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Protein

Valine--tRNA ligase

Gene

valS

Organism
Thermus thermophilus
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the attachment of valine to tRNA(Val). As ValRS can inadvertently accommodate and process structurally similar amino acids such as threonine, to avoid such errors, it has a "posttransfer" editing activity that hydrolyzes mischarged Thr-tRNA(Val) in a tRNA-dependent manner.

Catalytic activityi

ATP + L-valine + tRNA(Val) = AMP + diphosphate + L-valyl-tRNA(Val).

Cofactori

Zn2+Note: Binds 2 Zn2+ ions per subunit.

Kineticsi

  1. KM=0.7 µM for tRNA(Val)1 Publication

    Sites

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Binding sitei50Val-AMP intermediate adenyl group1
    Binding sitei53Val-AMP intermediate phosphate group1
    Metal bindingi176Zinc 11
    Metal bindingi179Zinc 11
    Metal bindingi344Zinc 11
    Metal bindingi347Zinc 11
    Metal bindingi417Zinc 21
    Metal bindingi420Zinc 21
    Metal bindingi438Zinc 21
    Metal bindingi441Zinc 21
    Binding sitei531ATPBy similarity1

    GO - Molecular functioni

    GO - Biological processi

    Complete GO annotation...

    Keywords - Molecular functioni

    Aminoacyl-tRNA synthetase, Ligase

    Keywords - Biological processi

    Protein biosynthesis

    Keywords - Ligandi

    ATP-binding, Metal-binding, Nucleotide-binding, Zinc

    Enzyme and pathway databases

    BRENDAi6.1.1.9. 2305.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Valine--tRNA ligase (EC:6.1.1.9)
    Alternative name(s):
    Valyl-tRNA synthetase
    Short name:
    ValRS
    Gene namesi
    Name:valS
    OrganismiThermus thermophilus
    Taxonomic identifieri274 [NCBI]
    Taxonomic lineageiBacteriaDeinococcus-ThermusDeinococciThermalesThermaceaeThermus

    Subcellular locationi

    GO - Cellular componenti

    Complete GO annotation...

    Keywords - Cellular componenti

    Cytoplasm

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Mutagenesisi216R → A: Decrease in posttransfer editing activity. No change in aminoacylation activity. 1 Publication1
    Mutagenesisi264F → A: Decrease in posttransfer editing activity. No change in aminoacylation activity. 1 Publication1
    Mutagenesisi270K → A: Strong decrease in posttransfer editing activity. Slight decrease in Val-tRNA(Val) formation, which could be due to deacylation of the synthesized Val-tRNA(Val). 1 Publication1
    Mutagenesisi272T → A: Decrease in posttransfer editing activity. No change in aminoacylation activity. 1 Publication1
    Mutagenesisi276D → A: No change in aminoacylation and posttransfer editing activities. 1 Publication1
    Mutagenesisi279D → A: Strong decrease in posttransfer editing activity. No change in aminoacylation activity. 1 Publication1
    Mutagenesisi818R → A: Increase in Km for tRNA(Val), without change in Kcat; when associated with A-843. 1 Publication1
    Mutagenesisi843R → A: Increase in Km for tRNA(Val), without change in Kcat; when associated with A-818. 1 Publication1

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    ChainiPRO_00001062401 – 862Valine--tRNA ligaseAdd BLAST862

    Interactioni

    Subunit structurei

    Monomer.3 Publications

    Sites

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Sitei81Interaction with valine in the Val-AMP intermediate1
    Sitei570Interaction with tRNA1

    Protein-protein interaction databases

    STRINGi262724.TTC0805.

    Structurei

    Secondary structure

    1862
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Helixi9 – 11Combined sources3
    Helixi13 – 22Combined sources10
    Beta strandi35 – 39Combined sources5
    Beta strandi44 – 47Combined sources4
    Helixi51 – 68Combined sources18
    Turni69 – 71Combined sources3
    Beta strandi72 – 77Combined sources6
    Beta strandi79 – 81Combined sources3
    Helixi85 – 92Combined sources8
    Turni93 – 99Combined sources7
    Helixi102 – 104Combined sources3
    Turni106 – 108Combined sources3
    Helixi109 – 131Combined sources23
    Helixi138 – 140Combined sources3
    Helixi147 – 161Combined sources15
    Beta strandi164 – 169Combined sources6
    Beta strandi172 – 176Combined sources5
    Turni177 – 180Combined sources4
    Beta strandi181 – 183Combined sources3
    Helixi185 – 187Combined sources3
    Beta strandi188 – 190Combined sources3
    Beta strandi196 – 204Combined sources9
    Beta strandi205 – 207Combined sources3
    Beta strandi209 – 215Combined sources7
    Helixi217 – 222Combined sources6
    Beta strandi225 – 228Combined sources4
    Turni233 – 235Combined sources3
    Helixi236 – 238Combined sources3
    Beta strandi242 – 244Combined sources3
    Beta strandi251 – 256Combined sources6
    Beta strandi267 – 271Combined sources5
    Turni273 – 275Combined sources3
    Helixi277 – 286Combined sources10
    Beta strandi293 – 295Combined sources3
    Beta strandi298 – 300Combined sources3
    Beta strandi302 – 305Combined sources4
    Helixi307 – 309Combined sources3
    Helixi314 – 327Combined sources14
    Beta strandi331 – 336Combined sources6
    Beta strandi342 – 344Combined sources3
    Turni345 – 347Combined sources3
    Beta strandi353 – 355Combined sources3
    Beta strandi358 – 361Combined sources4
    Helixi363 – 376Combined sources14
    Beta strandi380 – 384Combined sources5
    Helixi386 – 395Combined sources10
    Beta strandi407 – 409Combined sources3
    Beta strandi415 – 417Combined sources3
    Turni418 – 420Combined sources3
    Helixi428 – 430Combined sources3
    Turni439 – 441Combined sources3
    Beta strandi446 – 448Combined sources3
    Helixi455 – 459Combined sources5
    Helixi465 – 467Combined sources3
    Turni468 – 470Combined sources3
    Helixi474 – 478Combined sources5
    Beta strandi481 – 483Combined sources3
    Beta strandi485 – 488Combined sources4
    Helixi489 – 491Combined sources3
    Turni492 – 495Combined sources4
    Helixi496 – 506Combined sources11
    Beta strandi507 – 509Combined sources3
    Beta strandi511 – 518Combined sources8
    Beta strandi526 – 528Combined sources3
    Turni531 – 534Combined sources4
    Helixi539 – 546Combined sources8
    Helixi548 – 558Combined sources11
    Helixi569 – 592Combined sources24
    Beta strandi593 – 595Combined sources3
    Helixi605 – 625Combined sources21
    Turni626 – 628Combined sources3
    Helixi630 – 644Combined sources15
    Turni645 – 648Combined sources4
    Helixi649 – 658Combined sources10
    Helixi662 – 679Combined sources18
    Turni680 – 682Combined sources3
    Helixi684 – 695Combined sources12
    Helixi700 – 702Combined sources3
    Helixi713 – 736Combined sources24
    Beta strandi744 – 751Combined sources8
    Helixi753 – 757Combined sources5
    Helixi759 – 766Combined sources8
    Beta strandi768 – 770Combined sources3
    Beta strandi776 – 782Combined sources7
    Beta strandi784 – 791Combined sources8
    Helixi798 – 823Combined sources26
    Turni826 – 828Combined sources3
    Beta strandi829 – 832Combined sources4
    Helixi836 – 860Combined sources25

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    1GAXX-ray2.90A/B1-862[»]
    1IVSX-ray2.90A/B1-862[»]
    1IYWX-ray4.00A/B1-862[»]
    1WK9X-ray1.75A193-337[»]
    1WKAX-ray1.70A193-338[»]
    ProteinModelPortaliP96142.
    SMRiP96142.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP96142.

    Family & Domainsi

    Region

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Regioni41 – 53Interaction with valine in the Val-AMP intermediateAdd BLAST13
    Regioni261 – 279Interaction with the Thr-AMP intermediateAdd BLAST19
    Regioni487 – 491Interaction with AMP in the Val-AMP intermediate5
    Regioni518 – 521Interaction with AMP in the Val-AMP intermediate4
    Regioni576 – 587Interaction with tRNAAdd BLAST12
    Regioni646 – 651Interaction with tRNA6
    Regioni815 – 847Interaction with tRNAAdd BLAST33

    Coiled coil

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Coiled coili802 – 862Sequence analysisAdd BLAST61

    Motif

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Motifi44 – 53"HIGH" region10
    Motifi528 – 532"KMSKS" region5

    Domaini

    ValRS has two distinct active sites: one for aminoacylation and one for editing. The misactivated threonine is translocated from the active site to the editing site.
    The C-terminal coiled-coil domain is crucial for aminoacylation activity.

    Sequence similaritiesi

    Keywords - Domaini

    Coiled coil

    Phylogenomic databases

    eggNOGiENOG4105CA4. Bacteria.
    COG0525. LUCA.

    Family and domain databases

    CDDicd07962. Anticodon_Ia_Val. 1 hit.
    Gene3Di1.10.287.380. 1 hit.
    1.10.730.10. 1 hit.
    3.40.50.620. 2 hits.
    3.90.740.10. 1 hit.
    HAMAPiMF_02004. Val_tRNA_synth_type1. 1 hit.
    InterProiIPR001412. aa-tRNA-synth_I_CS.
    IPR002300. aa-tRNA-synth_Ia.
    IPR033705. Anticodon_Ia_Val.
    IPR013155. M/V/L/I-tRNA-synth_anticd-bd.
    IPR014729. Rossmann-like_a/b/a_fold.
    IPR010978. tRNA-bd_arm.
    IPR009080. tRNAsynth_Ia_anticodon-bd.
    IPR019499. Val-tRNA_synth_tRNA-bd.
    IPR009008. Val/Leu/Ile-tRNA-synth_edit.
    IPR002303. Valyl-tRNA_ligase.
    [Graphical view]
    PANTHERiPTHR11946:SF5. PTHR11946:SF5. 2 hits.
    PfamiPF08264. Anticodon_1. 1 hit.
    PF00133. tRNA-synt_1. 1 hit.
    PF10458. Val_tRNA-synt_C. 1 hit.
    [Graphical view]
    PRINTSiPR00986. TRNASYNTHVAL.
    SUPFAMiSSF46589. SSF46589. 1 hit.
    SSF47323. SSF47323. 1 hit.
    SSF50677. SSF50677. 1 hit.
    TIGRFAMsiTIGR00422. valS. 1 hit.
    PROSITEiPS00178. AA_TRNA_LIGASE_I. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    P96142-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MDLPKAYDPK SVEPKWAEKW AKNPFVANPK SGKPPFVIFM PPPNVTGSLH
    60 70 80 90 100
    MGHALDNSLQ DALIRYKRMR GFEAVWLPGT DHAGIATQVV VERLLLKEGK
    110 120 130 140 150
    TRHDLGREKF LERVWQWKEE SGGTILKQLK RLGASADWSR EAFTMDEKRS
    160 170 180 190 200
    RAVRYAFSRY YHEGLAYRAP RLVNWCPRCE TTLSDLEVET EPTPGKLYTL
    210 220 230 240 250
    RYEVEGGGFI EIATVRPETV FADQAIAVHP EDERYRHLLG KRARIPLTEV
    260 270 280 290 300
    WIPILADPAV EKDFGTGALK VTPAHDPLDY EIGERHGLKP VSVINLEGRM
    310 320 330 340 350
    EGERVPEALR GLDRFEARRK AVELFREAGH LVKEEDYTIA LATCSRCGTP
    360 370 380 390 400
    IEYAIFPQWW LRMRPLAEEV LKGLRRGDIA FVPERWKKVN MDWLENVKDW
    410 420 430 440 450
    NISRQLWWGH QIPAWYCEDC QAVNVPRPER YLEDPTSCEA CGSPRLKRDE
    460 470 480 490 500
    DVFDTWFSSA LWPLSTLGWP EETEDLKAFY PGDVLVTGYD ILFLWVSRME
    510 520 530 540 550
    VSGYHFMGER PFKTVLLHGL VLDEKGQKMS KSKGNVIDPL EMVERYGADA
    560 570 580 590 600
    LRFALIYLAT GGQDIRLDLR WLEMARNFAN KLYNAARFVL LSREGFQAKE
    610 620 630 640 650
    DTPTLADRFM RSRLSRGVEE ITALYEALDL AQAAREVYEL VWSEFCDWYL
    660 670 680 690 700
    EAAKPALKAG NAHTLRTLEE VLAVLLKLLH PMMPFLTSEL YQALTGKEEL
    710 720 730 740 750
    ALEAWPEPGG RDEEAERAFE ALKQAVTAVR ALKAEAGLPP AQEVRVYLEG
    760 770 780 790 800
    ETAPVEENLE VFRFLSRADL LPERPAKALV KAMPRVTARM PLEGLLDVEE
    810 820 830 840 850
    WRRRQEKRLK ELLALAERSQ RKLASPGFRE KAPKEVVEAE EARLKENLEQ
    860
    AERIREALSQ IG
    Length:862
    Mass (Da):98,775
    Last modified:June 1, 2001 - v2
    Checksum:i90504DC65780942F
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AB080140 Genomic DNA. Translation: BAB85225.1.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AB080140 Genomic DNA. Translation: BAB85225.1.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    1GAXX-ray2.90A/B1-862[»]
    1IVSX-ray2.90A/B1-862[»]
    1IYWX-ray4.00A/B1-862[»]
    1WK9X-ray1.75A193-337[»]
    1WKAX-ray1.70A193-338[»]
    ProteinModelPortaliP96142.
    SMRiP96142.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    STRINGi262724.TTC0805.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Phylogenomic databases

    eggNOGiENOG4105CA4. Bacteria.
    COG0525. LUCA.

    Enzyme and pathway databases

    BRENDAi6.1.1.9. 2305.

    Miscellaneous databases

    EvolutionaryTraceiP96142.

    Family and domain databases

    CDDicd07962. Anticodon_Ia_Val. 1 hit.
    Gene3Di1.10.287.380. 1 hit.
    1.10.730.10. 1 hit.
    3.40.50.620. 2 hits.
    3.90.740.10. 1 hit.
    HAMAPiMF_02004. Val_tRNA_synth_type1. 1 hit.
    InterProiIPR001412. aa-tRNA-synth_I_CS.
    IPR002300. aa-tRNA-synth_Ia.
    IPR033705. Anticodon_Ia_Val.
    IPR013155. M/V/L/I-tRNA-synth_anticd-bd.
    IPR014729. Rossmann-like_a/b/a_fold.
    IPR010978. tRNA-bd_arm.
    IPR009080. tRNAsynth_Ia_anticodon-bd.
    IPR019499. Val-tRNA_synth_tRNA-bd.
    IPR009008. Val/Leu/Ile-tRNA-synth_edit.
    IPR002303. Valyl-tRNA_ligase.
    [Graphical view]
    PANTHERiPTHR11946:SF5. PTHR11946:SF5. 2 hits.
    PfamiPF08264. Anticodon_1. 1 hit.
    PF00133. tRNA-synt_1. 1 hit.
    PF10458. Val_tRNA-synt_C. 1 hit.
    [Graphical view]
    PRINTSiPR00986. TRNASYNTHVAL.
    SUPFAMiSSF46589. SSF46589. 1 hit.
    SSF47323. SSF47323. 1 hit.
    SSF50677. SSF50677. 1 hit.
    TIGRFAMsiTIGR00422. valS. 1 hit.
    PROSITEiPS00178. AA_TRNA_LIGASE_I. 1 hit.
    [Graphical view]
    ProtoNetiSearch...

    Entry informationi

    Entry nameiSYV_THETH
    AccessioniPrimary (citable) accession number: P96142
    Secondary accession number(s): Q54A82
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: November 1, 1997
    Last sequence update: June 1, 2001
    Last modified: November 2, 2016
    This is version 107 of the entry and version 2 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure

    Documents

    1. Aminoacyl-tRNA synthetases
      List of aminoacyl-tRNA synthetase entries
    2. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    3. SIMILARITY comments
      Index of protein domains and families

    Similar proteinsi

    Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
    100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
    90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
    50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.