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P56690

- SYI_THET8

UniProt

P56690 - SYI_THET8

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Protein
Isoleucine--tRNA ligase
Gene
ileS, TTHA1067
Organism
Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Status
Reviewed - Annotation score: 5 out of 5 - Experimental evidence at protein leveli

Functioni

Catalyzes the attachment of isoleucine to tRNA(Ile). As IleRS can inadvertently accommodate and process structurally similar amino acids such as valine, to avoid such errors it has two additional distinct tRNA(Ile)-dependent editing activities. One activity is designated as 'pretransfer' editing and involves the hydrolysis of activated Val-AMP. The other activity is designated 'posttransfer' editing and involves deacylation of mischarged Val-tRNA(Ile) By similarity.UniRule annotation

Catalytic activityi

ATP + L-isoleucine + tRNA(Ile) = AMP + diphosphate + L-isoleucyl-tRNA(Ile).UniRule annotation

Cofactori

Binds 2 zinc ions per subunit.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei57 – 571Aminoacyl-adenylate
Metal bindingi181 – 1811Zinc 1
Metal bindingi184 – 1841Zinc 1
Binding sitei319 – 3191Valine
Binding sitei328 – 3281Valine
Metal bindingi389 – 3891Zinc 1
Metal bindingi392 – 3921Zinc 1
Metal bindingi461 – 4611Zinc 2
Metal bindingi464 – 4641Zinc 2
Metal bindingi502 – 5021Zinc 2
Metal bindingi504 – 5041Zinc 2
Binding sitei550 – 5501Aminoacyl-adenylate
Binding sitei553 – 5531Aminoacyl-adenylate
Binding sitei554 – 5541Aminoacyl-adenylate
Binding sitei581 – 5811Aminoacyl-adenylate
Binding sitei594 – 5941ATP By similarity

GO - Molecular functioni

  1. ATP binding Source: UniProtKB-HAMAP
  2. aminoacyl-tRNA editing activity Source: InterPro
  3. isoleucine-tRNA ligase activity Source: UniProtKB-HAMAP
  4. zinc ion binding Source: UniProtKB-HAMAP

GO - Biological processi

  1. isoleucyl-tRNA aminoacylation Source: UniProtKB-HAMAP
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

BioCyciTTHE300852:GH8R-1099-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Isoleucine--tRNA ligase (EC:6.1.1.5)
Alternative name(s):
Isoleucyl-tRNA synthetase
Short name:
IleRS
Gene namesi
Name:ileS
Ordered Locus Names:TTHA1067
OrganismiThermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Taxonomic identifieri300852 [NCBI]
Taxonomic lineageiBacteriaDeinococcus-ThermusDeinococciThermalesThermaceaeThermus
ProteomesiUP000000532: Chromosome

Subcellular locationi

Cytoplasm UniRule annotation

GO - Cellular componenti

  1. cytoplasm Source: UniProtKB-SubCell
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi228 – 2281T → A: Has some defects in posttransfer editing activity. 1 Publication
Mutagenesisi229 – 2291T → A: Has some defects in posttransfer editing activity. 1 Publication
Mutagenesisi230 – 2301T → A: No change in posttransfer editing activity. 1 Publication
Mutagenesisi233 – 2331T → A: No change in posttransfer editing activity. 1 Publication
Mutagenesisi328 – 3281D → A: Has some defects in posttransfer editing activity. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 10431043Isoleucine--tRNA ligaseUniRule annotation
PRO_0000098567Add
BLAST

Interactioni

Subunit structurei

Monomer.

Protein-protein interaction databases

STRINGi300852.TTHA1067.

Structurei

Secondary structure

Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi10 – 2314
Helixi26 – 338
Turni34 – 363
Helixi57 – 7317
Beta strandi81 – 844
Helixi88 – 9811
Helixi104 – 1107
Helixi112 – 12211
Turni123 – 1264
Helixi127 – 1304
Helixi133 – 1364
Beta strandi142 – 1487
Helixi152 – 16716
Beta strandi171 – 1744
Beta strandi177 – 1815
Turni182 – 1854
Helixi190 – 1956
Beta strandi204 – 2129
Helixi214 – 2174
Beta strandi220 – 22910
Helixi231 – 2366
Beta strandi239 – 2424
Beta strandi246 – 2538
Beta strandi256 – 2616
Helixi262 – 2698
Beta strandi275 – 2806
Helixi281 – 2844
Beta strandi302 – 3054
Beta strandi311 – 3144
Beta strandi318 – 3203
Helixi322 – 3243
Helixi326 – 33510
Beta strandi347 – 3493
Helixi352 – 3543
Helixi359 – 37214
Beta strandi376 – 3805
Beta strandi390 – 3923
Beta strandi397 – 4004
Beta strandi403 – 4064
Helixi408 – 4114
Helixi412 – 42110
Beta strandi422 – 4265
Helixi427 – 4293
Turni430 – 4345
Helixi435 – 4395
Beta strandi447 – 4493
Beta strandi451 – 4533
Beta strandi458 – 4658
Helixi473 – 4797
Beta strandi480 – 4823
Helixi492 – 4954
Beta strandi499 – 5013
Beta strandi505 – 5106
Helixi517 – 52711
Turni528 – 5336
Helixi536 – 5427
Beta strandi543 – 5519
Helixi552 – 5565
Helixi558 – 57013
Beta strandi574 – 5818
Beta strandi587 – 5893
Turni594 – 5974
Helixi602 – 6065
Turni607 – 6093
Helixi611 – 62111
Beta strandi624 – 6263
Helixi632 – 64110
Helixi643 – 66018
Helixi670 – 6723
Helixi675 – 69622
Helixi700 – 71415
Turni717 – 7193
Helixi720 – 7289
Beta strandi733 – 7353
Helixi738 – 75417
Turni755 – 7573
Helixi761 – 7699
Turni770 – 7734
Turni774 – 7763
Helixi781 – 7833
Turni791 – 7933
Helixi796 – 81217

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1ILEX-ray2.50A1-821[»]
1JZQX-ray3.00A1-821[»]
1JZSX-ray2.50A1-821[»]
1UDZX-ray1.80A/B201-381[»]
1UE0X-ray2.00A/B201-381[»]
1WK8X-ray1.70A/B196-388[»]
1WNYX-ray1.60A/B201-385[»]
1WNZX-ray1.70A201-385[»]
ProteinModelPortaliP56690.
SMRiP56690. Positions 1-821.

Miscellaneous databases

EvolutionaryTraceiP56690.

Family & Domainsi

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi47 – 5711"HIGH" regionUniRule annotation
Add
BLAST
Motifi591 – 5955"KMSKS" regionUniRule annotation

Domaini

IleRS has two distinct active sites: one for aminoacylation and one for editing. The misactivated valine is translocated from the active site to the editing site, which sterically excludes the correctly activated isoleucine. The single editing site contains two valyl binding pockets, one specific for each substrate (Val-AMP or Val-tRNA(Ile)) By similarity.UniRule annotation

Sequence similaritiesi

Phylogenomic databases

eggNOGiCOG0060.
HOGENOMiHOG000246403.
KOiK01870.
OMAiRVEHMVE.
OrthoDBiEOG644ZM1.
PhylomeDBiP56690.

Family and domain databases

Gene3Di1.10.730.10. 1 hit.
3.40.50.620. 2 hits.
3.90.740.10. 1 hit.
HAMAPiMF_02003. Ile_tRNA_synth_type2.
InterProiIPR001412. aa-tRNA-synth_I_CS.
IPR002300. aa-tRNA-synth_Ia.
IPR002301. Ile-tRNA-ligase.
IPR023586. Ile-tRNA-ligase_type2.
IPR014729. Rossmann-like_a/b/a_fold.
IPR009080. tRNAsynth_1a_anticodon-bd.
IPR013155. V/L/I-tRNA-synth_anticodon-bd.
IPR009008. Val/Leu/Ile-tRNA-synth_edit.
[Graphical view]
PfamiPF08264. Anticodon_1. 1 hit.
PF00133. tRNA-synt_1. 1 hit.
[Graphical view]
PRINTSiPR00984. TRNASYNTHILE.
SUPFAMiSSF47323. SSF47323. 1 hit.
SSF50677. SSF50677. 1 hit.
TIGRFAMsiTIGR00392. ileS. 1 hit.
PROSITEiPS00178. AA_TRNA_LIGASE_I. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P56690-1 [UniParc]FASTAAdd to Basket

« Hide

MFKEVGEPNF PKLEEEVLAF WKREKIFQKS VENRKGGPRY TVYEGPPTAN     50
GLPHVGHAQA RSYKDLFPRY KTMRGYYAPR RAGWDTHGLP VELEVEKKLG 100
LKSKREIEAY GIERFNQACR ESVFTYEKEW EAFTERIAYW VDLENAYATL 150
EPTYIESIWW SLKNLFDRGL LYRDHKVVPY CPRCGTPLSS HEVALGYKEI 200
QDPSVYVRFP LKEPKKLGLE KASLLIWTTT PWTLPGNVAA AVHPEYTYAA 250
FQVGDEALIL EEGLGRKLLG EGTPVLKTFP GKALEGLPYT PPYPQALEKG 300
YFVVLADYVS QEDGTGIVHQ APAFGAEDLE TARVYGLPLL KTVDEEGKLL 350
VEPFKGLYFR EANRAILRDL RGRGLLFKEE SYLHSYPHCW RCSTPLMYYA 400
TESWFIKNTL FKDELIRKNQ EIHWVPPHIK EGRYGEWLKN LVDWALSRNR 450
YWGTPLPIWV CQACGKEEAI GSFQELKARA TKPLPEPFDP HRPYVDQVEL 500
ACACGGTMRR VPYVIDVWYD SGAMPFASLH YPFEHEEVFR ESFPADFIAE 550
GIDQTRGWFN SLHQLGVMLF GSIAFKNVIC HGLILDEKGQ KMSKSKGNVV 600
DPWDIIREFG ADALRWYIYV SAPPEADRRF GPNLVRETVR DYFLTLWNVY 650
SFFVTYANLD RPDLKNPPPP EKRPEMDRWL LARMQDLIQR VTEALEAYDP 700
TTSARALRDF VVEDLSQWYV RRNRRRFWKN EDALDREAAY ATLYEALVLV 750
ATLAAPFTPF LAEVLWQNLV RSVRPEAKES VHLADWPEAD PALADEALVA 800
QMRAVLKVVD LARAARAKSG VKTRTPLPLL LVTAPTALER EGLKRFAHEI 850
AEELNVKEVR VLEPGEEILS YRVLPNLKLL GRKYGKLVPK IREALQRERE 900
RAAALALKGE AIPLEVEGEA LTLLPEEVLL EAEAPKGYQA LEKDGYVAAL 950
KVEVTEALRM EGLARDLIRL LQQARKDMGL KVSDRIRVGY EAEGPYLEAL 1000
KRHGPWIAEE VLATAFGEGL FGGFEARVED EEGKAVFHLA RAE 1043
Length:1,043
Mass (Da):119,247
Last modified:March 29, 2005 - v2
Checksum:i0F8010BBE8F83A30
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
AP008226 Genomic DNA. Translation: BAD70890.1.
RefSeqiWP_011228416.1. NC_006461.1.
YP_144333.1. NC_006461.1.

Genome annotation databases

EnsemblBacteriaiBAD70890; BAD70890; BAD70890.
GeneIDi3168241.
KEGGittj:TTHA1067.
PATRICi23957094. VBITheThe93045_1047.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
AP008226 Genomic DNA. Translation: BAD70890.1 .
RefSeqi WP_011228416.1. NC_006461.1.
YP_144333.1. NC_006461.1.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
1ILE X-ray 2.50 A 1-821 [» ]
1JZQ X-ray 3.00 A 1-821 [» ]
1JZS X-ray 2.50 A 1-821 [» ]
1UDZ X-ray 1.80 A/B 201-381 [» ]
1UE0 X-ray 2.00 A/B 201-381 [» ]
1WK8 X-ray 1.70 A/B 196-388 [» ]
1WNY X-ray 1.60 A/B 201-385 [» ]
1WNZ X-ray 1.70 A 201-385 [» ]
ProteinModelPortali P56690.
SMRi P56690. Positions 1-821.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

STRINGi 300852.TTHA1067.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai BAD70890 ; BAD70890 ; BAD70890 .
GeneIDi 3168241.
KEGGi ttj:TTHA1067.
PATRICi 23957094. VBITheThe93045_1047.

Phylogenomic databases

eggNOGi COG0060.
HOGENOMi HOG000246403.
KOi K01870.
OMAi RVEHMVE.
OrthoDBi EOG644ZM1.
PhylomeDBi P56690.

Enzyme and pathway databases

BioCyci TTHE300852:GH8R-1099-MONOMER.

Miscellaneous databases

EvolutionaryTracei P56690.

Family and domain databases

Gene3Di 1.10.730.10. 1 hit.
3.40.50.620. 2 hits.
3.90.740.10. 1 hit.
HAMAPi MF_02003. Ile_tRNA_synth_type2.
InterProi IPR001412. aa-tRNA-synth_I_CS.
IPR002300. aa-tRNA-synth_Ia.
IPR002301. Ile-tRNA-ligase.
IPR023586. Ile-tRNA-ligase_type2.
IPR014729. Rossmann-like_a/b/a_fold.
IPR009080. tRNAsynth_1a_anticodon-bd.
IPR013155. V/L/I-tRNA-synth_anticodon-bd.
IPR009008. Val/Leu/Ile-tRNA-synth_edit.
[Graphical view ]
Pfami PF08264. Anticodon_1. 1 hit.
PF00133. tRNA-synt_1. 1 hit.
[Graphical view ]
PRINTSi PR00984. TRNASYNTHILE.
SUPFAMi SSF47323. SSF47323. 1 hit.
SSF50677. SSF50677. 1 hit.
TIGRFAMsi TIGR00392. ileS. 1 hit.
PROSITEi PS00178. AA_TRNA_LIGASE_I. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  1. "Complete genome sequence of Thermus thermophilus HB8."
    Masui R., Kurokawa K., Nakagawa N., Tokunaga F., Koyama Y., Shibata T., Oshima T., Yokoyama S., Yasunaga T., Kuramitsu S.
    Submitted (NOV-2004) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: HB8 / ATCC 27634 / DSM 579.
  2. "Enzyme structure with two catalytic sites for double-sieve selection of substrate."
    Nureki O., Vassylyev D.G., Tateno M., Shimada A., Nakama T., Fukai S., Konno M., Hendrickson T.L., Schimmel P., Yokoyama S.
    Science 280:578-582(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS) OF 1-821 IN COMPLEX WITH ZINC IONS.
  3. "Structural basis for the recognition of isoleucyl-adenylate and an antibiotic, mupirocin, by isoleucyl-tRNA synthetase."
    Nakama T., Nureki O., Yokoyama S.
    J. Biol. Chem. 276:47387-47393(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS) OF 1-821 IN COMPLEX WITH ZINC IONS; ILE-ADENYLATE AND MUPIROCIN.
  4. "Crystal structures of the CP1 domain from Thermus thermophilus isoleucyl-tRNA synthetase and its complex with L-valine."
    Fukunaga R., Fukai S., Ishitani R., Nureki O., Yokoyama S.
    J. Biol. Chem. 279:8396-8402(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS) OF APOENZYME AND IN COMPLEX WITH VAL, MUTAGENESIS OF THR-228; THR-229; THR-230; THR-233 AND ASP-328.

Entry informationi

Entry nameiSYI_THET8
AccessioniPrimary (citable) accession number: P56690
Secondary accession number(s): Q5SJE7
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 15, 1999
Last sequence update: March 29, 2005
Last modified: September 3, 2014
This is version 102 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Miscellaneous

The ATP consumption with regard to L-valine is nonproductive and is solely for substrate selection, which demonstrates the high cost of accuracy.

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

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

External Data

Dasty 3

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