Reviewed, UniProtKB/Swiss-Prot P00952 (SYY_BACST)

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

Organism

Bacillus stearothermophilus (Geobacillus stearothermophilus)

Taxonomic identifier

1422 [NCBI]

Taxonomic lineage

Bacteria › Firmicutes › Bacillales › Bacillaceae › Geobacillus

Protein attributes

Sequence length	419 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level.

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. HAMAP MF_02006
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.
Biophysicochemical properties	Kinetic parameters: KM=1.35 mM for ATP HAMAP MF_02006 KM=1.8 µM for tyrosine

Ontologies

Keywords
Biological process	Protein biosynthesis
Cellular component	Cytoplasm
Ligand	ATP-binding Nucleotide-binding RNA-binding
Molecular function	Aminoacyl-tRNA synthetase Ligase
Technical term	3D-structure
Gene Ontology (GO)
Biological process	tyrosyl-tRNA aminoacylation Inferred from electronic annotation. Source: HAMAP
Cellular component	cytoplasm Inferred from electronic annotation. Source: UniProtKB-SubCell
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...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 419

419

Tyrosyl-tRNA synthetase HAMAP MF_02006

PRO_0000055642

Regions

Domain

352 – 419

68

S4 RNA-binding

Motif

39 – 48

10

"HIGH" region HAMAP MF_02006

Motif

230 – 234

5

"KMSKS" region HAMAP MF_02006

Sites

Binding site

34

1

Tyrosine By similarity

Binding site

169

1

Tyrosine By similarity

Binding site

173

1

Tyrosine By similarity

Binding site

233

1

ATP By similarity

Experimental info

Mutagenesis

40

1

T → A: Destabilizes the transition states for both steps of the reaction. Ref.7

Mutagenesis

45

1

H → A: Does not affect the second step of the reaction. Ref.7 Ref.5

Mutagenesis

45

1

H → N: Decreases the rate of formation of Tyr-AMP and, as a consequence, abolishes the aminoacylation activity. Strongly increases the toxicity; when associated with A-152. Ref.7 Ref.5

Mutagenesis

48

1

H → A: Does not affect the second step of the reaction. Ref.7

Mutagenesis

78

1

D → A: Does not affect the initial binding of tRNA(Tyr) and the stability of the transition state for the second step of the reaction. Ref.8

Mutagenesis

82

1

K → A: Destabilizes the transition states for both steps of the reaction. Ref.7

Mutagenesis

86

1

R → A: Destabilizes the transition states for both steps of the reaction. Ref.7

Mutagenesis

152

1

E → A: Mischarges tRNA(Phe) with tyrosine in vitro. Toxic for the cell, probably because it alters the discrimination of TyrRS against non-cognate tRNAs. The toxicity is abolished; when associated with N-410 or N-411. Strongly increases toxicity; when associated with N-45. Enhances the toxicity; when associated with A-224. Ref.5

Mutagenesis

152

1

E → D: Does not charge tRNA(Phe) in vitro with tyrosine. Ref.5

Mutagenesis

152

1

E → Q: Mischarges tRNA(Phe) with tyrosine in vitro but this mutation is not toxic in vivo. Ref.5

Mutagenesis

169

1

Y → A: Does not affect the initial binding of tRNA(Tyr) and the stability of the transition state for the second step of the reaction. Ref.8

Mutagenesis

173

1

Q → A: Destabilizes the transition state for the second step of the reaction. Ref.8

Mutagenesis

194

1

D → A: Destabilizes the transition state for the first step of the reaction, but does not affect the transition state for the second step. Ref.8

Mutagenesis

195

1

Q → A: Destabilizes the transition state for the first step of the reaction, but does not affect the transition state for the second step. Ref.8

Mutagenesis

224

1

T → A: Is not toxic in itself. Enhances the toxicity; when associated with A-152. Ref.5

Mutagenesis

230

1

K → A: Decreases the binding affinity between tRNA(Tyr) and TyrRS-Tyr-AMP complex. Ref.6

Mutagenesis

231

1

F → L: No effect on the binding affinity between tRNA(Tyr) and TyrRS-Tyr-AMP complex. Ref.6

Mutagenesis

232

1

G → A: No effect on the binding affinity between tRNA(Tyr) and TyrRS-Tyr-AMP complex. Ref.6

Mutagenesis

233

1

K → A: Decreases the binding affinity between tRNA(Tyr) and TyrRS-Tyr-AMP complex. Ref.6

Mutagenesis

234

1

T → A: No effect on the binding affinity between tRNA(Tyr) and TyrRS-Tyr-AMP complex. Ref.6

Mutagenesis

322

1

L → P: 50-fold decrease in charging of tRNA(Tyr) with tyrosine. Ref.9

Mutagenesis

323

1

F → A: 90-fold decrease in charging of tRNA(Tyr) with tyrosine, without effect on the first step of the reaction. Ref.9

Mutagenesis

323

1

F → L: 67-fold decrease in charging of tRNA(Tyr) with tyrosine, without effect on the first step of the reaction. Ref.9

Mutagenesis

323

1

F → W: Weak decrease in charging of tRNA(Tyr) with tyrosine, without effect on the first step of the reaction. Ref.9

Mutagenesis

323

1

F → Y: 3-fold decrease in charging of tRNA(Tyr) with tyrosine, without effect on the first step of the reaction. Ref.9

Mutagenesis

324

1

S → A: 2-fold increase in charging of tRNA(Tyr) with tyrosine. Ref.9

Mutagenesis

325

1

G → A: 5-fold increase in charging of tRNA(Tyr) with tyrosine. Ref.9

Mutagenesis

339

1

F → L: Has no effect on charging of tRNA(Tyr) with tyrosine. Ref.9

Mutagenesis

410

1

K → N: Decreases the binding of tRNA(Tyr), without affecting the formation of Tyr-AMP. Abolishes the toxicity; when associated with A-152. Ref.5

Mutagenesis

411

1

K → N: Decreases the binding of tRNA(Tyr), without affecting the formation of Tyr-AMP. Abolishes the toxicity; when associated with A-152. Ref.5

Secondary structure

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419

Helix Strand Turn

Details...

Helix

2 – 10

9

Beta strand

14 – 17

4

Helix

19 – 28

10

Beta strand

32 – 37

6

Beta strand

40 – 43

4

Helix

46 – 48

3

Helix

49 – 60

12

Beta strand

64 – 69

6

Helix

73 – 75

3

Helix

91 – 105

15

Beta strand

114 – 116

3

Beta strand

119 – 122

4

Helix

124 – 127

4

Helix

132 – 138

7

Helix

140 – 142

3

Helix

145 – 149

5

Helix

152 – 155

4

Turn

156 – 160

5

Helix

164 – 184

21

Beta strand

186 – 192

7

Helix

193 – 195

3

Helix

196 – 210

15

Beta strand

216 – 220

5

Beta strand

240 – 242

3

Turn

243 – 245

3

Helix

248 – 256

9

Helix

260 – 270

11

Helix

275 – 287

13

Helix

293 – 307

15

Helix

309 – 318

10

Beta strand

325 – 327

3

Helix

332 – 339

8

Beta strand

344 – 347

4

Helix

354 – 361

8

Helix

367 – 375

9

Beta strand

379 – 381

3

Turn

389 – 391

3

Turn

396 – 398

3

Beta strand

399 – 408

10

Beta strand

413 – 418

6

Sequences

	Sequence		Length	Mass (Da)
	P00952-1 [UniParc]. Last modified July 21, 1986. Version 1. Checksum: B9CB64AEEEE2010F	FASTA	419	47,303
	10 20 30 40 50 60 MDLLAELQWR GLVNQTTDED GLRKLLNEER VTLYCGFDPT ADSLHIGHLA TILTMRRFQQ 70 80 90 100 110 120 AGHRPIALVG GATGLIGDPS GKKSERTLNA KETVEAWSAR IKEQLGRFLD FEADGNPAKI 130 140 150 160 170 180 KNNYDWIGPL DVITFLRDVG KHFSVNYMMA KESVQSRIET GISFTEFSYM MLQAYDFLRL 190 200 210 220 230 240 YETEGCRLQI GGSDQWGNIT AGLELIRKTK GEARAFGLTI PLVTKADGTK FGKTESGTIW 250 260 270 280 290 300 LDKEKTSPYE FYQFWINTDD RDVIRYLKYF TFLSKEEIEA LEQELREAPE KRAAQKTLAE 310 320 330 340 350 360 EVTKLVHGEE ALRQAIRISE ALFSGDIANL TAAEIEQGFK DVPSFVHEGG DVPLVELLVS 370 380 390 400 410 AGISPSKRQA REDIQNGAIY VNGERLQDVG AILTAEHRLE GRFTVIRRGK KKYYLIRYA

References

[1]	"The amino acid sequence of the tyrosyl-tRNA synthetase from Bacillus stearothermophilus." Winter G., Koch G.L.E., Hartley B.S., Barker D.G. Eur. J. Biochem. 132:383-387(1983) [PubMed: 6840095] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]	"A transcription terminator in the 5' non-coding region of the tyrosyl tRNA synthetase gene from Bacillus stearothermophilus." Waye M.M.Y., Winter G. Eur. J. Biochem. 158:505-510(1986) [PubMed: 3525162] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-11.
[3]	"Deletion mutagenesis using an 'M13 splint': the N-terminal structural domain of tyrosyl-tRNA synthetase (B. stearothermophilus) catalyses the formation of tyrosyl adenylate." Waye M.M.Y., Winter G., Wilkinson A.J., Fersht A.R. EMBO J. 2:1827-1829(1983) [PubMed: 6315404] [Abstract] Cited for: BIOPHYSICOCHEMICAL PROPERTIES.
[4]	"Construction of heterodimer tyrosyl-tRNA synthetase shows tRNATyr interacts with both subunits." Carter P., Bedouelle H., Winter G. Proc. Natl. Acad. Sci. U.S.A. 83:1189-1192(1986) [PubMed: 3006039] [Abstract] Cited for: INTERACTION WITH TRNA(TYR).
[5]	"Role of residue Glu152 in the discrimination between transfer RNAs by tyrosyl-tRNA synthetase from Bacillus stearothermophilus." Vidal-Cros A., Bedouelle H. J. Mol. Biol. 223:801-810(1992) [PubMed: 1542120] [Abstract] Cited for: MUTAGENESIS OF HIS-45; GLU-152; THR-224; LYS-410 AND LYS-411.
[6]	"The 'KMSKS' motif in tyrosyl-tRNA synthetase participates in the initial binding of tRNA(Tyr)." Xin Y., Li W., First E.A. Biochemistry 39:340-347(2000) [PubMed: 10630994] [Abstract] Cited for: MUTAGENESIS OF LYS-230; PHE-231; GLY-232; LYS-233 AND THR-234.
[7]	"Correlating amino acid conservation with function in tyrosyl-tRNA synthetase." Xin Y., Li W., Dwyer D.S., First E.A. J. Mol. Biol. 303:287-298(2000) [PubMed: 11023793] [Abstract] Cited for: MUTAGENESIS OF THR-40; HIS-45; HIS-48; LYS-82 AND ARG-86.
[8]	"Stabilization of the transition state for the transfer of tyrosine to tRNA(Tyr) by tyrosyl-tRNA synthetase." Xin Y., Li W., First E.A. J. Mol. Biol. 303:299-310(2000) [PubMed: 11023794] [Abstract] Cited for: MUTAGENESIS OF ASP-78; TYR-169; GLN-173; ASP-194 AND GLN-195.
[9]	"An essential residue in the flexible peptide linking the two idiosynchratic domains of bacterial tyrosyl-tRNA synthetases." Gaillard C., Bedouelle H. Biochemistry 40:7192-7199(2001) [PubMed: 11401566] [Abstract] Cited for: MUTAGENESIS OF LEU-322; PHE-323; SER-324; GLY-325 AND PHE-339.
[10]	"Tyrosyl-tRNA synthetase forms a mononucleotide-binding fold." Bhat T.N., Blow D.M., Brick P., Nyborg J. J. Mol. Biol. 158:699-709(1982) [PubMed: 7120416] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (3.0 ANGSTROMS).
[11]	"Structure of tyrosyl-tRNA synthetase refined at 2.3-A resolution. Interaction of the enzyme with the tyrosyl adenylate intermediate." Brick P., Bhat T.N., Blow D.M. J. Mol. Biol. 208:83-98(1989) [PubMed: 2504923] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS).
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

J01546 Genomic DNA. No translation available.
X04193 Genomic DNA. Translation: CAA27784.1.

PIR

SYBSYF. A01179.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1JH3	NMR	-	A	321-419	[»]
1TYA	X-ray	2.80	E	1-319	[»]
1TYB	X-ray	2.50	E	1-319	[»]
1TYC	X-ray	2.50	A	1-319	[»]
1TYD	X-ray	2.50	E	1-319	[»]
2TS1	X-ray	2.30	A	1-419	[»]
3TS1	X-ray	2.70	A	1-419	[»]
4TS1	X-ray	2.50	A/B	1-317	[»]

DisProt

DP00095.

ModBase

Search...

Enzyme and pathway databases

BRENDA

6.1.1.1. 266715.

Family and domain databases

HAMAP

MF_02006. Tyr_tRNA_synth_type1.
[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...

Entry information

Entry name

SYY_BACST

Accession

Primary (citable) accession number: P00952

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 21, 1986
Last sequence update:	July 21, 1986
Last modified:	February 9, 2010
This is version 84 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

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