning to the query:
7nbcCCC structure of human serine racemase in complex with DSiP fragment Z2856434779, XChem fragment screen (see paper)
32% identity, 93% coverage: 7:314/330 of query aligns to 6:314/323 of 7nbcCCC
- active site: K53 (= K54), S81 (= S79), E207 (= E209), A211 (≠ F213), D213 (= D215), G236 (≠ A238), L309 (≠ A309), S310 (≠ T310)
- binding biphenyl-4-ylacetic acid: T78 (≠ A76), H79 (≠ C77), H84 (= H82), V148 (≠ I146), H149 (≠ K147), P150 (= P148)
- binding calcium ion: E207 (= E209), A211 (≠ F213), D213 (= D215)
- binding pyridoxal-5'-phosphate: F52 (= F53), K53 (= K54), N83 (= N81), G182 (= G184), G183 (= G185), G184 (= G186), G185 (= G187), M186 (≠ L188), G236 (≠ A238), V237 (≠ I239), T282 (≠ G285), S310 (≠ T310), G311 (= G311)
7nbcAAA structure of human serine racemase in complex with DSiP fragment Z2856434779, XChem fragment screen (see paper)
32% identity, 93% coverage: 7:314/330 of query aligns to 6:314/323 of 7nbcAAA
- active site: K53 (= K54), S81 (= S79), E207 (= E209), A211 (≠ F213), D213 (= D215), G236 (≠ A238), L309 (≠ A309), S310 (≠ T310)
- binding calcium ion: E207 (= E209), A211 (≠ F213), D213 (= D215)
- binding magnesium ion: N244 (≠ I247)
- binding pyridoxal-5'-phosphate: F52 (= F53), K53 (= K54), N83 (= N81), G182 (= G184), G183 (= G185), G184 (= G186), G185 (= G187), M186 (≠ L188), G236 (≠ A238), V237 (≠ I239), T282 (≠ G285), S310 (≠ T310), G311 (= G311)
Sites not aligning to the query:
7nbgAAA structure of human serine racemase in complex with DSiP fragment Z52314092, XChem fragment screen (see paper)
32% identity, 93% coverage: 7:314/330 of query aligns to 6:314/322 of 7nbgAAA
- active site: K53 (= K54), S81 (= S79), E207 (= E209), A211 (≠ F213), D213 (= D215), G236 (≠ A238), L309 (≠ A309), S310 (≠ T310)
- binding calcium ion: E207 (= E209), A211 (≠ F213), D213 (= D215)
- binding pyridoxal-5'-phosphate: F52 (= F53), K53 (= K54), N83 (= N81), G182 (= G184), G183 (= G185), G184 (= G186), G185 (= G187), M186 (≠ L188), G236 (≠ A238), V237 (≠ I239), T282 (≠ G285), S310 (≠ T310), G311 (= G311)
- binding ~{N}-[2-(2-methylphenyl)ethyl]ethanamide: S81 (= S79), G85 (≠ A83), Q86 (= Q84), I101 (= I99), K111 (= K109), I115 (≠ T113), Y118 (≠ L116)
7nbhAAA structure of human serine racemase in complex with DSiP fragment Z26781964, XChem fragment screen (see paper)
32% identity, 93% coverage: 7:314/330 of query aligns to 6:314/320 of 7nbhAAA
- active site: K53 (= K54), S81 (= S79), E207 (= E209), A211 (≠ F213), D213 (= D215), G236 (≠ A238), L309 (≠ A309), S310 (≠ T310)
- binding calcium ion: E207 (= E209), A211 (≠ F213), D213 (= D215)
- binding N-[(1H-benzimidazol-2-yl)methyl]furan-2-carboxamide: S81 (= S79), G85 (≠ A83), Q86 (= Q84), K111 (= K109), I115 (≠ T113), Y118 (≠ L116), D235 (= D237), P281 (= P284), N313 (= N313), V314 (= V314)
Sites not aligning to the query:
3l6bA X-ray crystal structure of human serine racemase in complex with malonate a potent inhibitor (see paper)
32% identity, 93% coverage: 7:314/330 of query aligns to 7:310/322 of 3l6bA
- active site: K54 (= K54), S77 (= S79), E203 (= E209), A207 (≠ F213), D209 (= D215), G232 (≠ A238), T278 (≠ G285), L305 (≠ A309), S306 (≠ T310)
- binding malonate ion: K54 (= K54), S76 (= S78), S77 (= S79), N79 (= N81), H80 (= H82), R128 (= R130), G232 (≠ A238)
- binding manganese (ii) ion: E203 (= E209), A207 (≠ F213), D209 (= D215)
- binding pyridoxal-5'-phosphate: F53 (= F53), K54 (= K54), N79 (= N81), G178 (= G184), G179 (= G185), G180 (= G186), G181 (= G187), M182 (≠ L188), V233 (≠ I239), E276 (= E283), T278 (≠ G285), S306 (≠ T310), G307 (= G311)
7nbgDDD structure of human serine racemase in complex with DSiP fragment Z52314092, XChem fragment screen (see paper)
32% identity, 93% coverage: 7:314/330 of query aligns to 6:309/310 of 7nbgDDD
- active site: K53 (= K54), S76 (= S79), E202 (= E209), A206 (≠ F213), D208 (= D215), G231 (≠ A238), L304 (≠ A309), S305 (≠ T310)
- binding calcium ion: E202 (= E209), A206 (≠ F213), D208 (= D215)
- binding magnesium ion: N239 (≠ I247)
- binding ortho-xylene: S76 (= S79), Q81 (= Q84), I96 (= I99), Y113 (≠ L116)
- binding pyridoxal-5'-phosphate: F52 (= F53), K53 (= K54), N78 (= N81), G177 (= G184), G178 (= G185), G179 (= G186), G180 (= G187), M181 (≠ L188), G231 (≠ A238), V232 (≠ I239), E275 (= E283), T277 (≠ G285), S305 (≠ T310), G306 (= G311)
Sites not aligning to the query:
1ve5D Crystal structure of t.Th. Hb8 threonine deaminase
42% identity, 88% coverage: 5:294/330 of query aligns to 1:257/280 of 1ve5D
- active site: K50 (= K54), S56 (≠ A60), S72 (= S79), E172 (= E209), A176 (≠ F213), D178 (= D215), G201 (≠ A238)
- binding calcium ion: E172 (= E209), A176 (≠ F213), D178 (= D215)
- binding pyridoxal-5'-phosphate: F49 (= F53), K50 (= K54), N74 (= N81), G147 (= G184), G148 (= G185), G149 (= G186), G150 (= G187), V202 (≠ I239), E246 (= E283), T248 (≠ G285)
Sites not aligning to the query:
Q9QZX7 Serine racemase; D-serine ammonia-lyase; D-serine dehydratase; L-serine ammonia-lyase; L-serine dehydratase; EC 5.1.1.18; EC 4.3.1.18; EC 4.3.1.17 from Mus musculus (Mouse) (see paper)
32% identity, 93% coverage: 7:314/330 of query aligns to 9:317/339 of Q9QZX7
- C113 (≠ P108) modified: S-nitrosocysteine; mutation to S: Abolishes S-nitrosylation.
Query Sequence
>3609317 Dshi_2702 Pyridoxal-5'-phosphate-dependent protein beta subunit (RefSeq)
MSGAPDFDRIKAAEARLDGHVRRTPILSAPALDALAGRRVLVKAECLQHTGSFKARGGWA
AVSALPAAVRARGVIACSSGNHAQGVARAAAAHGTRALIVMPGDAPAPKVENTRALGAEV
VFYDRAREDRDGLTATLAERDGLTLIKPYDDTEVIAGQATTGLEIAAQAAAEGVHAAEVL
VCCGGGGLSAGIALALAETAPRMRVRPVEPDGFDDMARSLAAGTRLANSARDGSICDAIL
TPMPGEITFPVLASRAGPGLVVTEGEVLRTMKLAFQHLKLVLEPGGAVALAAALFRPDAL
SGDAVIAVATGGNVSAEVFARALSMPPTRA
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