SYI1_STAAU
ID SYI1_STAAU Reviewed; 917 AA.
AC P41972;
DT 01-NOV-1995, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1995, sequence version 1.
DT 03-AUG-2022, entry version 142.
DE RecName: Full=Isoleucine--tRNA ligase;
DE EC=6.1.1.5;
DE AltName: Full=Isoleucyl-tRNA synthetase;
DE Short=IleRS;
GN Name=ileS;
OS Staphylococcus aureus.
OC Bacteria; Firmicutes; Bacilli; Bacillales; Staphylococcaceae;
OC Staphylococcus.
OX NCBI_TaxID=1280;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND PARTIAL PROTEIN SEQUENCE.
RC STRAIN=ATCC 9144 / DSM 683 / NCIB 6571 / NCTC 6571 / NRRL B-314 / Oxford;
RX PubMed=8163160; DOI=10.1016/0378-1119(94)90135-x;
RA Chalker A.F., Ward J.M., Fosberry A.P., Hodgson J.E.;
RT "Analysis and toxic overexpression in Escherichia coli of a staphylococcal
RT gene encoding isoleucyl-tRNA synthetase.";
RL Gene 141:103-108(1994).
RN [2] {ECO:0007744|PDB:1FFY, ECO:0007744|PDB:1QU2, ECO:0007744|PDB:1QU3}
RP X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS) IN COMPLEX WITH ZINC IONS; TRNA(ILE)
RP AND MUPIROCIN, AND COFACTOR.
RX PubMed=10446055; DOI=10.1126/science.285.5430.1074;
RA Silvian L.F., Wang J., Steitz T.A.;
RT "Insights into editing from an Ile-tRNA synthetase structure with tRNAIle
RT and mupirocin.";
RL Science 285:1074-1077(1999).
CC -!- FUNCTION: Catalyzes the attachment of isoleucine to tRNA(Ile). As IleRS
CC can inadvertently accommodate and process structurally similar amino
CC acids such as valine, to avoid such errors it has two additional
CC distinct tRNA(Ile)-dependent editing activities. One activity is
CC designated as 'pretransfer' editing and involves the hydrolysis of
CC activated Val-AMP. The other activity is designated 'posttransfer'
CC editing and involves deacylation of mischarged Val-tRNA(Ile) (By
CC similarity). {ECO:0000250}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=ATP + L-isoleucine + tRNA(Ile) = AMP + diphosphate + L-
CC isoleucyl-tRNA(Ile); Xref=Rhea:RHEA:11060, Rhea:RHEA-COMP:9666,
CC Rhea:RHEA-COMP:9695, ChEBI:CHEBI:30616, ChEBI:CHEBI:33019,
CC ChEBI:CHEBI:58045, ChEBI:CHEBI:78442, ChEBI:CHEBI:78528,
CC ChEBI:CHEBI:456215; EC=6.1.1.5;
CC -!- COFACTOR:
CC Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
CC Evidence={ECO:0000305|PubMed:10446055};
CC Note=Binds 1 zinc ion per subunit. {ECO:0000269|PubMed:10446055};
CC -!- SUBUNIT: Monomer. {ECO:0000269|PubMed:10446055}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm.
CC -!- DOMAIN: IleRS has two distinct active sites: one for aminoacylation and
CC one for editing. The misactivated valine is translocated from the
CC active site to the editing site, which sterically excludes the
CC correctly activated isoleucine. The single editing site contains two
CC valyl binding pockets, one specific for each substrate (Val-AMP or Val-
CC tRNA(Ile)) (By similarity). {ECO:0000250}.
CC -!- SIMILARITY: Belongs to the class-I aminoacyl-tRNA synthetase family.
CC IleS type 1 subfamily. {ECO:0000305}.
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DR EMBL; X74219; CAA52296.1; -; Genomic_DNA.
DR PIR; S40178; S40178.
DR RefSeq; WP_000384706.1; NZ_WKIW01000024.1.
DR PDB; 1FFY; X-ray; 2.20 A; A=1-917.
DR PDB; 1QU2; X-ray; 2.20 A; A=1-917.
DR PDB; 1QU3; X-ray; 2.90 A; A=1-917.
DR PDBsum; 1FFY; -.
DR PDBsum; 1QU2; -.
DR PDBsum; 1QU3; -.
DR AlphaFoldDB; P41972; -.
DR SMR; P41972; -.
DR BindingDB; P41972; -.
DR ChEMBL; CHEMBL1982; -.
DR DrugBank; DB00410; Mupirocin.
DR DrugCentral; P41972; -.
DR BRENDA; 6.1.1.5; 3352.
DR SABIO-RK; P41972; -.
DR EvolutionaryTrace; P41972; -.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0002161; F:aminoacyl-tRNA editing activity; IEA:InterPro.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-UniRule.
DR GO; GO:0004822; F:isoleucine-tRNA ligase activity; IEA:UniProtKB-UniRule.
DR GO; GO:0000049; F:tRNA binding; IEA:InterPro.
DR GO; GO:0008270; F:zinc ion binding; IEA:UniProtKB-UniRule.
DR GO; GO:0006428; P:isoleucyl-tRNA aminoacylation; IEA:UniProtKB-UniRule.
DR CDD; cd07960; Anticodon_Ia_Ile_BEm; 1.
DR Gene3D; 3.40.50.620; -; 2.
DR HAMAP; MF_02002; Ile_tRNA_synth_type1; 1.
DR InterPro; IPR001412; aa-tRNA-synth_I_CS.
DR InterPro; IPR002300; aa-tRNA-synth_Ia.
DR InterPro; IPR033708; Anticodon_Ile_BEm.
DR InterPro; IPR002301; Ile-tRNA-ligase.
DR InterPro; IPR023585; Ile-tRNA-ligase_type1.
DR InterPro; IPR013155; M/V/L/I-tRNA-synth_anticd-bd.
DR InterPro; IPR014729; Rossmann-like_a/b/a_fold.
DR InterPro; IPR009080; tRNAsynth_Ia_anticodon-bd.
DR InterPro; IPR009008; Val/Leu/Ile-tRNA-synth_edit.
DR InterPro; IPR010663; Znf_FPG/IleRS.
DR Pfam; PF08264; Anticodon_1; 1.
DR Pfam; PF00133; tRNA-synt_1; 1.
DR Pfam; PF06827; zf-FPG_IleRS; 1.
DR PRINTS; PR00984; TRNASYNTHILE.
DR SUPFAM; SSF47323; SSF47323; 1.
DR SUPFAM; SSF50677; SSF50677; 1.
DR TIGRFAMs; TIGR00392; ileS; 1.
DR PROSITE; PS00178; AA_TRNA_LIGASE_I; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Aminoacyl-tRNA synthetase; ATP-binding; Cytoplasm;
KW Direct protein sequencing; Ligase; Metal-binding; Nucleotide-binding;
KW Protein biosynthesis; Zinc.
FT CHAIN 1..917
FT /note="Isoleucine--tRNA ligase"
FT /id="PRO_0000098463"
FT MOTIF 57..67
FT /note="'HIGH' region"
FT MOTIF 595..599
FT /note="'KMSKS' region"
FT BINDING 56
FT /ligand="L-isoleucyl-5'-AMP"
FT /ligand_id="ChEBI:CHEBI:178002"
FT /evidence="ECO:0000250|UniProtKB:P56690"
FT BINDING 67
FT /ligand="L-isoleucyl-5'-AMP"
FT /ligand_id="ChEBI:CHEBI:178002"
FT /evidence="ECO:0000250|UniProtKB:P56690"
FT BINDING 554
FT /ligand="L-isoleucyl-5'-AMP"
FT /ligand_id="ChEBI:CHEBI:178002"
FT /evidence="ECO:0000250|UniProtKB:P56690"
FT BINDING 555
FT /ligand="L-isoleucyl-5'-AMP"
FT /ligand_id="ChEBI:CHEBI:178002"
FT /evidence="ECO:0000250|UniProtKB:P56690"
FT BINDING 557
FT /ligand="L-isoleucyl-5'-AMP"
FT /ligand_id="ChEBI:CHEBI:178002"
FT /evidence="ECO:0000250|UniProtKB:P56690"
FT BINDING 558
FT /ligand="L-isoleucyl-5'-AMP"
FT /ligand_id="ChEBI:CHEBI:178002"
FT /evidence="ECO:0000250|UniProtKB:P56690"
FT BINDING 585
FT /ligand="L-isoleucyl-5'-AMP"
FT /ligand_id="ChEBI:CHEBI:178002"
FT /evidence="ECO:0000250|UniProtKB:P56690"
FT BINDING 598
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250"
FT BINDING 632
FT /ligand="tRNA(Ile)"
FT /ligand_id="ChEBI:CHEBI:29174"
FT /evidence="ECO:0007744|PDB:1QU2"
FT BINDING 640
FT /ligand="tRNA(Ile)"
FT /ligand_id="ChEBI:CHEBI:29174"
FT /evidence="ECO:0007744|PDB:1QU2"
FT BINDING 886
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0007744|PDB:1FFY, ECO:0007744|PDB:1QU2"
FT BINDING 889
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0007744|PDB:1FFY, ECO:0007744|PDB:1QU2"
FT BINDING 906
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0007744|PDB:1FFY, ECO:0007744|PDB:1QU2"
FT BINDING 909
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0007744|PDB:1FFY, ECO:0007744|PDB:1QU2"
FT HELIX 4..6
FT /evidence="ECO:0007829|PDB:1FFY"
FT HELIX 20..33
FT /evidence="ECO:0007829|PDB:1FFY"
FT HELIX 36..43
FT /evidence="ECO:0007829|PDB:1FFY"
FT TURN 44..46
FT /evidence="ECO:0007829|PDB:1FFY"
FT STRAND 58..61
FT /evidence="ECO:0007829|PDB:1FFY"
FT HELIX 65..82
FT /evidence="ECO:0007829|PDB:1FFY"
FT TURN 83..85
FT /evidence="ECO:0007829|PDB:1FFY"
FT STRAND 93..95
FT /evidence="ECO:0007829|PDB:1FFY"
FT HELIX 99..108
FT /evidence="ECO:0007829|PDB:1FFY"
FT HELIX 117..140
FT /evidence="ECO:0007829|PDB:1FFY"
FT TURN 141..143
FT /evidence="ECO:0007829|PDB:1FFY"
FT HELIX 157..172
FT /evidence="ECO:0007829|PDB:1FFY"
FT STRAND 176..186
FT /evidence="ECO:0007829|PDB:1FFY"
FT TURN 187..190
FT /evidence="ECO:0007829|PDB:1FFY"
FT HELIX 195..197
FT /evidence="ECO:0007829|PDB:1FFY"
FT STRAND 198..209
FT /evidence="ECO:0007829|PDB:1FFY"
FT STRAND 212..214
FT /evidence="ECO:0007829|PDB:1QU3"
FT HELIX 220..222
FT /evidence="ECO:0007829|PDB:1FFY"
FT STRAND 230..232
FT /evidence="ECO:0007829|PDB:1FFY"
FT HELIX 234..236
FT /evidence="ECO:0007829|PDB:1FFY"
FT HELIX 237..239
FT /evidence="ECO:0007829|PDB:1QU3"
FT STRAND 242..245
FT /evidence="ECO:0007829|PDB:1QU3"
FT TURN 256..259
FT /evidence="ECO:0007829|PDB:1FFY"
FT TURN 265..268
FT /evidence="ECO:0007829|PDB:1FFY"
FT HELIX 269..272
FT /evidence="ECO:0007829|PDB:1FFY"
FT TURN 273..276
FT /evidence="ECO:0007829|PDB:1FFY"
FT TURN 290..292
FT /evidence="ECO:0007829|PDB:1FFY"
FT HELIX 301..303
FT /evidence="ECO:0007829|PDB:1QU3"
FT STRAND 306..312
FT /evidence="ECO:0007829|PDB:1QU3"
FT STRAND 318..320
FT /evidence="ECO:0007829|PDB:1FFY"
FT HELIX 333..336
FT /evidence="ECO:0007829|PDB:1FFY"
FT TURN 337..339
FT /evidence="ECO:0007829|PDB:1FFY"
FT STRAND 340..342
FT /evidence="ECO:0007829|PDB:1FFY"
FT STRAND 351..353
FT /evidence="ECO:0007829|PDB:1FFY"
FT STRAND 363..365
FT /evidence="ECO:0007829|PDB:1FFY"
FT HELIX 369..372
FT /evidence="ECO:0007829|PDB:1FFY"
FT HELIX 375..377
FT /evidence="ECO:0007829|PDB:1FFY"
FT HELIX 380..383
FT /evidence="ECO:0007829|PDB:1FFY"
FT STRAND 388..397
FT /evidence="ECO:0007829|PDB:1FFY"
FT TURN 398..400
FT /evidence="ECO:0007829|PDB:1FFY"
FT STRAND 405..414
FT /evidence="ECO:0007829|PDB:1FFY"
FT HELIX 416..428
FT /evidence="ECO:0007829|PDB:1FFY"
FT STRAND 430..434
FT /evidence="ECO:0007829|PDB:1FFY"
FT HELIX 435..447
FT /evidence="ECO:0007829|PDB:1FFY"
FT STRAND 454..456
FT /evidence="ECO:0007829|PDB:1FFY"
FT STRAND 458..460
FT /evidence="ECO:0007829|PDB:1FFY"
FT STRAND 469..471
FT /evidence="ECO:0007829|PDB:1QU3"
FT HELIX 477..490
FT /evidence="ECO:0007829|PDB:1FFY"
FT HELIX 493..497
FT /evidence="ECO:0007829|PDB:1FFY"
FT HELIX 500..503
FT /evidence="ECO:0007829|PDB:1FFY"
FT STRAND 504..507
FT /evidence="ECO:0007829|PDB:1QU3"
FT STRAND 511..513
FT /evidence="ECO:0007829|PDB:1QU3"
FT HELIX 527..532
FT /evidence="ECO:0007829|PDB:1FFY"
FT HELIX 534..537
FT /evidence="ECO:0007829|PDB:1FFY"
FT TURN 538..541
FT /evidence="ECO:0007829|PDB:1FFY"
FT STRAND 547..555
FT /evidence="ECO:0007829|PDB:1FFY"
FT HELIX 556..559
FT /evidence="ECO:0007829|PDB:1FFY"
FT HELIX 562..574
FT /evidence="ECO:0007829|PDB:1FFY"
FT STRAND 578..585
FT /evidence="ECO:0007829|PDB:1FFY"
FT STRAND 591..594
FT /evidence="ECO:0007829|PDB:1QU3"
FT STRAND 598..601
FT /evidence="ECO:0007829|PDB:1FFY"
FT HELIX 606..612
FT /evidence="ECO:0007829|PDB:1FFY"
FT HELIX 615..623
FT /evidence="ECO:0007829|PDB:1FFY"
FT HELIX 635..657
FT /evidence="ECO:0007829|PDB:1FFY"
FT HELIX 664..667
FT /evidence="ECO:0007829|PDB:1FFY"
FT HELIX 671..673
FT /evidence="ECO:0007829|PDB:1FFY"
FT HELIX 676..697
FT /evidence="ECO:0007829|PDB:1FFY"
FT HELIX 701..713
FT /evidence="ECO:0007829|PDB:1FFY"
FT HELIX 714..719
FT /evidence="ECO:0007829|PDB:1FFY"
FT HELIX 720..728
FT /evidence="ECO:0007829|PDB:1FFY"
FT HELIX 736..756
FT /evidence="ECO:0007829|PDB:1FFY"
FT TURN 757..759
FT /evidence="ECO:0007829|PDB:1FFY"
FT HELIX 761..768
FT /evidence="ECO:0007829|PDB:1FFY"
FT STRAND 775..778
FT /evidence="ECO:0007829|PDB:1FFY"
FT HELIX 779..781
FT /evidence="ECO:0007829|PDB:1FFY"
FT HELIX 792..817
FT /evidence="ECO:0007829|PDB:1FFY"
FT HELIX 824..826
FT /evidence="ECO:0007829|PDB:1FFY"
FT STRAND 827..832
FT /evidence="ECO:0007829|PDB:1FFY"
FT HELIX 839..842
FT /evidence="ECO:0007829|PDB:1FFY"
FT HELIX 843..845
FT /evidence="ECO:0007829|PDB:1FFY"
FT HELIX 849..852
FT /evidence="ECO:0007829|PDB:1FFY"
FT STRAND 855..860
FT /evidence="ECO:0007829|PDB:1FFY"
FT STRAND 868..871
FT /evidence="ECO:0007829|PDB:1FFY"
FT STRAND 874..880
FT /evidence="ECO:0007829|PDB:1FFY"
FT STRAND 882..885
FT /evidence="ECO:0007829|PDB:1FFY"
FT TURN 887..889
FT /evidence="ECO:0007829|PDB:1FFY"
FT STRAND 892..894
FT /evidence="ECO:0007829|PDB:1FFY"
FT STRAND 897..899
FT /evidence="ECO:0007829|PDB:1FFY"
FT STRAND 902..905
FT /evidence="ECO:0007829|PDB:1FFY"
FT HELIX 907..914
FT /evidence="ECO:0007829|PDB:1FFY"
SQ SEQUENCE 917 AA; 104885 MW; 8A2B644A03A85636 CRC64;
MDYKETLLMP KTDFPMRGGL PNKEPQIQEK WDAEDQYHKA LEKNKGNETF ILHDGPPYAN
GNLHMGHALN KILKDFIVRY KTMQGFYAPY VPGWDTHGLP IEQALTKKGV DRKKMSTAEF
REKCKEFALE QIELQKKDFR RLGVRGDFND PYITLKPEYE AAQIRIFGEM ADKGLIYKGK
KPVYWSPSSE SSLAEAEIEY HDKRSASIYV AFNVKDDKGV VDADAKFIIW TTTPWTIPSN
VAITVHPELK YGQYNVNGEK YIIAEALSDA VAEALDWDKA SIKLEKEYTG KELEYVVAQH
PFLDRESLVI NGDHVTTDAG TGCVHTAPGH GEDDYIVGQK YELPVISPID DKGVFTEEGG
QFEGMFYDKA NKAVTDLLTE KGALLKLDFI THSYPHDWRT KKPVIFRATP QWFASISKVR
QDILDAIENT NFKVNWGKTR IYNMVRDRGE WVISRQRVWG VPLPVFYAEN GEIIMTKETV
NHVADLFAEH GSNIWFEREA KDLLPEGFTH PGSPNGTFTK ETDIMDVWFD SGSSHRGVLE
TRPELSFPAD MYLEGSDQYR GWFNSSITTS VATRGVSPYK FLLSHGFVMD GEGKKMSKSL
GNVIVPDQVV KQKGADIARL WVSSTDYLAD VRISDEILKQ TSDVYRKIRN TLRFMLGNIN
DFNPDTDSIP ESELLEVDRY LLNRLREFTA STINNYENFD YLNIYQEVQN FINVELSNFY
LDYGKDILYI EQRDSHIRRS MQTVLYQILV DMTKLLAPIL VHTAEEVWSH TPHVKEESVH
LADMPKVVEV DQALLDKWRT FMNLRDDVNR ALETARNEKV IGKSLEAKVT IASNDKFNAS
EFLTSFDALH QLFIVSQVKV VDKLDDQATA YEHGDIVIEH ADGEKCERCW NYSEDLGAVD
ELTHLCPRCQ QVVKSLV
