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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)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei50 – 501Val-AMP intermediate adenyl group
    Binding sitei53 – 531Val-AMP intermediate phosphate group
    Metal bindingi176 – 1761Zinc 1
    Metal bindingi179 – 1791Zinc 1
    Metal bindingi344 – 3441Zinc 1
    Metal bindingi347 – 3471Zinc 1
    Metal bindingi417 – 4171Zinc 2
    Metal bindingi420 – 4201Zinc 2
    Metal bindingi438 – 4381Zinc 2
    Metal bindingi441 – 4411Zinc 2
    Binding sitei531 – 5311ATPBy similarity

    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)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi216 – 2161R → A: Decrease in posttransfer editing activity. No change in aminoacylation activity. 1 Publication
    Mutagenesisi264 – 2641F → A: Decrease in posttransfer editing activity. No change in aminoacylation activity. 1 Publication
    Mutagenesisi270 – 2701K → 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 Publication
    Mutagenesisi272 – 2721T → A: Decrease in posttransfer editing activity. No change in aminoacylation activity. 1 Publication
    Mutagenesisi276 – 2761D → A: No change in aminoacylation and posttransfer editing activities. 1 Publication
    Mutagenesisi279 – 2791D → A: Strong decrease in posttransfer editing activity. No change in aminoacylation activity. 1 Publication
    Mutagenesisi818 – 8181R → A: Increase in Km for tRNA(Val), without change in Kcat; when associated with A-843. 1 Publication
    Mutagenesisi843 – 8431R → A: Increase in Km for tRNA(Val), without change in Kcat; when associated with A-818. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 862862Valine--tRNA ligasePRO_0000106240Add
    BLAST

    Interactioni

    Subunit structurei

    Monomer.3 Publications

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sitei81 – 811Interaction with valine in the Val-AMP intermediate
    Sitei570 – 5701Interaction with tRNA

    Protein-protein interaction databases

    STRINGi262724.TTC0805.

    Structurei

    Secondary structure

    1
    862
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi9 – 113Combined sources
    Helixi13 – 2210Combined sources
    Beta strandi35 – 395Combined sources
    Beta strandi44 – 474Combined sources
    Helixi51 – 6818Combined sources
    Turni69 – 713Combined sources
    Beta strandi72 – 776Combined sources
    Beta strandi79 – 813Combined sources
    Helixi85 – 928Combined sources
    Turni93 – 997Combined sources
    Helixi102 – 1043Combined sources
    Turni106 – 1083Combined sources
    Helixi109 – 13123Combined sources
    Helixi138 – 1403Combined sources
    Helixi147 – 16115Combined sources
    Beta strandi164 – 1696Combined sources
    Beta strandi172 – 1765Combined sources
    Turni177 – 1804Combined sources
    Beta strandi181 – 1833Combined sources
    Helixi185 – 1873Combined sources
    Beta strandi188 – 1903Combined sources
    Beta strandi196 – 2049Combined sources
    Beta strandi205 – 2073Combined sources
    Beta strandi209 – 2157Combined sources
    Helixi217 – 2226Combined sources
    Beta strandi225 – 2284Combined sources
    Turni233 – 2353Combined sources
    Helixi236 – 2383Combined sources
    Beta strandi242 – 2443Combined sources
    Beta strandi251 – 2566Combined sources
    Beta strandi267 – 2715Combined sources
    Turni273 – 2753Combined sources
    Helixi277 – 28610Combined sources
    Beta strandi293 – 2953Combined sources
    Beta strandi298 – 3003Combined sources
    Beta strandi302 – 3054Combined sources
    Helixi307 – 3093Combined sources
    Helixi314 – 32714Combined sources
    Beta strandi331 – 3366Combined sources
    Beta strandi342 – 3443Combined sources
    Turni345 – 3473Combined sources
    Beta strandi353 – 3553Combined sources
    Beta strandi358 – 3614Combined sources
    Helixi363 – 37614Combined sources
    Beta strandi380 – 3845Combined sources
    Helixi386 – 39510Combined sources
    Beta strandi407 – 4093Combined sources
    Beta strandi415 – 4173Combined sources
    Turni418 – 4203Combined sources
    Helixi428 – 4303Combined sources
    Turni439 – 4413Combined sources
    Beta strandi446 – 4483Combined sources
    Helixi455 – 4595Combined sources
    Helixi465 – 4673Combined sources
    Turni468 – 4703Combined sources
    Helixi474 – 4785Combined sources
    Beta strandi481 – 4833Combined sources
    Beta strandi485 – 4884Combined sources
    Helixi489 – 4913Combined sources
    Turni492 – 4954Combined sources
    Helixi496 – 50611Combined sources
    Beta strandi507 – 5093Combined sources
    Beta strandi511 – 5188Combined sources
    Beta strandi526 – 5283Combined sources
    Turni531 – 5344Combined sources
    Helixi539 – 5468Combined sources
    Helixi548 – 55811Combined sources
    Helixi569 – 59224Combined sources
    Beta strandi593 – 5953Combined sources
    Helixi605 – 62521Combined sources
    Turni626 – 6283Combined sources
    Helixi630 – 64415Combined sources
    Turni645 – 6484Combined sources
    Helixi649 – 65810Combined sources
    Helixi662 – 67918Combined sources
    Turni680 – 6823Combined sources
    Helixi684 – 69512Combined sources
    Helixi700 – 7023Combined sources
    Helixi713 – 73624Combined sources
    Beta strandi744 – 7518Combined sources
    Helixi753 – 7575Combined sources
    Helixi759 – 7668Combined sources
    Beta strandi768 – 7703Combined sources
    Beta strandi776 – 7827Combined sources
    Beta strandi784 – 7918Combined sources
    Helixi798 – 82326Combined sources
    Turni826 – 8283Combined sources
    Beta strandi829 – 8324Combined sources
    Helixi836 – 86025Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    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. Positions 1-862.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP96142.

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni41 – 5313Interaction with valine in the Val-AMP intermediateAdd
    BLAST
    Regioni261 – 27919Interaction with the Thr-AMP intermediateAdd
    BLAST
    Regioni487 – 4915Interaction with AMP in the Val-AMP intermediate
    Regioni518 – 5214Interaction with AMP in the Val-AMP intermediate
    Regioni576 – 58712Interaction with tRNAAdd
    BLAST
    Regioni646 – 6516Interaction with tRNA
    Regioni815 – 84733Interaction with tRNAAdd
    BLAST

    Coiled coil

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Coiled coili802 – 86261Sequence analysisAdd
    BLAST

    Motif

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Motifi44 – 5310"HIGH" region
    Motifi528 – 5325"KMSKS" region

    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

    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.
    InterProiIPR001412. aa-tRNA-synth_I_CS.
    IPR002300. aa-tRNA-synth_Ia.
    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
    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. Positions 1-862.
    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

    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.
    InterProiIPR001412. aa-tRNA-synth_I_CS.
    IPR002300. aa-tRNA-synth_Ia.
    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...

    Publicationsi

    1. Fukai S., Nureki O., Sekine S., Shimada A., Vassylyev D.G., Yokoyama S.
      Submitted (FEB-2002) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    2. "Structural basis for double-sieve discrimination of L-valine from L-isoleucine and L-threonine by the complex of tRNA(Val) and valyl-tRNA synthetase."
      Fukai S., Nureki O., Sekine S., Shimada A., Tao J., Vassylyev D.G., Yokoyama S.
      Cell 103:793-803(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.9 ANGSTROMS) IN COMPLEX WITH TRNA(VAL) AND VAL-AMP ANALOG.
    3. "Mechanism of molecular interactions for tRNA(Val) recognition by valyl-tRNA synthetase."
      Fukai S., Nureki O., Sekine S., Shimada A., Vassylyev D.G., Yokoyama S.
      RNA 9:100-111(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.9 ANGSTROMS) IN COMPLEX WITH TRNA(VAL) AND VAL-AMP ANALOG, INTERACTION OF COILED-COIL DOMAIN WITH TRNA, KINETIC PARAMETERS, MUTAGENESIS OF ARG-818 AND ARG-843.
    4. "Structural basis for non-cognate amino acid discrimination by the valyl-tRNA synthetase editing domain."
      Fukunaga R., Yokoyama S.
      J. Biol. Chem. 280:29937-29945(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.7 ANGSTROMS) OF 195-337 IN COMPLEX WITH THR-AMP ANALOG, MUTAGENESIS OF ARG-216; PHE-264; LYS-270; THR-272; ASP-276 AND ASP-279.

    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: July 6, 2016
    This is version 104 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.