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B8DPD6

- SYI_DESVM

UniProt

B8DPD6 - SYI_DESVM

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Protein

Isoleucine--tRNA ligase

Gene
ileS, DvMF_0266
Organism
Desulfovibrio vulgaris (strain Miyazaki F / DSM 19637)
Status
Reviewed - Annotation score: 3 out of 5 - Protein inferred from homologyi

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 1 zinc ion per subunit By similarity.UniRule annotation

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei565 – 5651Aminoacyl-adenylate By similarity
Binding sitei609 – 6091ATP By similarity
Metal bindingi905 – 9051Zinc By similarity
Metal bindingi908 – 9081Zinc By similarity
Metal bindingi925 – 9251Zinc By similarity
Metal bindingi928 – 9281Zinc By similarity

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

Enzyme and pathway databases

BioCyciDVUL883:GCJ5-281-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:DvMF_0266
OrganismiDesulfovibrio vulgaris (strain Miyazaki F / DSM 19637)
Taxonomic identifieri883 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaDeltaproteobacteriaDesulfovibrionalesDesulfovibrionaceaeDesulfovibrio
ProteomesiUP000001361: Chromosome

Subcellular locationi

Cytoplasm By similarity UniRule annotation

GO - Cellular componenti

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

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 938938Isoleucine--tRNA ligaseUniRule annotationPRO_1000189152Add
BLAST

Proteomic databases

PRIDEiB8DPD6.

Interactioni

Subunit structurei

Monomer By similarity.UniRule annotation

Protein-protein interaction databases

STRINGi883.DvMF_0266.

Structurei

3D structure databases

ProteinModelPortaliB8DPD6.

Family & Domainsi

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi58 – 6811"HIGH" regionUniRule annotationAdd
BLAST
Motifi606 – 6105"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.
HOGENOMiHOG000246402.
KOiK01870.
OMAiERLMLHQ.
OrthoDBiEOG644ZM1.

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.
[Graphical view]
PANTHERiPTHR11946:SF9. PTHR11946:SF9. 1 hit.
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.

B8DPD6-1 [UniParc]FASTAAdd to Basket

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MSDYKKTLHL PDTKFPMKAN LTQREPEMLK FWEGIDAYAA MAQASGQKGQ    50
YVLHDGPPYA NGHIHLGTAL NKILKDMVVK SRNMQGYAAR YVPGWDCHGL 100
PIEHKVEQEL GEKKKELPAH VVRKRCRQYA EKYLDIQRKE FKRLGVLGAW 150
DKPYMTMDPA YESATARELG NFVAAGNVVR SKKPIYWCCS CQTALAEAEV 200
EYYDHTSPSI FVRFPLRDPK VADVLNVDPA SAWIVIWTTT PWTLPDNMAV 250
AVHPDHDYAV VRHDGAHYVL AAALVESSAK TFGWENCEVV STVPGAKLEG 300
LVATHPFYDR PSPVVLADYV VLDSGTGCVH TAPGHGREDY ETGLRYGLEI 350
LSPLNDEGRF LDSVPFFAGL TVFEANPKVI EKLREVGNLL AERKISHSYP 400
HCWRCKKPVI FRATTQWFIA MEKNDLRARA LSAIRNDVRW IPAWGEERIH 450
NMIEFRPDWC ISRQRTWGVP IIALLCEGCG EAWNDAAWMR DIADRFAKHP 500
TGCDYWYETP LEGIVPAGLA CPHCGGNHWK KETDILDVWF DSGTSFSAVL 550
EQRGDTAFPA DLYLEGSDQH RGWFHSSLLA SMGTRGVPPY RAVLTHGYVV 600
DGEGRKMSKS IGNVIAPQEI IDKYGAEILR LWVASVDYRE DIRISDEILS 650
RLVDAYRRIR NTCRYLLGNI DDLTPEEIVP FSVMDPLDRY ALDIVTDAHA 700
RIQEAYSEFE FHKVFHTLHN LCVTDLSAFY LDVLKDRLYA SAKDSPERRS 750
AQTALLHILL VLVRDMAPVL SFTAEEVFRH IPEALRPAAA TVFALRGSDT 800
PLYNVSSDES ERWEAVLAVR SEVTKAIEPL RKAGTVGHSL DTHVTLYADH 850
KLADLLRATG TDLRAVFIVS KLNIAPLEDA PQDAFASDEV KGLRIGVAKA 900
PGAKCERCWI YHEELGADPG YPGACARCTT VLRTSGAE 938
Length:938
Mass (Da):105,282
Last modified:March 3, 2009 - v1
Checksum:i2B910B49EA2CFE00
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
CP001197 Genomic DNA. Translation: ACL07223.1.
RefSeqiWP_012611417.1. NC_011769.1.
YP_002434691.1. NC_011769.1.

Genome annotation databases

EnsemblBacteriaiACL07223; ACL07223; DvMF_0266.
GeneIDi7172148.
KEGGidvm:DvMF_0266.
PATRICi21770443. VBIDesVul86729_0276.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
CP001197 Genomic DNA. Translation: ACL07223.1 .
RefSeqi WP_012611417.1. NC_011769.1.
YP_002434691.1. NC_011769.1.

3D structure databases

ProteinModelPortali B8DPD6.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

STRINGi 883.DvMF_0266.

Proteomic databases

PRIDEi B8DPD6.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai ACL07223 ; ACL07223 ; DvMF_0266 .
GeneIDi 7172148.
KEGGi dvm:DvMF_0266.
PATRICi 21770443. VBIDesVul86729_0276.

Phylogenomic databases

eggNOGi COG0060.
HOGENOMi HOG000246402.
KOi K01870.
OMAi ERLMLHQ.
OrthoDBi EOG644ZM1.

Enzyme and pathway databases

BioCyci DVUL883:GCJ5-281-MONOMER.

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.
[Graphical view ]
PANTHERi PTHR11946:SF9. PTHR11946:SF9. 1 hit.
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

  1. "Complete sequence of Desulfovibrio vulgaris str. 'Miyazaki F'."
    Lucas S., Copeland A., Lapidus A., Glavina del Rio T., Dalin E., Tice H., Bruce D., Goodwin L., Pitluck S., Sims D., Brettin T., Detter J.C., Han C., Larimer F., Land M., Hauser L., Kyrpides N., Mikhailova N., Hazen T.C., Richardson P.
    Submitted (OCT-2008) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: Miyazaki F / DSM 19637.

Entry informationi

Entry nameiSYI_DESVM
AccessioniPrimary (citable) accession number: B8DPD6
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 28, 2009
Last sequence update: March 3, 2009
Last modified: September 3, 2014
This is version 42 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

Complete proteome

Documents

  1. Aminoacyl-tRNA synthetases
    List of aminoacyl-tRNA synthetase entries
  2. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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