Reviewed, UniProtKB/Swiss-Prot Q57834 (SYY_METJA)

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:	MJ0389

Organism

Methanocaldococcus jannaschii (Methanococcus jannaschii) [Complete proteome] [HAMAP]

Taxonomic identifier

2190 [NCBI]

Taxonomic lineage

Archaea › Euryarchaeota › Methanococci › Methanococcales › Methanocaldococcaceae › Methanocaldococcus

Protein attributes

Sequence length	306 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is not processed.
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). Ref.2
Catalytic activity	ATP + L-tyrosine + tRNA(Tyr) = AMP + diphosphate + L-tyrosyl-tRNA(Tyr). HAMAP MF_02008
Subunit structure	Homodimer. Ref.2 Ref.4
Subcellular location	Cytoplasm. HAMAP MF_02008
Sequence similarities	Belongs to the class-I aminoacyl-tRNA synthetase family. TyrS type 3 subfamily.
Biophysicochemical properties	Kinetic parameters: KM=15 µM for tRNA(Tyr) (at 45 degrees Celsius) Ref.2

Ontologies

Keywords
Biological process	Protein biosynthesis
Cellular component	Cytoplasm
Ligand	ATP-binding Nucleotide-binding
Molecular function	Aminoacyl-tRNA synthetase Ligase
Technical term	3D-structure Complete proteome
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 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 – 306

306

Tyrosyl-tRNA synthetase HAMAP MF_02008

PRO_0000055669

Regions

Region

151 – 158

8

Tyrosine HAMAP MF_02008

Region

228 – 231

4

Interaction with t-RNA HAMAP MF_02008

Region

283 – 288

6

Interaction with t-RNA HAMAP MF_02008

Motif

37 – 45

9

"HIGH" region HAMAP MF_02008

Motif

204 – 208

5

"KMSKS" region HAMAP MF_02008

Sites

Binding site

32

1

Tyrosine HAMAP MF_02008

Binding site

36

1

Tyrosine HAMAP MF_02008

Binding site

173

1

Tyrosine HAMAP MF_02008

Binding site

207

1

ATP Potential

Site

143

1

Interaction with t-RNA HAMAP MF_02008

Experimental info

Mutagenesis

32

1

Y → Q: Confers specificity for the non-natural amino acid O-methyl-tyrosine; when associated with T-107; A-158 and P-162.

Mutagenesis

107

1

E → T: Confers specificity for the non-natural amino acid O-methyl-tyrosine; when associated with Q-32; A-158 and P-162.

Mutagenesis

158

1

D → A: Confers specificity for the non-natural amino acid O-methyl-tyrosine; when associated with Q-32; T-107 and P-162.

Mutagenesis

162

1

L → P: Confers specificity for the non-natural amino acid O-methyl-tyrosine; when associated with Q-32; T-107 and A-158.

Mutagenesis

286

1

D → A: Decreases the rate of aminoacylation more than 10-fold, without effect on tyrosyl adenylate synthesis. Ref.4 Ref.3

Mutagenesis

286

1

D → R: Decreases the rate of aminoacylation with wild-type tRNA and increases aminoacylation with amber suppressor tRNA 8-fold. Decreases affinity for wild-type tRNA and increases affinity for amber suppressor tRNA. Ref.4 Ref.3

Mutagenesis

288

1

K → A: Decreases the rate of aminoacylation more than 200-fold, without effect on tyrosyl adenylate synthesis. Ref.3

Secondary structure

1

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306

Helix Strand Turn

Details...

Helix

3 – 8

6

Beta strand

12 – 15

4

Helix

17 – 25

9

Beta strand

26 – 35

10

Helix

43 – 57

15

Beta strand

60 – 66

7

Helix

68 – 73

6

Helix

79 – 95

17

Beta strand

101 – 104

4

Helix

105 – 107

3

Turn

108 – 110

3

Helix

112 – 124

13

Helix

127 – 133

7

Turn

134 – 137

4

Helix

147 – 162

16

Beta strand

165 – 170

6

Helix

171 – 173

3

Helix

174 – 183

10

Beta strand

184 – 186

3

Beta strand

189 – 193

5

Helix

219 – 228

10

Helix

240 – 247

8

Beta strand

251 – 255

5

Helix

259 – 261

3

Beta strand

265 – 269

5

Helix

270 – 278

9

Helix

284 – 304

21

Sequences

	Sequence		Length	Mass (Da)
	Q57834-1 [UniParc]. Last modified November 1, 1997. Version 1. Checksum: 1887760ABAF2DD5E	FASTA	306	35,049
	10 20 30 40 50 60 MDEFEMIKRN TSEIISEEEL REVLKKDEKS AYIGFEPSGK IHLGHYLQIK KMIDLQNAGF 70 80 90 100 110 120 DIIILLADLH AYLNQKGELD EIRKIGDYNK KVFEAMGLKA KYVYGSEFQL DKDYTLNVYR 130 140 150 160 170 180 LALKTTLKRA RRSMELIARE DENPKVAEVI YPIMQVNDIH YLGVDVAVGG MEQRKIHMLA 190 200 210 220 230 240 RELLPKKVVC IHNPVLTGLD GEGKMSSSKG NFIAVDDSPE EIRAKIKKAY CPAGVVEGNP 250 260 270 280 290 300 IMEIAKYFLE YPLTIKRPEK FGGDLTVNSY EELESLFKNK ELHPMDLKNA VAEELIKILE PIRKRL

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Complete genome sequence of the methanogenic archaeon, Methanococcus jannaschii." Bult C.J., White O., Olsen G.J., Zhou L., Fleischmann R.D., Sutton G.G., Blake J.A., FitzGerald L.M., Clayton R.A., Gocayne J.D., Kerlavage A.R., Dougherty B.A., Tomb J.-F., Adams M.D., Reich C.I., Overbeek R., Kirkness E.F., Weinstock K.G. , Merrick J.M., Glodek A., Scott J.L., Geoghagen N.S.M., Weidman J.F., Fuhrmann J.L., Nguyen D., Utterback T.R., Kelley J.M., Peterson J.D., Sadow P.W., Hanna M.C., Cotton M.D., Roberts K.M., Hurst M.A., Kaine B.P., Borodovsky M., Klenk H.-P., Fraser C.M., Smith H.O., Woese C.R., Venter J.C. Science 273:1058-1073(1996) [PubMed: 8688087] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440.
[2]	"Major anticodon-binding region missing from an archaebacterial tRNA synthetase." Steer B.A., Schimmel P. J. Biol. Chem. 274:35601-35606(1999) [PubMed: 10585437] [Abstract] Cited for: FUNCTION, SUBUNIT, KINETIC PARAMETERS.
[3]	"Domain-domain communication in a miniature archaebacterial tRNA synthetase." Steer B.A., Schimmel P. Proc. Natl. Acad. Sci. U.S.A. 96:13644-13649(1999) [PubMed: 10570126] [Abstract] Cited for: MUTAGENESIS OF ASP-286 AND LYS-288.
[4]	"Structural basis for orthogonal tRNA specificities of tyrosyl-tRNA synthetases for genetic code expansion." Kobayashi T., Nureki O., Ishitani R., Yaremchuk A., Tukalo M., Cusack S., Sakamoto K., Yokoyama S. Nat. Struct. Biol. 10:425-432(2003) [PubMed: 12754495] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.95 ANGSTROMS) IN COMPLEX WITH TRNA(TYR) AND TYROSINE, MUTAGENESIS OF ASP-286, SUBUNIT.
[5]	"Crystal structures of apo wild-type M. jannaschii tyrosyl-tRNA synthetase (TyrRS) and an engineered TyrRS specific for O-methyl-L-tyrosine." Zhang Y., Wang L., Schultz P.G., Wilson I.A. Protein Sci. 14:1340-1349(2005) [PubMed: 15840835] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.66 ANGSTROMS) OF WILD-TYPE AND O-METHYL-TYROSINE-SPECIFIC MUTANT APOENZYME.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBLGenBankDDBJ

L77117 Genomic DNA. Translation: AAB98375.1.

PIR

E64348.

RefSeq

NP_247363.1.

3D structure databases

PDBPDBe

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1J1U	X-ray	1.95	A	1-306	[»]
1U7D	X-ray	2.65	A/B	1-306	[»]
1U7X	X-ray	3.00	A/B	1-306	[»]
1ZH0	X-ray	1.90	A	1-306	[»]
1ZH6	X-ray	2.50	A	1-306	[»]
2AG6	X-ray	1.90	A	1-306	[»]
2HGZ	X-ray	2.50	A	2-306	[»]
2PXH	X-ray	1.97	A	1-306	[»]
2ZP1	X-ray	1.70	A	1-306	[»]
3D6U	X-ray	2.20	A	1-306	[»]
3D6V	X-ray	2.20	A	1-306	[»]

ModBase

Search...

Genome annotation databases

GeneID

1451246.

GenomeReviews

Gene locus MJ0389 in contig L77117_GR.

KEGG

mja:MJ0389.

NMPDR

fig|243232.1.peg.400.

TIGR

MJ0389.

Phylogenomic databases

HOGENOM

Q57834.

OMA

GMEQRKI.

Enzyme and pathway databases

BioCyc

MJAN243232:MJ_0389-MON.

Family and domain databases

HAMAP

MF_02008.
[Tree]

InterPro

IPR001412. aa-tRNA-synth_I_CS.
IPR002305. aa-tRNA-synth_Ib.
IPR014729. Rossmann-like_a/b/a_fold.
IPR015624. Tyr-tRNA-synth_Ib_arc/euk.
IPR002307. Tyr-tRNA-synth_Ib_bac/mito.
IPR016485. TyrRS_arch_euk.
[Graphical view]

Gene3D

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

PANTHER

PTHR11946:SF8. Tyr-tRNA_synth. 1 hit.

Pfam

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

PIRSF

PIRSF006588. TyrRS_arch_euk. 1 hit.

PRINTS

PR01040. TRNASYNTHTYR.

TIGRFAMs

TIGR00234. tyrS. 1 hit.

PROSITE

PS00178. AA_TRNA_LIGASE_I. 1 hit.
[Graphical view]

ProtoNet

Search...

Entry information

Entry name

SYY_METJA

Accession

Primary (citable) accession number: Q57834

Entry history

Integrated into UniProtKB/Swiss-Prot:	November 1, 1997
Last sequence update:	November 1, 1997
Last modified:	November 3, 2009
This is version 66 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)