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P96142 (SYV_THETH) Reviewed, UniProtKB/Swiss-Prot

Last modified April 3, 2013. Version 91. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (3) | Third-party data text xml rdf/xml gff fasta
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to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Valine--tRNA ligase
EC=6.1.1.9
Alternative name(s):
Valyl-tRNA synthetase
Short name=ValRS
Gene names
Name:valS
OrganismThermus thermophilus
Taxonomic identifier274 [NCBI]
Taxonomic lineageBacteria › Deinococcus-Thermus › Deinococci › Thermales › Thermaceae › Thermus

Protein attributes

Sequence length862 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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. HAMAP-Rule MF_02004

Catalytic activity

ATP + L-valine + tRNA(Val) = AMP + diphosphate + L-valyl-tRNA(Val). HAMAP-Rule MF_02004

Cofactor

Binds 2 zinc ions per subunit.

Subunit structure

Monomer.

Subcellular location

Cytoplasm HAMAP-Rule MF_02004.

Domain

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. Ref.3

The C-terminal coiled-coil domain is crucial for aminoacylation activity. Ref.3

Sequence similarities

Belongs to the class-I aminoacyl-tRNA synthetase family. ValS type 1 subfamily.

Biophysicochemical properties

Kinetic parameters:

KM=0.7 µM for tRNA(Val) Ref.3

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 862862Valine--tRNA ligase HAMAP-Rule MF_02004
PRO_0000106240

Regions

Region41 – 5313Interaction with valine in the Val-AMP intermediate HAMAP-Rule MF_02004
Region261 – 27919Interaction with the Thr-AMP intermediate HAMAP-Rule MF_02004
Region487 – 4915Interaction with AMP in the Val-AMP intermediate HAMAP-Rule MF_02004
Region518 – 5214Interaction with AMP in the Val-AMP intermediate HAMAP-Rule MF_02004
Region576 – 58712Interaction with tRNA HAMAP-Rule MF_02004
Region646 – 6516Interaction with tRNA HAMAP-Rule MF_02004
Region815 – 84733Interaction with tRNA HAMAP-Rule MF_02004
Coiled coil802 – 86261 Potential
Motif44 – 5310"HIGH" region HAMAP-Rule MF_02004
Motif528 – 5325"KMSKS" region HAMAP-Rule MF_02004

Sites

Metal binding1761Zinc 1
Metal binding1791Zinc 1
Metal binding3441Zinc 1
Metal binding3471Zinc 1
Metal binding4171Zinc 2
Metal binding4201Zinc 2
Metal binding4381Zinc 2
Metal binding4411Zinc 2
Binding site501Val-AMP intermediate adenyl group
Binding site531Val-AMP intermediate phosphate group
Binding site5311ATP By similarity
Site811Interaction with valine in the Val-AMP intermediate
Site5701Interaction with tRNA

Experimental info

Mutagenesis2161R → A: Decrease in posttransfer editing activity. No change in aminoacylation activity. Ref.4
Mutagenesis2641F → A: Decrease in posttransfer editing activity. No change in aminoacylation activity. Ref.4
Mutagenesis2701K → 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). Ref.4
Mutagenesis2721T → A: Decrease in posttransfer editing activity. No change in aminoacylation activity. Ref.4
Mutagenesis2761D → A: No change in aminoacylation and posttransfer editing activities. Ref.4
Mutagenesis2791D → A: Strong decrease in posttransfer editing activity. No change in aminoacylation activity. Ref.4
Mutagenesis8181R → A: Increase in Km for tRNA(Val), without change in Kcat; when associated with A-843. Ref.3
Mutagenesis8431R → A: Increase in Km for tRNA(Val), without change in Kcat; when associated with A-818. Ref.3

Secondary structure

1 ............................................................................................................................................................. 862
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P96142 [UniParc].

Last modified June 1, 2001. Version 2.
Checksum: 90504DC65780942F

FASTA86298,775
        10         20         30         40         50         60 
MDLPKAYDPK SVEPKWAEKW AKNPFVANPK SGKPPFVIFM PPPNVTGSLH MGHALDNSLQ 

        70         80         90        100        110        120 
DALIRYKRMR GFEAVWLPGT DHAGIATQVV VERLLLKEGK TRHDLGREKF LERVWQWKEE 

       130        140        150        160        170        180 
SGGTILKQLK RLGASADWSR EAFTMDEKRS RAVRYAFSRY YHEGLAYRAP RLVNWCPRCE 

       190        200        210        220        230        240 
TTLSDLEVET EPTPGKLYTL RYEVEGGGFI EIATVRPETV FADQAIAVHP EDERYRHLLG 

       250        260        270        280        290        300 
KRARIPLTEV WIPILADPAV EKDFGTGALK VTPAHDPLDY EIGERHGLKP VSVINLEGRM 

       310        320        330        340        350        360 
EGERVPEALR GLDRFEARRK AVELFREAGH LVKEEDYTIA LATCSRCGTP IEYAIFPQWW 

       370        380        390        400        410        420 
LRMRPLAEEV LKGLRRGDIA FVPERWKKVN MDWLENVKDW NISRQLWWGH QIPAWYCEDC 

       430        440        450        460        470        480 
QAVNVPRPER YLEDPTSCEA CGSPRLKRDE DVFDTWFSSA LWPLSTLGWP EETEDLKAFY 

       490        500        510        520        530        540 
PGDVLVTGYD ILFLWVSRME VSGYHFMGER PFKTVLLHGL VLDEKGQKMS KSKGNVIDPL 

       550        560        570        580        590        600 
EMVERYGADA LRFALIYLAT GGQDIRLDLR WLEMARNFAN KLYNAARFVL LSREGFQAKE 

       610        620        630        640        650        660 
DTPTLADRFM RSRLSRGVEE ITALYEALDL AQAAREVYEL VWSEFCDWYL EAAKPALKAG 

       670        680        690        700        710        720 
NAHTLRTLEE VLAVLLKLLH PMMPFLTSEL YQALTGKEEL ALEAWPEPGG RDEEAERAFE 

       730        740        750        760        770        780 
ALKQAVTAVR ALKAEAGLPP AQEVRVYLEG ETAPVEENLE VFRFLSRADL LPERPAKALV 

       790        800        810        820        830        840 
KAMPRVTARM PLEGLLDVEE WRRRQEKRLK ELLALAERSQ RKLASPGFRE KAPKEVVEAE 

       850        860 
EARLKENLEQ AERIREALSQ IG

« Hide

References

[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.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ		AB080140 Genomic DNA. Translation: BAB85225.1.

3D structure databases

PDBe
RCSB PDB
PDBj
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[»]
ProteinModelPortalP96142.
SMRP96142. Positions 1-862.
ModBaseSearch...

Protein-protein interaction databases

STRING262724.TTC0805.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Family and domain databases

Gene3D1.10.287.380. 1 hit.
3.40.50.620. 2 hits.
3.90.740.10. 1 hit.
HAMAPMF_02004. Val_tRNA_synth_type1.
InterProIPR001412. aa-tRNA-synth_I_CS.
IPR002300. aa-tRNA-synth_Ia.
IPR014729. Rossmann-like_a/b/a_fold.
IPR010978. tRNA-bd_arm.
IPR009080. tRNAsynth_1a_anticodon-bd.
IPR013155. V/L/I-tRNA-synth_anticodon-bd.
IPR019499. Val-tRNA_synth_tRNA-bd.
IPR009008. Val/Leu/Ile-tRNA-synth_edit.
IPR002303. Valyl-tRNA_ligase.
[Graphical view]
PANTHERPTHR11946:SF5. PTHR11946:SF5. 1 hit.
PfamPF08264. Anticodon_1. 1 hit.
PF00133. tRNA-synt_1. 1 hit.
PF10458. Val_tRNA-synt_C. 1 hit.
[Graphical view]
PRINTSPR00986. TRNASYNTHVAL.
SUPFAMSSF46589. tRNA_binding_arm. 1 hit.
SSF47323. tRNAsyn_1a_bind. 1 hit.
SSF50677. ValRS_IleRS_edit. 1 hit.
TIGRFAMsTIGR00422. valS. 1 hit.
PROSITEPS00178. AA_TRNA_LIGASE_I. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceP96142.

Entry information

Entry nameSYV_THETH
AccessionPrimary (citable) accession number: P96142
Secondary accession number(s): Q54A82
Entry history
Integrated into UniProtKB/Swiss-Prot: November 1, 1997
Last sequence update: June 1, 2001
Last modified: April 3, 2013
This is version 91 of the entry and version 2 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

Aminoacyl-tRNA synthetases

List of aminoacyl-tRNA synthetase entries

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families

to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents