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P41972

- SYI1_STAAU

UniProt

P41972 - SYI1_STAAU

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Protein

Isoleucine--tRNA ligase

Gene

ileS

Organism
Staphylococcus aureus
Status
Reviewed - Annotation score: 4 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).By similarity

Catalytic activityi

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

Cofactori

Binds 1 zinc ion per subunit.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei554 – 5541Aminoacyl-adenylate
Binding sitei598 – 5981ATPBy similarity
Binding sitei632 – 6321tRNA
Binding sitei640 – 6401tRNA
Metal bindingi886 – 8861Zinc
Metal bindingi889 – 8891Zinc
Metal bindingi906 – 9061Zinc
Metal bindingi909 – 9091Zinc

GO - Molecular functioni

  1. aminoacyl-tRNA editing activity Source: InterPro
  2. ATP binding Source: UniProtKB-HAMAP
  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

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
OrganismiStaphylococcus aureus
Taxonomic identifieri1280 [NCBI]
Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesStaphylococcus

Subcellular locationi

GO - Cellular componenti

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

Keywords - Cellular componenti

Cytoplasm

Pathology & Biotechi

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 917917Isoleucine--tRNA ligasePRO_0000098463Add
BLAST

Proteomic databases

PRIDEiP41972.

Interactioni

Subunit structurei

Monomer.1 Publication

Structurei

Secondary structure

1
917
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi4 – 63
Helixi20 – 3314
Helixi36 – 438
Turni44 – 463
Beta strandi58 – 614
Helixi65 – 8218
Turni83 – 853
Beta strandi93 – 953
Helixi99 – 10810
Helixi117 – 14024
Turni141 – 1433
Helixi157 – 17216
Beta strandi176 – 18611
Turni187 – 1904
Helixi195 – 1973
Beta strandi198 – 20912
Beta strandi212 – 2143
Helixi220 – 2223
Beta strandi230 – 2323
Helixi234 – 2363
Helixi237 – 2393
Beta strandi242 – 2454
Turni256 – 2594
Turni265 – 2684
Helixi269 – 2724
Turni273 – 2764
Turni290 – 2923
Helixi301 – 3033
Beta strandi306 – 3127
Beta strandi318 – 3203
Helixi333 – 3364
Turni337 – 3393
Beta strandi340 – 3423
Beta strandi351 – 3533
Beta strandi363 – 3653
Helixi369 – 3724
Helixi375 – 3773
Helixi380 – 3834
Beta strandi388 – 39710
Turni398 – 4003
Beta strandi405 – 41410
Helixi416 – 42813
Beta strandi430 – 4345
Helixi435 – 44713
Beta strandi454 – 4563
Beta strandi458 – 4603
Beta strandi469 – 4713
Helixi477 – 49014
Helixi493 – 4975
Helixi500 – 5034
Beta strandi504 – 5074
Beta strandi511 – 5133
Helixi527 – 5326
Helixi534 – 5374
Turni538 – 5414
Beta strandi547 – 5559
Helixi556 – 5594
Helixi562 – 57413
Beta strandi578 – 5858
Beta strandi591 – 5944
Beta strandi598 – 6014
Helixi606 – 6127
Helixi615 – 6239
Helixi635 – 65723
Helixi664 – 6674
Helixi671 – 6733
Helixi676 – 69722
Helixi701 – 71313
Helixi714 – 7196
Helixi720 – 7289
Helixi736 – 75621
Turni757 – 7593
Helixi761 – 7688
Beta strandi775 – 7784
Helixi779 – 7813
Helixi792 – 81726
Helixi824 – 8263
Beta strandi827 – 8326
Helixi839 – 8424
Helixi843 – 8453
Helixi849 – 8524
Beta strandi855 – 8606
Beta strandi868 – 8714
Beta strandi874 – 8807
Beta strandi882 – 8854
Turni887 – 8893
Beta strandi892 – 8943
Beta strandi897 – 8993
Beta strandi902 – 9054
Helixi907 – 9148

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1FFYX-ray2.20A1-917[»]
1QU2X-ray2.20A1-917[»]
1QU3X-ray2.90A1-917[»]
ProteinModelPortaliP41972.
SMRiP41972. Positions 1-917.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP41972.

Family & Domainsi

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi57 – 6711"HIGH" regionAdd
BLAST
Motifi595 – 5995"KMSKS" region

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).By similarity

Sequence similaritiesi

Family and domain databases

Gene3Di1.10.730.10. 1 hit.
3.40.50.620. 2 hits.
3.90.740.10. 1 hit.
HAMAPiMF_02002. Ile_tRNA_synth_type1.
InterProiIPR001412. aa-tRNA-synth_I_CS.
IPR002300. aa-tRNA-synth_Ia.
IPR002301. Ile-tRNA-ligase.
IPR023585. Ile-tRNA-ligase_type1.
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.
IPR010663. Znf_DNA_glyclase/IsotRNA_synth.
[Graphical view]
PANTHERiPTHR11946:SF9. PTHR11946:SF9. 1 hit.
PfamiPF08264. Anticodon_1. 1 hit.
PF00133. tRNA-synt_1. 1 hit.
PF06827. zf-FPG_IleRS. 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.

P41972-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MDYKETLLMP KTDFPMRGGL PNKEPQIQEK WDAEDQYHKA LEKNKGNETF
60 70 80 90 100
ILHDGPPYAN GNLHMGHALN KILKDFIVRY KTMQGFYAPY VPGWDTHGLP
110 120 130 140 150
IEQALTKKGV DRKKMSTAEF REKCKEFALE QIELQKKDFR RLGVRGDFND
160 170 180 190 200
PYITLKPEYE AAQIRIFGEM ADKGLIYKGK KPVYWSPSSE SSLAEAEIEY
210 220 230 240 250
HDKRSASIYV AFNVKDDKGV VDADAKFIIW TTTPWTIPSN VAITVHPELK
260 270 280 290 300
YGQYNVNGEK YIIAEALSDA VAEALDWDKA SIKLEKEYTG KELEYVVAQH
310 320 330 340 350
PFLDRESLVI NGDHVTTDAG TGCVHTAPGH GEDDYIVGQK YELPVISPID
360 370 380 390 400
DKGVFTEEGG QFEGMFYDKA NKAVTDLLTE KGALLKLDFI THSYPHDWRT
410 420 430 440 450
KKPVIFRATP QWFASISKVR QDILDAIENT NFKVNWGKTR IYNMVRDRGE
460 470 480 490 500
WVISRQRVWG VPLPVFYAEN GEIIMTKETV NHVADLFAEH GSNIWFEREA
510 520 530 540 550
KDLLPEGFTH PGSPNGTFTK ETDIMDVWFD SGSSHRGVLE TRPELSFPAD
560 570 580 590 600
MYLEGSDQYR GWFNSSITTS VATRGVSPYK FLLSHGFVMD GEGKKMSKSL
610 620 630 640 650
GNVIVPDQVV KQKGADIARL WVSSTDYLAD VRISDEILKQ TSDVYRKIRN
660 670 680 690 700
TLRFMLGNIN DFNPDTDSIP ESELLEVDRY LLNRLREFTA STINNYENFD
710 720 730 740 750
YLNIYQEVQN FINVELSNFY LDYGKDILYI EQRDSHIRRS MQTVLYQILV
760 770 780 790 800
DMTKLLAPIL VHTAEEVWSH TPHVKEESVH LADMPKVVEV DQALLDKWRT
810 820 830 840 850
FMNLRDDVNR ALETARNEKV IGKSLEAKVT IASNDKFNAS EFLTSFDALH
860 870 880 890 900
QLFIVSQVKV VDKLDDQATA YEHGDIVIEH ADGEKCERCW NYSEDLGAVD
910
ELTHLCPRCQ QVVKSLV
Length:917
Mass (Da):104,885
Last modified:November 1, 1995 - v1
Checksum:i8A2B644A03A85636
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
X74219 Genomic DNA. Translation: CAA52296.1.
PIRiS40178.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
X74219 Genomic DNA. Translation: CAA52296.1 .
PIRi S40178.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
1FFY X-ray 2.20 A 1-917 [» ]
1QU2 X-ray 2.20 A 1-917 [» ]
1QU3 X-ray 2.90 A 1-917 [» ]
ProteinModelPortali P41972.
SMRi P41972. Positions 1-917.
ModBasei Search...
MobiDBi Search...

Chemistry

ChEMBLi CHEMBL1982.
DrugBanki DB00410. Mupirocin.

Proteomic databases

PRIDEi P41972.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Miscellaneous databases

EvolutionaryTracei P41972.

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_02002. Ile_tRNA_synth_type1.
InterProi IPR001412. aa-tRNA-synth_I_CS.
IPR002300. aa-tRNA-synth_Ia.
IPR002301. Ile-tRNA-ligase.
IPR023585. Ile-tRNA-ligase_type1.
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.
IPR010663. Znf_DNA_glyclase/IsotRNA_synth.
[Graphical view ]
PANTHERi PTHR11946:SF9. PTHR11946:SF9. 1 hit.
Pfami PF08264. Anticodon_1. 1 hit.
PF00133. tRNA-synt_1. 1 hit.
PF06827. zf-FPG_IleRS. 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

  1. "Analysis and toxic overexpression in Escherichia coli of a staphylococcal gene encoding isoleucyl-tRNA synthetase."
    Chalker A.F., Ward J.M., Fosberry A.P., Hodgson J.E.
    Gene 141:103-108(1994) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PARTIAL PROTEIN SEQUENCE.
    Strain: ATCC 9144 / Oxford / NCIB 6571 / NCTC 6571.
  2. "Insights into editing from an Ile-tRNA synthetase structure with tRNAIle and mupirocin."
    Silvian L.F., Wang J., Steitz T.A.
    Science 285:1074-1077(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS) IN COMPLEX WITH METAL IONS; ILE-TRNA AND MUPIROCIN.

Entry informationi

Entry nameiSYI1_STAAU
AccessioniPrimary (citable) accession number: P41972
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1995
Last sequence update: November 1, 1995
Last modified: October 29, 2014
This is version 100 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Direct protein sequencing

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