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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

Zn2+Note: 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 – 63Combined sources
Helixi20 – 3314Combined sources
Helixi36 – 438Combined sources
Turni44 – 463Combined sources
Beta strandi58 – 614Combined sources
Helixi65 – 8218Combined sources
Turni83 – 853Combined sources
Beta strandi93 – 953Combined sources
Helixi99 – 10810Combined sources
Helixi117 – 14024Combined sources
Turni141 – 1433Combined sources
Helixi157 – 17216Combined sources
Beta strandi176 – 18611Combined sources
Turni187 – 1904Combined sources
Helixi195 – 1973Combined sources
Beta strandi198 – 20912Combined sources
Beta strandi212 – 2143Combined sources
Helixi220 – 2223Combined sources
Beta strandi230 – 2323Combined sources
Helixi234 – 2363Combined sources
Helixi237 – 2393Combined sources
Beta strandi242 – 2454Combined sources
Turni256 – 2594Combined sources
Turni265 – 2684Combined sources
Helixi269 – 2724Combined sources
Turni273 – 2764Combined sources
Turni290 – 2923Combined sources
Helixi301 – 3033Combined sources
Beta strandi306 – 3127Combined sources
Beta strandi318 – 3203Combined sources
Helixi333 – 3364Combined sources
Turni337 – 3393Combined sources
Beta strandi340 – 3423Combined sources
Beta strandi351 – 3533Combined sources
Beta strandi363 – 3653Combined sources
Helixi369 – 3724Combined sources
Helixi375 – 3773Combined sources
Helixi380 – 3834Combined sources
Beta strandi388 – 39710Combined sources
Turni398 – 4003Combined sources
Beta strandi405 – 41410Combined sources
Helixi416 – 42813Combined sources
Beta strandi430 – 4345Combined sources
Helixi435 – 44713Combined sources
Beta strandi454 – 4563Combined sources
Beta strandi458 – 4603Combined sources
Beta strandi469 – 4713Combined sources
Helixi477 – 49014Combined sources
Helixi493 – 4975Combined sources
Helixi500 – 5034Combined sources
Beta strandi504 – 5074Combined sources
Beta strandi511 – 5133Combined sources
Helixi527 – 5326Combined sources
Helixi534 – 5374Combined sources
Turni538 – 5414Combined sources
Beta strandi547 – 5559Combined sources
Helixi556 – 5594Combined sources
Helixi562 – 57413Combined sources
Beta strandi578 – 5858Combined sources
Beta strandi591 – 5944Combined sources
Beta strandi598 – 6014Combined sources
Helixi606 – 6127Combined sources
Helixi615 – 6239Combined sources
Helixi635 – 65723Combined sources
Helixi664 – 6674Combined sources
Helixi671 – 6733Combined sources
Helixi676 – 69722Combined sources
Helixi701 – 71313Combined sources
Helixi714 – 7196Combined sources
Helixi720 – 7289Combined sources
Helixi736 – 75621Combined sources
Turni757 – 7593Combined sources
Helixi761 – 7688Combined sources
Beta strandi775 – 7784Combined sources
Helixi779 – 7813Combined sources
Helixi792 – 81726Combined sources
Helixi824 – 8263Combined sources
Beta strandi827 – 8326Combined sources
Helixi839 – 8424Combined sources
Helixi843 – 8453Combined sources
Helixi849 – 8524Combined sources
Beta strandi855 – 8606Combined sources
Beta strandi868 – 8714Combined sources
Beta strandi874 – 8807Combined sources
Beta strandi882 – 8854Combined sources
Turni887 – 8893Combined sources
Beta strandi892 – 8943Combined sources
Beta strandi897 – 8993Combined sources
Beta strandi902 – 9054Combined sources
Helixi907 – 9148Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
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:
EMBLi
GenBanki
DDBJi
Links Updated
X74219 Genomic DNA. Translation: CAA52296.1.
PIRiS40178.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X74219 Genomic DNA. Translation: CAA52296.1 .
PIRi S40178.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
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: November 26, 2014
This is version 101 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