SitesBLAST
Comparing PP_5338 FitnessBrowser__Putida:PP_5338 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)
6wngA Crystal structure of an aspartate ammonia-lyase from elizabethkingia anophelis nuhp1
60% identity, 97% coverage: 11:472/478 of query aligns to 3:463/466 of 6wngA
3oceA Crystal structure of fumarate lyase:delta crystallin from brucella melitensis bound to cobalt
61% identity, 96% coverage: 12:471/478 of query aligns to 3:460/461 of 3oceA
P0AC38 Aspartate ammonia-lyase; Aspartase; EC 4.3.1.1 from Escherichia coli (strain K12) (see 3 papers)
57% identity, 97% coverage: 10:471/478 of query aligns to 4:465/478 of P0AC38
- D10 (= D16) mutation to A: Loss of activity.; mutation to N: 5.4-fold decrease in kcat. 3.5-fold increase in KM for L-aspartate.
- R15 (≠ L21) mutation to A: No effect on kcat. 2.7-fold increase in KM for L-aspartate.
- H26 (≠ Q32) mutation to Q: No effect on kcat. 3.1-fold increase in KM for L-aspartate.
- R29 (= R35) mutation to A: No effect on kcat. 44-fold increase in KM for L-aspartate.
- K55 (= K61) mutation to C: Produced exclusively as an inclusion body, and only the higher molecular weight oligomers are observed.; mutation to R: Loss of activity. Forms high molecular weight oligomers. May cause extensive changes in the structure. Treatment of this mutant for extended periods of time in the presence of high concentrations of the denaturant guanidinium chloride leads to the dissociation of the high molecular weight oligomers and results in the recovery of a substantial fraction of the wild-type activity. Upon removal of the denaturant this mutant slowly reverts to its inactive and insoluble form.
- H124 (= H129) mutation to L: 30% decrease in Vmax. KM for L-aspartate is almost unaffected.
- S143 (= S148) mutation to G: 9-fold decrease in kcat. 4-fold increase in KM for L-aspartate.; mutation to T: 68-fold decrease in kcat. 2.9-fold increase in KM for L-aspartate.
- K327 (= K333) mutation to R: Retains only 0.3% of the activity. 5-fold increase in KM for L-aspartate.
- C390 (= C396) mutation C->A,S: No significant change in kinetic parameters.
3r6vG Crystal structure of aspartase from bacillus sp. Ym55-1 with bound l- aspartate (see paper)
50% identity, 96% coverage: 12:471/478 of query aligns to 3:459/463 of 3r6vG
3r6qA A triclinic-lattice structure of aspartase from bacillus sp. Ym55-1 (see paper)
50% identity, 96% coverage: 12:471/478 of query aligns to 2:458/462 of 3r6qA
Q9LCC6 Aspartate ammonia-lyase; Aspartase; EC 4.3.1.1 from Bacillus sp. (see 3 papers)
50% identity, 96% coverage: 12:471/478 of query aligns to 6:462/468 of Q9LCC6
- T101 (= T109) binding ; mutation to A: 7100-fold decrease in catalytic efficiency. Does not result in any major conformational changes.; mutation to S: 80-fold decrease in catalytic efficiency.
- H134 (≠ D142) mutation to A: Retains full activity. Shows a slightly stronger affinity for L-aspartate. Does not affect tertiary structure.
- S140 (= S148) binding ; mutation to A: 27-fold decrease in catalytic efficiency. Does not result in any major conformational changes.; mutation S->K,R: Loss of activity.
- T141 (= T149) binding ; mutation to A: 15-fold decrease in catalytic efficiency. Does not result in any major conformational changes.; mutation to K: 40000-fold decrease in catalytic efficiency.; mutation T->V,R: Loss of activity.
- N142 (= N150) binding ; mutation to A: Loss of activity. Does not result in any major conformational changes.; mutation to Q: 3000-fold decrease in catalytic efficiency.
- K183 (= K191) mutation to A: Loss of activity. Does not affect tertiary structure.
- T187 (= T195) binding ; mutation to A: 6280-fold decrease in catalytic efficiency. Does not result in any major conformational changes.; mutation to S: 2.3-fold decrease in catalytic efficiency.
- H188 (≠ Q196) binding ; mutation to A: 100-fold decrease in catalytic efficiency. Does not result in any major conformational changes.; mutation H->K,Q,R: Loss of activity.
- S318 (= S327) mutation to A: Loss of activity.
- S319 (= S328) binding ; mutation to A: Almost no change in catalytic efficiency.
- I320 (= I329) mutation to A: 50-fold decrease in catalytic efficiency.
- M321 (= M330) mutation to A: 338-fold decrease in catalytic efficiency.
- P322 (= P331) mutation to A: Almost no change in catalytic efficiency.
- K324 (= K333) binding ; mutation to A: Loss of activity. Does not result in any major conformational changes.; mutation K->D,H,R,S,V: Loss of activity.
- N326 (= N335) mutation to A: 22500-fold decrease in catalytic efficiency. Does not result in any major conformational changes.; mutation to Q: 168750-fold decrease in catalytic efficiency.
P07954 Fumarate hydratase, mitochondrial; Fumarase; HsFH; EC 4.2.1.2 from Homo sapiens (Human) (see 4 papers)
42% identity, 98% coverage: 5:472/478 of query aligns to 44:510/510 of P07954
- S46 (= S7) mutation to A: Does not affect phosphorylation by PRKDC.
- T147 (= T109) mutation to A: Does not affect phosphorylation by PRKDC.
- S187 (≠ T149) mutation to A: Does not affect phosphorylation by PRKDC.
- K230 (= K191) to R: in FMRD and HLRCC; dbSNP:rs752232718
- R233 (= R194) to H: in HLRCC; catalytically inactive mutant; abolished ability to promote DNA repair; dbSNP:rs121913123
- T236 (≠ L197) modified: Phosphothreonine; by PRKDC; mutation to A: Abolished interaction with H2AZ1 and localization to chromatin in response to DNA damage.; mutation to D: Phosphomimetic mutant; promotes interaction with H2AZ1, leading to increased localization to chromatin in response to DNA damage.
Sites not aligning to the query:
- 1 modified: Initiator methionine, Removed
- 1:43 modified: Variant sequence, Missing (in isoform Cytoplasmic)
7lubB Crystal structure of recombinant human fumarase in complex with d-2- amino-3-phosphono-propionic acid (see paper)
42% identity, 97% coverage: 10:472/478 of query aligns to 1:462/462 of 7lubB
P08417 Fumarate hydratase, mitochondrial; Fumarase; EC 4.2.1.2 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) (see 2 papers)
42% identity, 97% coverage: 9:472/478 of query aligns to 26:488/488 of P08417
- 29:44 (vs. 12:27, 50% identical) mutation Missing: Does not affect subcellular location.
- H154 (= H138) mutation to R: Abolished fumarate hydratase activity and ability to participate in DNA repair.
Sites not aligning to the query:
- 1:24 modified: transit peptide, Mitochondrion
- 24 M→S: Does not affect processing by the mitochondrial processing peptidase. Localizes both in the mitochondrion and cytosol. Exhibits high fumarate hydratase activity.; mutation M->V,I: Abolishes processing by the mitochondrial processing peptidase. Mainly localizes in the cytosol, with a small fraction in the mitochondrion. Reduced fumarate hydratase activity.
- 24:25 MN→SF: Does not affect processing by the mitochondrial processing peptidase. Localizes both in the mitochondrion and cytosol. Exhibits high fumarate hydratase activity.
P05042 Fumarate hydratase class II; Fumarase C; Aerobic fumarase; Iron-independent fumarase; EC 4.2.1.2 from Escherichia coli (strain K12) (see 4 papers)
41% identity, 96% coverage: 10:469/478 of query aligns to 3:460/467 of P05042
- R126 (≠ Q135) binding ; mutation to A: 10-fold decrease of fumarase activity.
- K127 (≠ Y136) mutation to D: No effect.
- H129 (= H138) mutation to N: No effect on fumarase activity and essentially same conformation compared to the wild-type, but appears to dramatically reduce binding of ligands at the B-site.
- HPND 129:132 (≠ HPNN 138:141) binding in site B
- SSN 139:141 (≠ STN 148:150) binding
- H188 (≠ Q196) active site, Proton donor/acceptor; mutation to N: 200-fold decrease of fumarase activity.
- E315 (≠ Q324) mutation to Q: There is essentially no effect on the affinity values for both S-malate and fumarate. In contrast, the catalytic efficiency values have been lowered by 10-fold in both directions.
Q9ZCQ4 Fumarate hydratase class II; Fumarase C; Aerobic fumarase; Iron-independent fumarase; EC 4.2.1.2 from Rickettsia prowazekii (strain Madrid E) (see paper)
41% identity, 96% coverage: 10:470/478 of query aligns to 3:461/461 of Q9ZCQ4
1fuqA Fumarase with bound 3-trimethylsilylsuccinic acid (see paper)
42% identity, 96% coverage: 12:468/478 of query aligns to 2:456/456 of 1fuqA
- active site: N104 (= N116), T184 (= T195), H185 (≠ Q196), S315 (= S327), K321 (= K333), E328 (= E340)
- binding citric acid: T97 (= T109), S136 (= S148), S137 (≠ T149), N138 (= N150)
- binding 3-trimethylsilylsuccinic acid: R123 (≠ Q135), H126 (= H138), P127 (= P139), N128 (= N140), D129 (≠ N141)
1fuoA FumarasE C with bound citrate (see paper)
42% identity, 96% coverage: 12:468/478 of query aligns to 2:456/456 of 1fuoA
1fupA Fumarase with bound pyromellitic acid (see paper)
42% identity, 96% coverage: 12:468/478 of query aligns to 1:455/455 of 1fupA
7c18B Crystal structure of fumarasec from mannheimia succiniciproducens in complex with fumarate
41% identity, 96% coverage: 10:469/478 of query aligns to 2:460/464 of 7c18B
- binding fumaric acid: T100 (= T109), S139 (= S148), S140 (≠ T149), N141 (= N150), T187 (= T195), H188 (≠ Q196), C318 (≠ S327), S319 (= S328), M321 (= M330), K324 (= K333), N326 (= N335)
P9WN93 Fumarate hydratase class II; Fumarase C; Aerobic fumarase; Iron-independent fumarase; EC 4.2.1.2 from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (see 2 papers)
43% identity, 97% coverage: 6:470/478 of query aligns to 5:462/474 of P9WN93
4adlA Crystal structures of rv1098c in complex with malate (see paper)
43% identity, 96% coverage: 10:470/478 of query aligns to 1:454/459 of 4adlA
4apbD Crystal structure of mycobacterium tuberculosis fumarase (rv1098c) s318c in complex with fumarate (see paper)
43% identity, 96% coverage: 10:470/478 of query aligns to 1:454/462 of 4apbD
- active site: H179 (≠ Q196), C310 (≠ S327), K316 (= K333), E323 (= E340)
- binding fumaric acid: T98 (= T109), S130 (= S148), S131 (≠ T149), N132 (= N150), T178 (= T195), H179 (≠ Q196), C310 (≠ S327), S311 (= S328), M313 (= M330), K316 (= K333), N318 (= N335)
6s88A Fumarate hydratase of mycobacterium tuberculosis in complex with formate and allosteric modulator n-(2-methoxy-5-((1,2,4,5-tetrahydro- 3h-benzo[d]azepin-3-yl)sulfonyl)phenyl)-2-(4-oxo-3,4- dihydrophthalazin-1-yl)acetamide (see paper)
41% identity, 96% coverage: 11:470/478 of query aligns to 1:445/450 of 6s88A
6s7wA Fumarate hydratase of mycobacterium tuberculosis in complex with formate and allosteric modulator n-(5-(azepan-1-ylsulfonyl)-2- methoxyphenyl)-2-(quinolin-4-yl)acetamide (see paper)
41% identity, 96% coverage: 11:470/478 of query aligns to 1:445/450 of 6s7wA
Query Sequence
>PP_5338 FitnessBrowser__Putida:PP_5338
MIYIMSSAASFRVEKDLLGTLEVPADAYYGIQTLRAANNFHLSGVPLSHYPKLVVALAMV
KQAAADANRELGHLSDAKHAAISAACARLIKGDFHDQFVVDMIQGGAGTSTNMNANEVIA
NVALEAMGHQKGEYQYLHPNNDVNMAQSTNDAYPTAIRLGLLLGHDALLASLDSLIQAFA
AKGKEFDHVLKMGRTQLQDAVPMTLGQEFRAFATTMTEDLQRLRSLAPELLTEINLGGTA
IGTGINADPGYQALAVQRLATISGHPLVPAADLIEATSDMGAFVLFSGMLKRTAVKLSKI
CNDLRLLSSGPRTGINEINLPARQPGSSIMPGKVNPVIPEAVNQVAFAIMGNDLALTVAA
EGGQLQLNVMEPLIAYKIFDSIRLLQRAMDMLREHCIVGITANEQRCRELVEHSIGLVTA
LNPYIGYENATRIARVALESGRGVLELVREEKLLDDAMLDDILRPENMIAPRLVPLKA
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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