SYV_THETH
ID SYV_THETH Reviewed; 862 AA.
AC P96142; Q54A82;
DT 01-NOV-1997, integrated into UniProtKB/Swiss-Prot.
DT 01-JUN-2001, sequence version 2.
DT 03-AUG-2022, entry version 131.
DE RecName: Full=Valine--tRNA ligase;
DE EC=6.1.1.9;
DE AltName: Full=Valyl-tRNA synthetase;
DE Short=ValRS;
GN Name=valS;
OS Thermus thermophilus.
OC Bacteria; Deinococcus-Thermus; Deinococci; Thermales; Thermaceae; Thermus.
OX NCBI_TaxID=274;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RA Fukai S., Nureki O., Sekine S., Shimada A., Vassylyev D.G., Yokoyama S.;
RL Submitted (FEB-2002) to the EMBL/GenBank/DDBJ databases.
RN [2] {ECO:0007744|PDB:1GAX}
RP X-RAY CRYSTALLOGRAPHY (2.9 ANGSTROMS) IN COMPLEX WITH TRNA(VAL) AND VAL-AMP
RP ANALOG.
RX PubMed=11114335; DOI=10.1016/s0092-8674(00)00182-3;
RA Fukai S., Nureki O., Sekine S., Shimada A., Tao J., Vassylyev D.G.,
RA Yokoyama S.;
RT "Structural basis for double-sieve discrimination of L-valine from L-
RT isoleucine and L-threonine by the complex of tRNA(Val) and valyl-tRNA
RT synthetase.";
RL Cell 103:793-803(2000).
RN [3] {ECO:0007744|PDB:1IVS, ECO:0007744|PDB:1IYW}
RP X-RAY CRYSTALLOGRAPHY (2.9 ANGSTROMS) IN COMPLEX WITH TRNA(VAL) AND VAL-AMP
RP ANALOG, INTERACTION OF COILED-COIL DOMAIN WITH TRNA, KINETIC PARAMETERS,
RP AND MUTAGENESIS OF ARG-818 AND ARG-843.
RX PubMed=12554880; DOI=10.1261/rna.2760703;
RA Fukai S., Nureki O., Sekine S., Shimada A., Vassylyev D.G., Yokoyama S.;
RT "Mechanism of molecular interactions for tRNA(Val) recognition by valyl-
RT tRNA synthetase.";
RL RNA 9:100-111(2003).
RN [4] {ECO:0007744|PDB:1WK9, ECO:0007744|PDB:1WKA}
RP X-RAY CRYSTALLOGRAPHY (1.7 ANGSTROMS) OF 195-337 IN COMPLEX WITH THR-AMP
RP ANALOG, AND MUTAGENESIS OF ARG-216; PHE-264; LYS-270; THR-272; ASP-276 AND
RP ASP-279.
RX PubMed=15970591; DOI=10.1074/jbc.m502668200;
RA Fukunaga R., Yokoyama S.;
RT "Structural basis for non-cognate amino acid discrimination by the valyl-
RT tRNA synthetase editing domain.";
RL J. Biol. Chem. 280:29937-29945(2005).
CC -!- FUNCTION: Catalyzes the attachment of valine to tRNA(Val). As ValRS can
CC inadvertently accommodate and process structurally similar amino acids
CC such as threonine, to avoid such errors, it has a 'posttransfer'
CC editing activity that hydrolyzes mischarged Thr-tRNA(Val) in a tRNA-
CC dependent manner.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=ATP + L-valine + tRNA(Val) = AMP + diphosphate + L-valyl-
CC tRNA(Val); Xref=Rhea:RHEA:10704, Rhea:RHEA-COMP:9672, Rhea:RHEA-
CC COMP:9708, ChEBI:CHEBI:30616, ChEBI:CHEBI:33019, ChEBI:CHEBI:57762,
CC ChEBI:CHEBI:78442, ChEBI:CHEBI:78537, ChEBI:CHEBI:456215; EC=6.1.1.9;
CC -!- COFACTOR:
CC Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
CC Note=Binds 2 Zn(2+) ions per subunit.;
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=0.7 uM for tRNA(Val) {ECO:0000269|PubMed:12554880};
CC -!- SUBUNIT: Monomer. {ECO:0000269|PubMed:11114335,
CC ECO:0000269|PubMed:12554880, ECO:0000269|PubMed:15970591}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm.
CC -!- DOMAIN: ValRS has two distinct active sites: one for aminoacylation and
CC one for editing. The misactivated threonine is translocated from the
CC active site to the editing site.
CC -!- DOMAIN: The C-terminal coiled-coil domain is crucial for aminoacylation
CC activity.
CC -!- SIMILARITY: Belongs to the class-I aminoacyl-tRNA synthetase family.
CC ValS type 1 subfamily. {ECO:0000305}.
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DR EMBL; AB080140; BAB85225.1; -; Genomic_DNA.
DR RefSeq; WP_011228487.1; NC_006461.1.
DR PDB; 1GAX; X-ray; 2.90 A; A/B=1-862.
DR PDB; 1IVS; X-ray; 2.90 A; A/B=1-862.
DR PDB; 1IYW; X-ray; 4.00 A; A/B=1-862.
DR PDB; 1WK9; X-ray; 1.75 A; A=193-337.
DR PDB; 1WKA; X-ray; 1.70 A; A=193-338.
DR PDBsum; 1GAX; -.
DR PDBsum; 1IVS; -.
DR PDBsum; 1IYW; -.
DR PDBsum; 1WK9; -.
DR PDBsum; 1WKA; -.
DR AlphaFoldDB; P96142; -.
DR SMR; P96142; -.
DR PRIDE; P96142; -.
DR GeneID; 3169414; -.
DR BRENDA; 6.1.1.9; 2305.
DR SABIO-RK; P96142; -.
DR EvolutionaryTrace; P96142; -.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0002161; F:aminoacyl-tRNA editing activity; IEA:InterPro.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-UniRule.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0004832; F:valine-tRNA ligase activity; IEA:UniProtKB-UniRule.
DR GO; GO:0006438; P:valyl-tRNA aminoacylation; IEA:UniProtKB-UniRule.
DR CDD; cd07962; Anticodon_Ia_Val; 1.
DR Gene3D; 1.10.287.380; -; 1.
DR Gene3D; 3.40.50.620; -; 2.
DR Gene3D; 3.90.740.10; -; 1.
DR HAMAP; MF_02004; Val_tRNA_synth_type1; 1.
DR InterPro; IPR001412; aa-tRNA-synth_I_CS.
DR InterPro; IPR002300; aa-tRNA-synth_Ia.
DR InterPro; IPR033705; Anticodon_Ia_Val.
DR InterPro; IPR013155; M/V/L/I-tRNA-synth_anticd-bd.
DR InterPro; IPR014729; Rossmann-like_a/b/a_fold.
DR InterPro; IPR010978; tRNA-bd_arm.
DR InterPro; IPR009080; tRNAsynth_Ia_anticodon-bd.
DR InterPro; IPR037118; Val-tRNA_synth_C_sf.
DR InterPro; IPR019499; Val-tRNA_synth_tRNA-bd.
DR InterPro; IPR009008; Val/Leu/Ile-tRNA-synth_edit.
DR InterPro; IPR002303; Valyl-tRNA_ligase.
DR PANTHER; PTHR11946; PTHR11946; 1.
DR Pfam; PF08264; Anticodon_1; 1.
DR Pfam; PF00133; tRNA-synt_1; 1.
DR Pfam; PF10458; Val_tRNA-synt_C; 1.
DR PRINTS; PR00986; TRNASYNTHVAL.
DR SUPFAM; SSF46589; SSF46589; 1.
DR SUPFAM; SSF47323; SSF47323; 1.
DR SUPFAM; SSF50677; SSF50677; 1.
DR TIGRFAMs; TIGR00422; valS; 1.
DR PROSITE; PS00178; AA_TRNA_LIGASE_I; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Aminoacyl-tRNA synthetase; ATP-binding; Coiled coil;
KW Cytoplasm; Ligase; Metal-binding; Nucleotide-binding; Protein biosynthesis;
KW Zinc.
FT CHAIN 1..862
FT /note="Valine--tRNA ligase"
FT /id="PRO_0000106240"
FT REGION 42..44
FT /note="Valine"
FT /evidence="ECO:0000305|PubMed:11114335,
FT ECO:0000305|PubMed:12554880, ECO:0007744|PDB:1GAX,
FT ECO:0007744|PDB:1IVS"
FT REGION 50..53
FT /note="AMP"
FT /evidence="ECO:0000305|PubMed:11114335,
FT ECO:0000305|PubMed:12554880, ECO:0007744|PDB:1GAX,
FT ECO:0007744|PDB:1IVS"
FT REGION 487..490
FT /note="AMP"
FT /evidence="ECO:0000305|PubMed:11114335,
FT ECO:0000305|PubMed:12554880, ECO:0007744|PDB:1GAX,
FT ECO:0007744|PDB:1IVS"
FT REGION 518..521
FT /note="AMP"
FT /evidence="ECO:0000305|PubMed:11114335,
FT ECO:0000305|PubMed:12554880, ECO:0007744|PDB:1GAX,
FT ECO:0007744|PDB:1IVS"
FT REGION 576..587
FT /note="Interaction with tRNA"
FT REGION 646..651
FT /note="Interaction with tRNA"
FT REGION 815..847
FT /note="Interaction with tRNA"
FT COILED 802..862
FT /evidence="ECO:0000255"
FT MOTIF 44..53
FT /note="'HIGH' region"
FT MOTIF 528..532
FT /note="'KMSKS' region"
FT BINDING 81
FT /ligand="L-valine"
FT /ligand_id="ChEBI:CHEBI:57762"
FT /evidence="ECO:0000305|PubMed:11114335,
FT ECO:0000305|PubMed:12554880, ECO:0007744|PDB:1GAX,
FT ECO:0007744|PDB:1IVS"
FT BINDING 176
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT BINDING 179
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT BINDING 344
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT BINDING 347
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT BINDING 417
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT BINDING 420
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT BINDING 438
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT BINDING 441
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT BINDING 529
FT /ligand="AMP"
FT /ligand_id="ChEBI:CHEBI:456215"
FT /evidence="ECO:0000305|PubMed:11114335,
FT ECO:0000305|PubMed:12554880, ECO:0007744|PDB:1GAX,
FT ECO:0007744|PDB:1IVS"
FT BINDING 531
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250"
FT SITE 570
FT /note="Interaction with tRNA"
FT MUTAGEN 216
FT /note="R->A: Decrease in posttransfer editing activity. No
FT change in aminoacylation activity."
FT /evidence="ECO:0000269|PubMed:15970591"
FT MUTAGEN 264
FT /note="F->A: Decrease in posttransfer editing activity. No
FT change in aminoacylation activity."
FT /evidence="ECO:0000269|PubMed:15970591"
FT MUTAGEN 270
FT /note="K->A: Strong decrease in posttransfer editing
FT activity. Slight decrease in Val-tRNA(Val) formation, which
FT could be due to deacylation of the synthesized Val-
FT tRNA(Val)."
FT /evidence="ECO:0000269|PubMed:15970591"
FT MUTAGEN 272
FT /note="T->A: Decrease in posttransfer editing activity. No
FT change in aminoacylation activity."
FT /evidence="ECO:0000269|PubMed:15970591"
FT MUTAGEN 276
FT /note="D->A: No change in aminoacylation and posttransfer
FT editing activities."
FT /evidence="ECO:0000269|PubMed:15970591"
FT MUTAGEN 279
FT /note="D->A: Strong decrease in posttransfer editing
FT activity. No change in aminoacylation activity."
FT /evidence="ECO:0000269|PubMed:15970591"
FT MUTAGEN 818
FT /note="R->A: Increase in KM for tRNA(Val), without change
FT in kcat; when associated with A-843."
FT /evidence="ECO:0000269|PubMed:12554880"
FT MUTAGEN 843
FT /note="R->A: Increase in KM for tRNA(Val), without change
FT in kcat; when associated with A-818."
FT /evidence="ECO:0000269|PubMed:12554880"
FT HELIX 9..11
FT /evidence="ECO:0007829|PDB:1GAX"
FT HELIX 13..22
FT /evidence="ECO:0007829|PDB:1GAX"
FT STRAND 35..39
FT /evidence="ECO:0007829|PDB:1GAX"
FT STRAND 44..47
FT /evidence="ECO:0007829|PDB:1GAX"
FT HELIX 51..68
FT /evidence="ECO:0007829|PDB:1GAX"
FT TURN 69..71
FT /evidence="ECO:0007829|PDB:1GAX"
FT STRAND 72..77
FT /evidence="ECO:0007829|PDB:1GAX"
FT STRAND 79..81
FT /evidence="ECO:0007829|PDB:1GAX"
FT HELIX 85..92
FT /evidence="ECO:0007829|PDB:1GAX"
FT TURN 93..99
FT /evidence="ECO:0007829|PDB:1GAX"
FT HELIX 102..104
FT /evidence="ECO:0007829|PDB:1IVS"
FT TURN 106..108
FT /evidence="ECO:0007829|PDB:1IVS"
FT HELIX 109..131
FT /evidence="ECO:0007829|PDB:1GAX"
FT HELIX 138..140
FT /evidence="ECO:0007829|PDB:1GAX"
FT HELIX 147..161
FT /evidence="ECO:0007829|PDB:1GAX"
FT STRAND 164..169
FT /evidence="ECO:0007829|PDB:1GAX"
FT STRAND 172..176
FT /evidence="ECO:0007829|PDB:1GAX"
FT TURN 177..180
FT /evidence="ECO:0007829|PDB:1GAX"
FT STRAND 181..183
FT /evidence="ECO:0007829|PDB:1GAX"
FT HELIX 185..187
FT /evidence="ECO:0007829|PDB:1GAX"
FT STRAND 188..190
FT /evidence="ECO:0007829|PDB:1GAX"
FT STRAND 196..204
FT /evidence="ECO:0007829|PDB:1WKA"
FT STRAND 205..207
FT /evidence="ECO:0007829|PDB:1GAX"
FT STRAND 209..215
FT /evidence="ECO:0007829|PDB:1WKA"
FT HELIX 217..222
FT /evidence="ECO:0007829|PDB:1WKA"
FT STRAND 225..228
FT /evidence="ECO:0007829|PDB:1WKA"
FT TURN 233..235
FT /evidence="ECO:0007829|PDB:1WKA"
FT HELIX 236..238
FT /evidence="ECO:0007829|PDB:1WKA"
FT STRAND 242..244
FT /evidence="ECO:0007829|PDB:1WKA"
FT STRAND 251..256
FT /evidence="ECO:0007829|PDB:1WKA"
FT STRAND 267..271
FT /evidence="ECO:0007829|PDB:1WKA"
FT TURN 273..275
FT /evidence="ECO:0007829|PDB:1WKA"
FT HELIX 277..286
FT /evidence="ECO:0007829|PDB:1WKA"
FT STRAND 293..295
FT /evidence="ECO:0007829|PDB:1IVS"
FT STRAND 298..300
FT /evidence="ECO:0007829|PDB:1WKA"
FT STRAND 302..305
FT /evidence="ECO:0007829|PDB:1GAX"
FT HELIX 307..309
FT /evidence="ECO:0007829|PDB:1WKA"
FT HELIX 314..327
FT /evidence="ECO:0007829|PDB:1WKA"
FT STRAND 331..336
FT /evidence="ECO:0007829|PDB:1WKA"
FT STRAND 342..344
FT /evidence="ECO:0007829|PDB:1GAX"
FT TURN 345..347
FT /evidence="ECO:0007829|PDB:1GAX"
FT STRAND 353..355
FT /evidence="ECO:0007829|PDB:1GAX"
FT STRAND 358..361
FT /evidence="ECO:0007829|PDB:1GAX"
FT HELIX 363..376
FT /evidence="ECO:0007829|PDB:1GAX"
FT STRAND 380..384
FT /evidence="ECO:0007829|PDB:1GAX"
FT HELIX 386..395
FT /evidence="ECO:0007829|PDB:1GAX"
FT STRAND 407..409
FT /evidence="ECO:0007829|PDB:1GAX"
FT STRAND 415..417
FT /evidence="ECO:0007829|PDB:1GAX"
FT TURN 418..420
FT /evidence="ECO:0007829|PDB:1GAX"
FT HELIX 428..430
FT /evidence="ECO:0007829|PDB:1GAX"
FT TURN 439..441
FT /evidence="ECO:0007829|PDB:1GAX"
FT STRAND 446..448
FT /evidence="ECO:0007829|PDB:1GAX"
FT HELIX 455..459
FT /evidence="ECO:0007829|PDB:1GAX"
FT HELIX 465..467
FT /evidence="ECO:0007829|PDB:1GAX"
FT TURN 468..470
FT /evidence="ECO:0007829|PDB:1GAX"
FT HELIX 474..478
FT /evidence="ECO:0007829|PDB:1GAX"
FT STRAND 481..483
FT /evidence="ECO:0007829|PDB:1GAX"
FT STRAND 485..488
FT /evidence="ECO:0007829|PDB:1GAX"
FT HELIX 489..491
FT /evidence="ECO:0007829|PDB:1GAX"
FT TURN 492..495
FT /evidence="ECO:0007829|PDB:1GAX"
FT HELIX 496..506
FT /evidence="ECO:0007829|PDB:1GAX"
FT STRAND 507..509
FT /evidence="ECO:0007829|PDB:1GAX"
FT STRAND 511..518
FT /evidence="ECO:0007829|PDB:1GAX"
FT STRAND 526..528
FT /evidence="ECO:0007829|PDB:1IVS"
FT TURN 531..534
FT /evidence="ECO:0007829|PDB:1GAX"
FT HELIX 539..546
FT /evidence="ECO:0007829|PDB:1GAX"
FT HELIX 548..558
FT /evidence="ECO:0007829|PDB:1GAX"
FT HELIX 569..592
FT /evidence="ECO:0007829|PDB:1GAX"
FT STRAND 593..595
FT /evidence="ECO:0007829|PDB:1GAX"
FT HELIX 605..625
FT /evidence="ECO:0007829|PDB:1GAX"
FT TURN 626..628
FT /evidence="ECO:0007829|PDB:1GAX"
FT HELIX 630..644
FT /evidence="ECO:0007829|PDB:1GAX"
FT TURN 645..648
FT /evidence="ECO:0007829|PDB:1GAX"
FT HELIX 649..658
FT /evidence="ECO:0007829|PDB:1GAX"
FT HELIX 662..679
FT /evidence="ECO:0007829|PDB:1GAX"
FT TURN 680..682
FT /evidence="ECO:0007829|PDB:1GAX"
FT HELIX 684..695
FT /evidence="ECO:0007829|PDB:1GAX"
FT HELIX 700..702
FT /evidence="ECO:0007829|PDB:1GAX"
FT HELIX 713..736
FT /evidence="ECO:0007829|PDB:1GAX"
FT STRAND 744..751
FT /evidence="ECO:0007829|PDB:1GAX"
FT HELIX 753..757
FT /evidence="ECO:0007829|PDB:1GAX"
FT HELIX 759..766
FT /evidence="ECO:0007829|PDB:1GAX"
FT STRAND 768..770
FT /evidence="ECO:0007829|PDB:1GAX"
FT STRAND 776..782
FT /evidence="ECO:0007829|PDB:1GAX"
FT STRAND 784..791
FT /evidence="ECO:0007829|PDB:1GAX"
FT HELIX 798..823
FT /evidence="ECO:0007829|PDB:1GAX"
FT TURN 826..828
FT /evidence="ECO:0007829|PDB:1GAX"
FT STRAND 829..832
FT /evidence="ECO:0007829|PDB:1GAX"
FT HELIX 836..860
FT /evidence="ECO:0007829|PDB:1GAX"
SQ SEQUENCE 862 AA; 98775 MW; 90504DC65780942F CRC64;
MDLPKAYDPK SVEPKWAEKW AKNPFVANPK SGKPPFVIFM PPPNVTGSLH MGHALDNSLQ
DALIRYKRMR GFEAVWLPGT DHAGIATQVV VERLLLKEGK TRHDLGREKF LERVWQWKEE
SGGTILKQLK RLGASADWSR EAFTMDEKRS RAVRYAFSRY YHEGLAYRAP RLVNWCPRCE
TTLSDLEVET EPTPGKLYTL RYEVEGGGFI EIATVRPETV FADQAIAVHP EDERYRHLLG
KRARIPLTEV WIPILADPAV EKDFGTGALK VTPAHDPLDY EIGERHGLKP VSVINLEGRM
EGERVPEALR GLDRFEARRK AVELFREAGH LVKEEDYTIA LATCSRCGTP IEYAIFPQWW
LRMRPLAEEV LKGLRRGDIA FVPERWKKVN MDWLENVKDW NISRQLWWGH QIPAWYCEDC
QAVNVPRPER YLEDPTSCEA CGSPRLKRDE DVFDTWFSSA LWPLSTLGWP EETEDLKAFY
PGDVLVTGYD ILFLWVSRME VSGYHFMGER PFKTVLLHGL VLDEKGQKMS KSKGNVIDPL
EMVERYGADA LRFALIYLAT GGQDIRLDLR WLEMARNFAN KLYNAARFVL LSREGFQAKE
DTPTLADRFM RSRLSRGVEE ITALYEALDL AQAAREVYEL VWSEFCDWYL EAAKPALKAG
NAHTLRTLEE VLAVLLKLLH PMMPFLTSEL YQALTGKEEL ALEAWPEPGG RDEEAERAFE
ALKQAVTAVR ALKAEAGLPP AQEVRVYLEG ETAPVEENLE VFRFLSRADL LPERPAKALV
KAMPRVTARM PLEGLLDVEE WRRRQEKRLK ELLALAERSQ RKLASPGFRE KAPKEVVEAE
EARLKENLEQ AERIREALSQ IG
