SitesBLAST
Comparing PP_3722 FitnessBrowser__Putida:PP_3722 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)
I6LNY0 Broad specificity amino-acid racemase; EC 5.1.1.10 from Pseudomonas putida (Arthrobacter siderocapsulatus) (see paper)
97% identity, 100% coverage: 1:409/409 of query aligns to 1:409/409 of I6LNY0
- C71 (= C71) modified: Disulfide link with 97
- K75 (= K75) modified: N6-(pyridoxal phosphate)lysine
- C97 (= C97) modified: Disulfide link with 71
- R174 (= R174) mutation R->A,K: Loss of catalytic activity.
- N175 (= N175) mutation to L: Loss of catalytic activity.
- A393 (= A393) mutation to Y: Reduces the catalytic activity towards L-Lys by 2-fold. Loss of racemase activity towards L-Arg.
4fs9A Complex structure of a broad specificity amino acid racemase (bar) within the reactive intermediate (see paper)
98% identity, 94% coverage: 26:409/409 of query aligns to 1:384/384 of 4fs9A
- active site: K50 (= K75), R149 (= R174), H180 (= H205), R236 (= R261), Y276 (= Y301), S323 (= S348), N325 (= N350)
- binding n~2~-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)-l-lysine: K50 (= K75), Y54 (= Y79), V96 (= V121), H180 (= H205), S221 (= S246), R236 (= R261), G238 (= G263), G239 (= G264), Y276 (= Y301), M324 (= M349)
I0J1I6 Broad specificity amino-acid racemase; Arginine racemase; Broad substrate specificity racemase; EC 5.1.1.10 from Pseudomonas taetrolens (see 2 papers)
73% identity, 100% coverage: 1:409/409 of query aligns to 1:408/409 of I0J1I6
- 1:23 (vs. 1:24, 54% identical) signal peptide
- C70 (= C71) modified: Disulfide link with 96; mutation to A: The catalytic efficiency with arginine, lysine, and ornithine is very similar to that of wild-type, and that with both L-alanine and D-alanine increases approximately five times; when associated with A-96.
- C96 (= C97) modified: Disulfide link with 70; mutation to A: The catalytic efficiency with arginine, lysine, and ornithine is very similar to that of wild-type, and that with both L-alanine and D-alanine increases approximately five times; when associated with A-70.
A0KLG5 Broad specificity amino-acid racemase; Broad spectrum racemase; EC 5.1.1.10 from Aeromonas hydrophila subsp. hydrophila (strain ATCC 7966 / DSM 30187 / BCRC 13018 / CCUG 14551 / JCM 1027 / KCTC 2358 / NCIMB 9240 / NCTC 8049) (see paper)
57% identity, 95% coverage: 18:405/409 of query aligns to 17:404/408 of A0KLG5
- K74 (= K75) modified: N6-(pyridoxal phosphate)lysine
4bf5A Structure of broad spectrum racemase from aeromonas hydrophila (see paper)
57% identity, 93% coverage: 25:405/409 of query aligns to 1:383/396 of 4bf5A
- active site: K53 (= K75), R152 (= R174), H183 (= H205), R239 (= R261), Y279 (= Y301), S326 (= S348), N328 (= N350)
- binding pyridoxal-5'-phosphate: K53 (= K75), Y57 (= Y79), H183 (= H205), S224 (= S246), R239 (= R261), G241 (= G263), G242 (= G264)
M4GGR9 Lysine racemase; EC 5.1.1.5 from Proteus mirabilis (see paper)
49% identity, 99% coverage: 5:409/409 of query aligns to 6:407/407 of M4GGR9
- K74 (= K75) modified: N6-(pyridoxal phosphate)lysine; mutation to L: Completely loss of racemase activity towards lysine.
- R173 (= R174) mutation R->A,K: Loss of racemase activity towards both L-lysine and L-arginine.
- N174 (= N175) mutation to L: Loss of racemase activity towards both L-lysine and L-arginine.
- T391 (≠ A393) mutation to Y: Reduces the racemization activity towards L-lysine by 2-fold. Does not affect racemase activity towards L-arginine.
- S394 (≠ Y396) mutation S->C,N,T,Y: Arginine racemization activity is increased by 1.5-1.8 fold compared to the wild-type enzyme, while activity towards L-lysine is decreased. Almost no change in affinity for L-lysine and L-arginine.
Q9KSE5 Broad specificity amino-acid racemase; Broad spectrum racemase; EC 5.1.1.10 from Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961) (see paper)
49% identity, 100% coverage: 1:408/409 of query aligns to 1:406/407 of Q9KSE5
- P25 (= P27) mutation to E: Completely abolishes the catalytic activity towards Ala and Met and dramatically impairs (70% reduction) activity towards Arg.
- C70 (= C71) mutation to A: Completely abolishes or highly reduces the catalytic activity towards Ala, Ser and large aliphatic side chains, while activity towards basic amino acids is preserved.
- K74 (= K75) modified: N6-(pyridoxal phosphate)lysine
- R119 (= R120) mutation to A: Highly reduces the catalytic activity towards Ala and Ser and completely abolishes activity towards Met, Leu, Asn, Gln, Lys and Arg.
- R121 (= R122) mutation to A: Completely abolishes or highly reduces the catalytic activity towards all the amino acids.
- A165 (= A166) mutation to K: Completely abolishes or highly reduces the catalytic activity towards all the amino acids except Gln.
- N167 (= N168) mutation to A: Completely abolishes or highly reduces the catalytic activity towards all the amino acids.
- G169 (≠ S170) mutation to A: Completely abolishes or highly reduces the catalytic activity towards all the amino acids except Gln and Arg.
- RN 173:174 (= RN 174:175) mutation to AA: Completely abolishes or highly reduces the catalytic activity towards all the amino acids.
- P391 (≠ A393) mutation to N: Completely abolishes the catalytic activity towards Ala, Ser and large aliphatic side chains, while activity towards basic amino acids is preserved.
4beuA Structure of vibrio cholerae broad spectrum racemase (see paper)
50% identity, 93% coverage: 27:408/409 of query aligns to 2:383/392 of 4beuA
- active site: K51 (= K75), R150 (= R174), H181 (= H205), R237 (= R261), Y276 (= Y301), S323 (= S348), N325 (= N350)
- binding pyridoxal-5'-phosphate: K51 (= K75), Y55 (= Y79), R150 (= R174), H181 (= H205), N221 (= N245), S222 (= S246), R237 (= R261), G239 (= G263), G240 (= G264)
4y2wA Crystal structure of a thermostable alanine racemase from thermoanaerobacter tengcongensis mb4 (see paper)
30% identity, 88% coverage: 46:406/409 of query aligns to 11:373/388 of 4y2wA
- active site: K40 (= K75), R138 (= R174), H168 (= H205), R224 (= R261), Y268 (= Y301), C315 (≠ S348), D317 (≠ N350)
- binding alanine: Y268 (= Y301), Y287 (= Y320), C315 (≠ S348), M316 (= M349)
- binding phosphate ion: N208 (= N245), A209 (≠ S246), I227 (≠ G264)
6q70A Crystal structure of the alanine racemase bsu17640 from bacillus subtilis in the presence of hepes (see paper)
28% identity, 89% coverage: 45:408/409 of query aligns to 9:379/386 of 6q70A
- active site: K39 (= K75), R139 (= R174), H169 (= H205), R225 (= R261), Y272 (= Y301), T319 (≠ S348), D321 (≠ N350)
- binding pyridoxal-5'-phosphate: V37 (= V73), K39 (= K75), Y43 (= Y79), L85 (≠ V121), R139 (= R174), H169 (= H205), T210 (≠ S246), R225 (= R261), G227 (= G263), I228 (≠ G264), Y364 (≠ A393)
5irpA Crystal structure of the alanine racemase bsu17640 from bacillus subtilis (see paper)
28% identity, 89% coverage: 45:408/409 of query aligns to 9:379/386 of 5irpA
- active site: K39 (= K75), R139 (= R174), H169 (= H205), R225 (= R261), Y272 (= Y301), T319 (≠ S348), D321 (≠ N350)
- binding magnesium ion: L155 (vs. gap), K156 (vs. gap), S158 (≠ Q194), L161 (= L197)
- binding 2-amino-2-hydroxymethyl-propane-1,3-diol: D174 (= D210), P235 (≠ V271), Y364 (≠ A393)
- binding (5-hydroxy-6-methylpyridin-3-yl)methyl dihydrogen phosphate: Y43 (= Y79), L85 (≠ V121), R139 (= R174), H169 (= H205), N209 (= N245), T210 (≠ S246), R225 (= R261), G227 (= G263), I228 (≠ G264), Y364 (≠ A393)
P9WQA9 Alanine racemase; EC 5.1.1.1 from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (see paper)
34% identity, 86% coverage: 48:397/409 of query aligns to 16:368/384 of P9WQA9
- K42 (= K75) modified: N6-(pyridoxal phosphate)lysine
6sczA Mycobacterium tuberculosis alanine racemase inhibited by dcs (see paper)
34% identity, 86% coverage: 48:397/409 of query aligns to 8:360/373 of 6sczA
- active site: K34 (= K75), R132 (= R174), H164 (= H205), R220 (= R261), Y263 (= Y301), C310 (≠ S348), D312 (≠ N350)
- binding (~{E})-[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylidene-[(4~{R})-3-oxidanylidene-1,2-oxazolidin-4-yl]azanium: K34 (= K75), Y38 (= Y79), W80 (≠ V121), H164 (= H205), S205 (= S246), R220 (= R261), G222 (= G263), I223 (≠ G264), Y356 (≠ A393)
- binding [2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methyl-(3-oxidanyl-1,2-oxazol-4-yl)azanium: Y38 (= Y79), W80 (≠ V121), H164 (= H205), N204 (= N245), S205 (= S246), R220 (= R261), G222 (= G263), I223 (≠ G264), Y263 (= Y301), Y282 (= Y320), M311 (= M349), Y356 (≠ A393)
- binding polyethylene glycol: D172 (= D212), A210 (≠ E251), P212 (= P253)
1xfcA The 1.9 a crystal structure of alanine racemase from mycobacterium tuberculosis contains a conserved entryway into the active site (see paper)
33% identity, 86% coverage: 48:397/409 of query aligns to 6:353/366 of 1xfcA
- active site: K32 (= K75), R130 (= R174), H162 (= H205), R213 (= R261), C303 (≠ S348), D305 (≠ N350)
- binding pyridoxal-5'-phosphate: K32 (= K75), Y36 (= Y79), W78 (≠ V121), H162 (= H205), S198 (= S246), R213 (= R261), G215 (= G263), I216 (≠ G264), Y349 (≠ A393)
4lusB Alanine racemase [clostridium difficile 630] (see paper)
28% identity, 82% coverage: 45:380/409 of query aligns to 7:333/374 of 4lusB
- active site: K37 (= K75), H160 (= H205), R213 (= R261), Y258 (= Y301), C304 (≠ S348), D306 (≠ N350)
- binding 3,3',3''-phosphanetriyltripropanoic acid: T77 (= T115), P79 (≠ Q117), K98 (≠ D136), C124 (≠ R162)
4lutA Alanine racemase [clostridium difficile 630] complex with cycloserine (see paper)
28% identity, 82% coverage: 45:380/409 of query aligns to 7:334/375 of 4lutA
- active site: K37 (= K75), H158 (= H205), R214 (= R261), Y259 (= Y301), C305 (≠ S348), D307 (≠ N350)
- binding d-[3-hydroxy-2-methyl-5-phosphonooxymethyl-pyridin-4-ylmethyl]-n,o-cycloserylamide: K37 (= K75), Y41 (= Y79), L83 (≠ V121), H158 (= H205), S199 (= S246), R214 (= R261), G216 (= G263), I217 (≠ G264), Y259 (= Y301), Y278 (= Y320), M306 (= M349)
Sites not aligning to the query:
5yycA Crystal structure of alanine racemase from bacillus pseudofirmus (of4) (see paper)
26% identity, 89% coverage: 43:405/409 of query aligns to 8:364/368 of 5yycA
- active site: K41 (= K75), R139 (= R174), H169 (= H205), R225 (= R261), Y269 (= Y301), C316 (≠ S348), D318 (≠ N350)
- binding pyridoxal-5'-phosphate: K41 (= K75), Y45 (= Y79), R139 (= R174), H169 (= H205), N209 (= N245), S210 (= S246), R225 (= R261), G227 (= G263), I228 (≠ G264), Y352 (≠ A393)
2vd9A The crystal structure of alanine racemase from bacillus anthracis (ba0252) with bound l-ala-p (see paper)
28% identity, 89% coverage: 43:408/409 of query aligns to 6:371/386 of 2vd9A
- active site: K38 (= K75), R135 (= R174), H165 (= H205), R221 (= R261), Y267 (= Y301), T313 (≠ S348), D315 (≠ N350)
- binding (1s)-1-[((1e)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylene)amino]ethylphosphonic acid: K38 (= K75), Y42 (= Y79), R135 (= R174), H165 (= H205), N205 (= N245), S206 (= S246), G223 (= G263), I224 (≠ G264), Y267 (= Y301), T313 (≠ S348), M314 (= M349), Y356 (≠ A393)
- binding {1-[(3-hydroxy-methyl-5-phosphonooxy-methyl-pyridin-4-ylmethyl)-amino]-ethyl}-phosphonic acid: K38 (= K75), Y42 (= Y79), R135 (= R174), H165 (= H205), S206 (= S246), R221 (= R261), G223 (= G263), I224 (≠ G264), Y267 (= Y301), T313 (≠ S348), M314 (= M349), Y356 (≠ A393)
- binding magnesium ion: T329 (≠ N366), K330 (≠ E367)
2vd8A The crystal structure of alanine racemase from bacillus anthracis (ba0252) (see paper)
28% identity, 89% coverage: 43:408/409 of query aligns to 7:372/387 of 2vd8A
- active site: K39 (= K75), R136 (= R174), H166 (= H205), R222 (= R261), Y268 (= Y301), T314 (≠ S348), D316 (≠ N350)
- binding pyridoxal-5'-phosphate: K39 (= K75), Y43 (= Y79), R136 (= R174), H166 (= H205), S207 (= S246), R222 (= R261), G224 (= G263), I225 (≠ G264), Y357 (≠ A393)
1vfsA Crystal structure of d-cycloserine-bound form of alanine racemase from d-cycloserine-producing streptomyces lavendulae (see paper)
28% identity, 90% coverage: 42:408/409 of query aligns to 4:374/383 of 1vfsA
- binding d-[3-hydroxy-2-methyl-5-phosphonooxymethyl-pyridin-4-ylmethyl]-n,o-cycloserylamide: K36 (= K75), Y40 (= Y79), W82 (≠ V121), R134 (= R174), H166 (= H205), S207 (= S246), R222 (= R261), G224 (= G263), Y268 (= Y301), Y287 (= Y320), M316 (= M349), Y359 (≠ A393)
Query Sequence
>PP_3722 FitnessBrowser__Putida:PP_3722
MPFRRTLLAASLALLITGQAPLYAAPPLSMDNGTNTLTVQNSNAWVEVSASALQHNIRTL
QAELAGKSKLCAVLKADAYGHGIGLVMPSIIAQGVPCVAVASNEEARVVRASGFTGQLVR
VRLASLSELEDGLQYDMEELVGSAEFARQADAIAARHGKTLRIHMALNSSGMSRNGVEMA
TWSGRGEALQITDQKHLKLVALMTHFAVEDKDDVRKGLAAFNEQTDWLIKHARLDRSKLT
LHAANSFATLEVPEARLDMVRTGGALFGDTVPARTEYKRAMQFKSHVAAVHSYPAGNTVG
YDRTFTLARDSRLANITVGYSDGYRRVFTNKGHVLINGHRVPVVGKVSMNTLMVDVTDFP
DVKGGNEVVLFGKQAGGEITQAEMEEINGALLADLYTVWGNSNPKILVD
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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