Tyrosyl-tRNA synthetase - Escherichia coli (strain K12)

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Reviewed, UniProtKB/Swiss-Prot P0AGJ9 (SYY_ECOLI)

Last modified November 3, 2009. Version 46. History...

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Names and origin · Protein attributes · General annotation (Comments) · Ontologies · Sequence annotation (Features) · Sequences · References · Cross-references · Entry information · Relevant documents

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Names and origin

Protein names

Recommended name:
    Tyrosyl-tRNA synthetase
    EC=6.1.1.1
Alternative name(s):
    Tyrosine--tRNA ligase
      Short name=TyrRS

Gene names

Name:	tyrS
Ordered Locus Names:	b1637, JW1629

Organism

Escherichia coli (strain K12) [Complete proteome] [HAMAP]

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia

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Protein attributes

Sequence length	424 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level.

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General annotation (Comments)

Function	Catalyzes the attachment of tyrosine to tRNA(Tyr) in a two-step reaction: tyrosine is first activated by ATP to form Tyr-AMP and then transferred to the acceptor end of tRNA(Tyr). HAMAP MF_02006
Catalytic activity	ATP + L-tyrosine + tRNA(Tyr) = AMP + diphosphate + L-tyrosyl-tRNA(Tyr). HAMAP MF_02006
Subunit structure	Homodimer. Ref.8
Subcellular location	Cytoplasm. HAMAP MF_02006
Sequence similarities	Belongs to the class-I aminoacyl-tRNA synthetase family. TyrS type 1 subfamily. Contains 1 S4 RNA-binding domain.

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Ontologies

Keywords
Biological process	Protein biosynthesis
Cellular component	Cytoplasm
Ligand	ATP-binding Nucleotide-binding RNA-binding
Molecular function	Aminoacyl-tRNA synthetase Ligase
PTM	Acetylation
Technical term	3D-structure Complete proteome Direct protein sequencing
Gene Ontology (GO)
Biological process	tyrosyl-tRNA aminoacylation Inferred from electronic annotation. Source: HAMAP
Cellular component	cytosol Inferred from direct assay. Source: UniProtKB membrane Inferred from direct assay. Source: UniProtKB
Molecular function	ATP binding Inferred from electronic annotation. Source: HAMAP RNA binding Inferred from electronic annotation. Source: UniProtKB-KW tyrosine-tRNA ligase activity Inferred from electronic annotation. Source: HAMAP
Complete GO annotation...

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Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Initiator methionine

Removed HAMAP MF_02006

Chain

2 – 424

423

Tyrosyl-tRNA synthetase HAMAP MF_02006

PRO_0000055652

Regions

Domain

357 – 414

S4 RNA-binding

Motif

42 – 51

"HIGH" region HAMAP MF_02006

Motif

235 – 239

"KMSKS" region HAMAP MF_02006

Sites

Binding site

Tyrosine HAMAP MF_02006

Binding site

175

Tyrosine HAMAP MF_02006

Binding site

179

Tyrosine HAMAP MF_02006

Binding site

198

Tyr-AMP intermediate adenyl group; via amide nitrogen HAMAP MF_02006

Binding site

200

Tyr-AMP intermediate adenyl group HAMAP MF_02006

Binding site

228

Tyr-AMP intermediate adenyl group; via carbonyl oxygen and amide nitrogen HAMAP MF_02006

Binding site

238

ATP By similarity

Site

231

Cross-linked with tRNA by periodate oxidation HAMAP MF_02006

Site

235

Cross-linked with tRNA by periodate oxidation; predominant HAMAP MF_02006

Site

238

Cross-linked with tRNA by periodate oxidation HAMAP MF_02006

Amino acid modifications

Modified residue

144

N6-acetyllysine Ref.6

Experimental info

Mutagenesis

Y → V: Confers specificity for the non-natural amino acid 3-iodo-tyrosine; when associated with C-195.

Mutagenesis

195

Q → C: Confers specificity for the non-natural amino acid 3-iodo-tyrosine; when associated with V-37.

Secondary structure

424

Helix Strand Turn

Details...

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Sequences

Sequence

Length

Mass (Da)

Tools

P0AGJ9-1 [UniParc].

Last modified January 23, 2007. Version 2.
Checksum: 98E7080D85B356A2
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FASTA

424

47,527

        10         20         30         40         50         60 
MASSNLIKQL QERGLVAQVT DEEALAERLA QGPIALYCGF DPTADSLHLG HLVPLLCLKR 

        70         80         90        100        110        120 
FQQAGHKPVA LVGGATGLIG DPSFKAAERK LNTEETVQEW VDKIRKQVAP FLDFDCGENS 

       130        140        150        160        170        180 
AIAANNYDWF GNMNVLTFLR DIGKHFSVNQ MINKEAVKQR LNREDQGISF TEFSYNLLQG 

       190        200        210        220        230        240 
YDFACLNKQY GVVLQIGGSD QWGNITSGID LTRRLHQNQV FGLTVPLITK ADGTKFGKTE 

       250        260        270        280        290        300 
GGAVWLDPKK TSPYKFYQFW INTADADVYR FLKFFTFMSI EEINALEEED KNSGKAPRAQ 

       310        320        330        340        350        360 
YVLAEQVTRL VHGEEGLQAA KRITECLFSG SLSALSEADF EQLAQDGVPM VEMEKGADLM 

       370        380        390        400        410        420 
QALVDSELQP SRGQARKTIA SNAITINGEK QSDPEYFFKE EDRLFGRFTL LRRGKKNYCL 


ICWK

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References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"The tyrosyl-tRNA synthetase from Escherichia coli. Complete nucleotide sequence of the structural gene." Barker D.G., Bruton C.J., Winter G. FEBS Lett. 150:419-423(1982) [PubMed: 6761148] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PARTIAL PROTEIN SEQUENCE.
[2]	"A 570-kb DNA sequence of the Escherichia coli K-12 genome corresponding to the 28.0-40.1 min region on the linkage map." Aiba H., Baba T., Fujita K., Hayashi K., Inada T., Isono K., Itoh T., Kasai H., Kashimoto K., Kimura S., Kitakawa M., Kitagawa M., Makino K., Miki T., Mizobuchi K., Mori H., Mori T., Motomura K. Horiuchi T. DNA Res. 3:363-377(1996) [PubMed: 9097039] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[3]	"The complete genome sequence of Escherichia coli K-12." Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V., Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B., Shao Y. Science 277:1453-1474(1997) [PubMed: 9278503] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / MG1655 / ATCC 47076.
[4]	"Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110." Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T. Mol. Syst. Biol. 2:E1-E5(2006) [PubMed: 16738553] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[5]	"Characterization of the complex pdxH-tyrS operon of Escherichia coli K-12 and pleiotropic phenotypes caused by pdxH insertion mutations." Lam H.-M., Winkler M.E. J. Bacteriol. 174:6033-6045(1992) [PubMed: 1356963] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-26. Strain: K12.
[6]	"Lysine acetylation is a highly abundant and evolutionarily conserved modification in Escherichia coli." Zhang J., Sprung R., Pei J., Tan X., Kim S., Zhu H., Liu C.F., Grishin N.V., Zhao Y. Mol. Cell. Proteomics 8:215-225(2009) [PubMed: 18723842] [Abstract] Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT LYS-144, MASS SPECTROMETRY.
[7]	"Structural snapshots of the KMSKS loop rearrangement for amino acid activation by bacterial tyrosyl-tRNA synthetase." Kobayashi T., Takimura T., Sekine R., Vincent K., Kamata K., Sakamoto K., Nishimura S., Yokoyama S. J. Mol. Biol. 346:105-117(2005) [PubMed: 15663931] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) OF 5-322 IN COMPLEX WITH TYROSINE AND TYR-AMP ANALOG.
[8]	"Structural basis of nonnatural amino acid recognition by an engineered aminoacyl-tRNA synthetase for genetic code expansion." Kobayashi T., Sakamoto K., Takimura T., Sekine R., Kelly V.P., Kamata K., Nishimura S., Yokoyama S. Proc. Natl. Acad. Sci. U.S.A. 102:1366-1371(2005) [PubMed: 15671170] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) OF 1-322 OF MUTANT VAL-37/CYS-195 IN COMPLEX WITH SUBSTRATE, SUBUNIT.

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Cross-references

Sequence databases

J01719 Genomic DNA. Translation: AAA24707.1.
U00096 Genomic DNA. Translation: AAC74709.1.
AP009048 Genomic DNA. Translation: BAA15398.1.
M92351 Genomic DNA. Translation: AAA24710.1.

PIR

SYECYT. A01178.

RefSeq

AP_002259.1.
NP_416154.1.

3D structure databases

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1VBM	X-ray	2.70	A/B	5-322	[»]
1VBN	X-ray	2.70	A/B	5-322	[»]
1WQ3	X-ray	2.00	A	1-322	[»]
1WQ4	X-ray	2.00	A	2-322	[»]
1X8X	X-ray	2.00	A	1-322	[»]
2YXN	X-ray	1.80	A	1-322	[»]

ModBase

Search...

Protein-protein interaction databases

IntAct

P0AGJ9. 8 interactions.

STRING

P0AGJ9.

2-D gel databases

SWISS-2DPAGE

P0AGJ9.

ECO2DBASE

G044.0. 6TH EDITION.

Genome annotation databases

GeneID

948855.

GenomeReviews

Gene locus JW1629 in contig AP009048_GR.
Gene locus b1637 in contig U00096_GR.

KEGG

ecj:JW1629.
eco:b1637.

Organism-specific databases

EchoBASE

EB1036.

EcoGene

EG11043. tyrS.

CMR

Search...

Phylogenomic databases

HOGENOM

P0AGJ9.

OMA

TFYIGFD.

Enzyme and pathway databases

BioCyc

EcoCyc:TYRS-MON.
MetaCyc:TYRS-MON.

Gene expression databases

Genevestigator

P0AGJ9.

Family and domain databases

HAMAP

MF_02006.
[Tree]

InterPro

IPR001412. aa-tRNA-synth_I_CS.
IPR002305. aa-tRNA-synth_Ib.
IPR014729. Rossmann-like_a/b/a_fold.
IPR002942. S4_RNA_bd.
IPR002307. Tyr-tRNA-synth_Ib_bac/mito.
[Graphical view]

Gene3D

G3DSA:3.40.50.620. Rossmann-like_a/b/a_fold. 1 hit.

PANTHER

PTHR11766. Tyr_tRNA-synt_1b. 1 hit.

Pfam

PF01479. S4. 1 hit.
PF00579. tRNA-synt_1b. 1 hit.
[Graphical view]

PRINTS

PR01040. TRNASYNTHTYR.

SMART

SM00363. S4. 1 hit.
[Graphical view]

TIGRFAMs

TIGR00234. tyrS. 1 hit.

PROSITE

PS00178. AA_TRNA_LIGASE_I. 1 hit.
PS50889. S4. 1 hit.
[Graphical view]

ProtoNet

Search...

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Entry information

Entry name

SYY_ECOLI

Accession

Primary (citable) accession number: P0AGJ9
Secondary accession number(s): P00951

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 21, 1986
Last sequence update:	January 23, 2007
Last modified:	November 3, 2009
This is version 46 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

HAMAP (High-quality Automated and Manual Annotation of microbial Proteomes)

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