SitesBLAST
Comparing WP_012675654.1 NCBI__GCF_000021565.1:WP_012675654.1 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)
P0A8N5 Lysine--tRNA ligase, heat inducible; Lysyl-tRNA synthetase; LysRS; EC 6.1.1.6 from Escherichia coli (strain K12) (see 2 papers)
51% identity, 76% coverage: 141:578/579 of query aligns to 67:505/505 of P0A8N5
- K114 (≠ E188) modified: N6-acetyllysine
- K156 (= K230) modified: N6-acetyllysine
Sites not aligning to the query:
- 1 modified: Initiator methionine, Removed
3e9iA Lysyl-tRNA synthetase from bacillus stearothermophilus complexed with l-lysine hydroxamate-amp (see paper)
54% identity, 75% coverage: 141:575/579 of query aligns to 55:483/484 of 3e9iA
- active site: R245 (= R337), E247 (= E339), R252 (≠ T344), H253 (= H345), E403 (= E495), N406 (= N498), R462 (= R554)
- binding 5'-O-{(R)-hydroxy[(L-lysylamino)oxy]phosphoryl}adenosine: G199 (= G291), E223 (= E315), R245 (= R337), H253 (= H345), N254 (= N346), F257 (= F349), M259 (= M351), E261 (= E353), Y263 (= Y355), E403 (= E495), H404 (≠ I496), N406 (= N498), F408 (≠ Y500), E410 (= E502), G459 (= G551)
3e9hA Lysyl-tRNA synthetase from bacillus stearothermophilus complexed with l-lysylsulfamoyl adenosine (see paper)
54% identity, 75% coverage: 141:575/579 of query aligns to 55:483/484 of 3e9hA
- active site: R245 (= R337), E247 (= E339), R252 (≠ T344), H253 (= H345), E403 (= E495), N406 (= N498), R462 (= R554)
- binding 5'-o-[(l-lysylamino)sulfonyl]adenosine: E223 (= E315), R245 (= R337), H253 (= H345), N254 (= N346), F257 (= F349), M259 (= M351), E261 (= E353), Y263 (= Y355), E403 (= E495), H404 (≠ I496), N406 (= N498), F408 (≠ Y500), E410 (= E502), G455 (= G547), G459 (= G551), R462 (= R554)
- binding magnesium ion: E396 (= E488), E403 (= E495), N406 (= N498)
3a74A Lysyl-tRNA synthetase from bacillus stearothermophilus complexed with diadenosine tetraphosphate (ap4a)
54% identity, 75% coverage: 141:575/579 of query aligns to 55:483/484 of 3a74A
- active site: R245 (= R337), E247 (= E339), R252 (≠ T344), H253 (= H345), E403 (= E495), N406 (= N498), R462 (= R554)
- binding bis(adenosine)-5'-tetraphosphate: R245 (= R337), E247 (= E339), R252 (≠ T344), H253 (= H345), N254 (= N346), F257 (= F349), M259 (= M351), E358 (= E450), E362 (= E454), E403 (= E495), N406 (= N498), G459 (= G551), R462 (= R554)
- binding 2,6-diamino-hexanoic acid amide: G199 (= G291), E223 (= E315), M259 (= M351), E261 (= E353), Y263 (= Y355), N406 (= N498), F408 (≠ Y500), E410 (= E502)
- binding magnesium ion: E396 (= E488), E396 (= E488), E403 (= E495), E403 (= E495)
1e24A Lysyl-tRNA synthetase (lysu) hexagonal form complexed with lysine and atp and mn2+ (see paper)
51% identity, 75% coverage: 141:576/579 of query aligns to 56:485/485 of 1e24A
- active site: R245 (= R337), E247 (= E339), R252 (≠ T344), H253 (= H345), E404 (= E495), N407 (= N498), R463 (= R554)
- binding adenosine-5'-triphosphate: R245 (= R337), R252 (≠ T344), H253 (= H345), N254 (= N346), F257 (= F349), M259 (= M351), E404 (= E495), I405 (= I496), G460 (= G551), R463 (= R554)
- binding lysine: G199 (= G291), E223 (= E315), E261 (= E353), Y263 (= Y355), N407 (= N498), F409 (≠ Y500), E411 (= E502), G456 (= G547), G458 (= G549)
- binding manganese (ii) ion: E397 (= E488), E404 (= E495)
1e22A Lysyl-tRNA synthetase (lysu) hexagonal form complexed with lysine and the non-hydrolysable atp analogue amp-pcp (see paper)
51% identity, 75% coverage: 141:576/579 of query aligns to 56:485/485 of 1e22A
- active site: R245 (= R337), E247 (= E339), R252 (≠ T344), H253 (= H345), E404 (= E495), N407 (= N498), R463 (= R554)
- binding phosphomethylphosphonic acid adenylate ester: R245 (= R337), R252 (≠ T344), H253 (= H345), N254 (= N346), F257 (= F349), E404 (= E495), I405 (= I496), G460 (= G551), R463 (= R554)
- binding lysine: G199 (= G291), E223 (= E315), M259 (= M351), E261 (= E353), Y263 (= Y355), N407 (= N498), F409 (≠ Y500), E411 (= E502), G456 (= G547), G458 (= G549)
- binding magnesium ion: E397 (= E488), E404 (= E495)
1e1tA Lysyl-tRNA synthetase (lysu) hexagonal form complexed with the lysyl_adenylate intermediate (see paper)
51% identity, 75% coverage: 141:576/579 of query aligns to 56:485/485 of 1e1tA
- active site: R245 (= R337), E247 (= E339), R252 (≠ T344), H253 (= H345), E404 (= E495), N407 (= N498), R463 (= R554)
- binding adenosine-5'-[lysyl-phosphate]: G199 (= G291), E223 (= E315), R245 (= R337), R252 (≠ T344), H253 (= H345), N254 (= N346), F257 (= F349), M259 (= M351), E261 (= E353), Y263 (= Y355), E404 (= E495), I405 (= I496), N407 (= N498), F409 (≠ Y500), E411 (= E502), G456 (= G547), G458 (= G549), G460 (= G551)
- binding magnesium ion: E397 (= E488), E404 (= E495)
- binding pyrophosphate 2-: H253 (= H345), E404 (= E495), R463 (= R554)
5yzxA Crystal structure of e.Coli lysu t146d mutant
50% identity, 75% coverage: 141:576/579 of query aligns to 55:484/484 of 5yzxA
- binding bis(adenosine)-5'-tetraphosphate: R244 (= R337), E246 (= E339), H252 (= H345), N253 (= N346), F256 (= F349), M258 (= M351), D358 (≠ E450), E403 (= E495), I404 (= I496), G459 (= G551), R462 (= R554)
- binding calcium ion: D358 (≠ E450), E396 (= E488), E396 (= E488), E403 (= E495), N406 (= N498)
1e1oA Lysyl-tRNA synthetase (lysu) hexagonal form, complexed with lysine (see paper)
51% identity, 75% coverage: 141:576/579 of query aligns to 56:484/484 of 1e1oA
- active site: R245 (= R337), E247 (= E339), H252 (= H345), E403 (= E495), N406 (= N498), R462 (= R554)
- binding lysine: G199 (= G291), E223 (= E315), E260 (= E353), Y262 (= Y355), N406 (= N498), F408 (≠ Y500), E410 (= E502), G455 (= G547), G457 (= G549)
1bbuA Lysyl-tRNA synthetase (lyss) complexed with lysine (see paper)
51% identity, 75% coverage: 141:576/579 of query aligns to 56:486/486 of 1bbuA
- active site: R246 (= R337), E248 (= E339), R253 (≠ T344), H254 (= H345), E405 (= E495), N408 (= N498), R464 (= R554)
- binding lysine: G200 (= G291), E224 (= E315), E262 (= E353), Y264 (= Y355), F410 (≠ Y500), E412 (= E502), G457 (= G547), G459 (= G549)
4up7A Crystal structure of entamoeba histolytica lysyl-tRNA synthetase in complex with lysyl-adenylate (see paper)
52% identity, 75% coverage: 142:577/579 of query aligns to 61:508/529 of 4up7A
- active site: R258 (= R337), E260 (= E339), T265 (= T344), H266 (= H345), E426 (= E495), N429 (= N498), R485 (= R554)
- binding adenosine-5'-[lysyl-phosphate]: E236 (= E315), R258 (= R337), H266 (= H345), F270 (= F349), E274 (= E353), Y276 (= Y355), E426 (= E495), I427 (= I496), Y431 (= Y500), E433 (= E502), G478 (= G547), R485 (= R554)
4ex5A Crystal structure of lysyl-tRNA synthetase lysrs from burkholderia thailandensis bound to lysine (see paper)
51% identity, 75% coverage: 141:575/579 of query aligns to 53:485/486 of 4ex5A
- active site: R242 (= R337), E244 (= E339), R249 (≠ T344), H250 (= H345), E405 (= E495), N408 (= N498), R464 (= R554)
- binding lysine: E220 (= E315), E258 (= E353), Y260 (= Y355), F410 (≠ Y500), E412 (= E502), G457 (= G547), G459 (= G549)
6wbdB Crystal structure of lysyl-tRNA synthetase from stenotrophomonas maltophilia with bound l-lysine
47% identity, 79% coverage: 121:576/579 of query aligns to 37:485/485 of 6wbdB
4up9A Crystal structure of entamoeba histolytica lysyl-tRNA synthetase in complex with atp (see paper)
51% identity, 75% coverage: 142:577/579 of query aligns to 58:493/514 of 4up9A
- active site: R255 (= R337), E257 (= E339), T262 (= T344), H263 (= H345), E418 (= E495), N421 (= N498), R470 (= R554)
- binding adenosine-5'-triphosphate: R255 (= R337), T262 (= T344), H263 (= H345), N264 (= N346), F267 (= F349), R470 (= R554)
4upaA Crystal structure of entamoeba histolytica lysyl-tRNA synthetase in complex with amppnp (see paper)
51% identity, 75% coverage: 142:577/579 of query aligns to 58:494/515 of 4upaA
- active site: R255 (= R337), E257 (= E339), T262 (= T344), H263 (= H345), E419 (= E495), N422 (= N498), R471 (= R554)
- binding phosphoaminophosphonic acid-adenylate ester: R255 (= R337), H263 (= H345), N264 (= N346), F267 (= F349), R471 (= R554)
Q15046 Lysine--tRNA ligase; Lysyl-tRNA synthetase; LysRS; EC 2.7.7.-; EC 6.1.1.6 from Homo sapiens (Human) (see 16 papers)
48% identity, 78% coverage: 129:577/579 of query aligns to 109:576/597 of Q15046
- G189 (≠ F203) to D: in LEPID; does not rescue the developmental defects caused by KARS1 depletion in xenopus
- P200 (≠ V214) to L: in DEAPLE and LEPID; reduces interaction with AIMP2. Reduces tRNA-lysine aminoacylation
- S207 (≠ T221) modified: Phosphoserine; mutation to A: Strongly reduced production of diadenosine tetraphosphate (Ap4A). Reduced protein phosphorylation.; mutation to D: Phosphomimetic mutant that strongly enhances translocation into the nucleus and production of diadenosine tetraphosphate (Ap4A). Almost complete loss of tRNA ligase activity.; mutation to R: Strongly decreased tRNA ligase activity.; mutation to Y: Almost complete loss of tRNA ligase activity.
- F263 (= F277) to V: in DEAPLE; reduces interaction with AIMP2. Reduces tRNA-lysine aminoacylation; dbSNP:rs772410450
- G277 (= G291) binding
- E301 (= E315) binding
- RNE 323:325 (= RNE 337:339) binding
- HN 331:332 (= HN 345:346) binding
- E339 (= E353) binding
- Y341 (= Y355) binding
- D346 (= D360) mutation to R: Induces protein aggregation. Releases from the subunit complex.
- L350 (= L364) to H: found in a patient with hypertrophic cardiomyopathy and mild intellectual disability together with proximal muscle weakness; uncertain significance
- P390 (= P397) to R: found in a patient with hypertrophic cardiomyopathy and mild intellectual disability together with proximal muscle weakness; uncertain significance
- R438 (vs. gap) to W: in LEPID; uncertain significance; dbSNP:rs761527468
- V448 (≠ F449) to F: in DEAPLE; uncertain significance
- R477 (= R478) to H: in DEAPLE and LEPID; decreases tRNA-lysine aminoacylation; induces protein aggregation; releases from the subunit complex; no effect on cytoplasmic location; no effect on oligomerization; dbSNP:rs778748895
- EI 494:495 (= EI 495:496) binding
- N497 (= N498) binding
- E501 (= E502) binding
- P505 (= P506) to S: in DEAPLE; decreases tRNA-lysine aminoacylation; slightly induces protein aggregation; no effect on cytoplasmic location; no effect on oligomerization; dbSNP:rs1555512658
- E525 (= E526) to K: in LEPID; uncertain significance; dbSNP:rs770522582
- G540 (= G541) mutation to Y: Disrupts interaction with AIMP2 and the multisynthase complex. Increases production of diadenosine tetraphosphate (Ap4A). Almost complete loss of tRNA ligase activity.
- GIDR 550:553 (= GIDR 551:554) binding
- L568 (≠ I569) to F: in LEPID; decreases tRNA-lysine aminoacylation activity of both the mitochondrial and cytosolic forms. Does not rescue the developmental defects caused by KARS1 depletion in xenopus
Sites not aligning to the query:
- 1 modified: Initiator methionine, Removed
- 1:65 mutation Missing: Loss of nuclear localization, but no effect on packaging into HIV-1.
- 2 modified: N-acetylalanine
- 80 R → H: in DEAPLE; uncertain significance; dbSNP:rs369114426
- 101 mutation V->D,R,W: Disrupts interaction with AIMP2 and the multisynthase complex.
- 105 L → H: in CMTRIB; severely affects enzyme activity; dbSNP:rs267607194
- 595 T → S: in dbSNP:rs6834
4ycuA Crystal structure of cladosporin in complex with human lysyl-tRNA synthetase (see paper)
48% identity, 78% coverage: 129:577/579 of query aligns to 38:505/505 of 4ycuA
- active site: R252 (= R337), E254 (= E339), T259 (= T344), H260 (= H345), E423 (= E495), N426 (= N498), R482 (= R554)
- binding cladosporin: E254 (= E339), H260 (= H345), N261 (= N346), F264 (= F349), N426 (= N498), G479 (= G551), R482 (= R554)
- binding lysine: G206 (= G291), E230 (= E315), E268 (= E353), Y270 (= Y355), N426 (= N498), Y428 (= Y500), E430 (= E502), G475 (= G547)
6chdA Crystal structure of human lysyl-tRNA synthetase complexed with l- lysylsulfamoyl adenosine
48% identity, 78% coverage: 129:577/579 of query aligns to 39:506/506 of 6chdA
- binding 5'-o-[(l-lysylamino)sulfonyl]adenosine: G207 (= G291), A229 (= A313), E231 (= E315), R253 (= R337), H261 (= H345), N262 (= N346), F265 (= F349), E269 (= E353), Y271 (= Y355), E424 (= E495), I425 (= I496), N427 (= N498), Y429 (= Y500), E431 (= E502), G476 (= G547), G478 (= G549), G480 (= G551), R483 (= R554)
3bjuA Crystal structure of tetrameric form of human lysyl-tRNA synthetase (see paper)
47% identity, 78% coverage: 129:577/579 of query aligns to 40:503/503 of 3bjuA
- active site: R250 (= R337), E252 (= E339), T257 (= T344), H258 (= H345), E421 (= E495), N424 (= N498), R480 (= R554)
- binding adenosine-5'-triphosphate: R250 (= R337), H258 (= H345), N259 (= N346), F262 (= F349), E421 (= E495), G477 (= G551), R480 (= R554)
- binding calcium ion: E414 (= E488), E421 (= E495)
- binding lysine: G204 (= G291), E228 (= E315), E266 (= E353), Y268 (= Y355), N424 (= N498), Y426 (= Y500), E428 (= E502), G473 (= G547)
4dpgA Crystal structure of human lysrs: p38/aimp2 complex i (see paper)
47% identity, 77% coverage: 129:576/579 of query aligns to 39:501/501 of 4dpgA
- active site: R249 (= R337), E251 (= E339), T256 (= T344), H257 (= H345), E420 (= E495), N423 (= N498), R479 (= R554)
- binding diphosphomethylphosphonic acid adenosyl ester: R249 (= R337), T256 (= T344), H257 (= H345), N258 (= N346), F261 (= F349), R479 (= R554)
- binding lysine: E227 (= E315), E265 (= E353), Y267 (= Y355), N423 (= N498), Y425 (= Y500), E427 (= E502), G472 (= G547)
- binding magnesium ion: E413 (= E488), E420 (= E495)
Query Sequence
>WP_012675654.1 NCBI__GCF_000021565.1:WP_012675654.1
MSEEIIESRRDLVKRLKEKGINPYPHKFSVTAKLDQIRKKYELPVERDKEYILKGRIKRV
SKREDRYIIRFADLTEPVEIQVIFPIDKGKVSPNTVCSFKGYLDRIDGKLTLVAEEVLEG
EEGTAVSEVKRVYDLDPGREKVSVAGRIVSFRDQGKAAFGHIQDADGKIQIYFRRDTLGD
EKYNEAMEILDIGDIVGVEGELFRTMTGELTVEVKDFKLLTKSLRALPEKWHGLKDVELR
YRRRYVDLIANPKAREIFKIRYKAIKSLREFLESEGFMEVETPILQSVASGAMARPFITH
HNALDIDMYLRIAPELYLKMLIVGGFNRVYELGRNFRNEGIDTTHNPEFTMVEFYAAYMD
YNDLMDLTERLMRKILMDTVGKLKITWEGQELDFSKPFRRLRFFDALKEKTGKDKEFFLD
EGKAREFAKEVGIPKAETLTHLKILDKLFEHFIEEDLVQPTFVIDFPKILSPLAKTHRDD
PDLVERFELIVNKQEIANAYTELNDPEDQRERFLQQLKEKAAGDEEAMDIDENFLTALEY
GLPPTGGEGIGIDRLVMMLTDSPSIREVILFPTLRPEKD
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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