P34945 (SYS_THET2) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Seryl-tRNA synthetase
EC=6.1.1.11

Alternative name(s):
Seryl-tRNA(Ser/Sec) synthetase
Serine--tRNA ligase
Short name=SerRS

Gene names

Name:	serS
Ordered Locus Names:	TT_C0520

Organism

Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039) [Complete proteome] [HAMAP]

Taxonomic identifier

262724 [NCBI]

Taxonomic lineage

Bacteria › Deinococcus-Thermus › Deinococci › Thermales › Thermaceae › Thermus

Protein attributes

Sequence length	421 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level.

General annotation (Comments)

Function	Catalyzes the attachment of serine to tRNA(Ser). Is also probably able to aminoacylate tRNA(Sec) with serine, to form the misacylated tRNA L-seryl-tRNA(Sec), which will be further converted into selenocysteinyl-tRNA(Sec). HAMAP MF_00176
Catalytic activity	ATP + L-serine + tRNA(Ser) = AMP + diphosphate + L-seryl-tRNA(Ser). HAMAP MF_00176 ATP + L-serine + tRNA(Sec) = AMP + diphosphate + L-seryl-tRNA(Sec). HAMAP MF_00176
Pathway	Aminoacyl-tRNA biosynthesis; selenocysteinyl-tRNA(Sec) biosynthesis; L-seryl-tRNA(Sec) from L-serine and tRNA(Sec): step 1/1. HAMAP MF_00176
Subunit structure	Homodimer. A single tRNA molecule binds across the dimer. Ref.2 Ref.4 Ref.5
Subcellular location	Cytoplasm By similarity HAMAP MF_00176.
Domain	Consists of two distinct domains, a catalytic core and a N-terminal extension that is involved in tRNA binding. HAMAP MF_00176
Sequence similarities	Belongs to the class-II aminoacyl-tRNA synthetase family. Type-1 seryl-tRNA synthetase subfamily.

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	seryl-tRNA aminoacylation Inferred from electronic annotation. Source: InterPro
Cellular component	cytoplasm Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular function	ATP binding Inferred from electronic annotation. Source: UniProtKB-KW serine-tRNA ligase activity Inferred from electronic annotation. Source: EC
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 421

421

Seryl-tRNA synthetase HAMAP MF_00176

PRO_0000122145

Regions

Nucleotide binding

256 – 258

3

ATP HAMAP MF_00176

Nucleotide binding

345 – 348

4

ATP HAMAP MF_00176

Region

225 – 227

3

Serine binding HAMAP MF_00176

Sites

Binding site

272

1

ATP; via amide nitrogen and carbonyl oxygen

Binding site

279

1

Serine

Binding site

380

1

Serine

Secondary structure

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421

Helix Strand Turn

Details...

Helix

4 – 9

6

Helix

11 – 21

11

Helix

27 – 36

10

Helix

90 – 98

9

Helix

114 – 116

3

Beta strand

118 – 124

7

Helix

136 – 143

8

Helix

150 – 154

5

Helix

164 – 182

19

Beta strand

186 – 189

4

Beta strand

192 – 195

4

Helix

196 – 201

6

Turn

205 – 208

4

Helix

209 – 211

3

Beta strand

218 – 222

5

Helix

227 – 232

6

Turn

233 – 236

4

Beta strand

238 – 240

3

Helix

241 – 243

3

Beta strand

245 – 255

11

Turn

265 – 270

6

Beta strand

273 – 284

12

Helix

288 – 309

22

Beta strand

313 – 317

5

Turn

320 – 322

3

Beta strand

328 – 337

10

Turn

338 – 341

4

Beta strand

342 – 351

10

Turn

353 – 356

4

Helix

357 – 360

4

Beta strand

363 – 365

3

Beta strand

371 – 373

3

Beta strand

375 – 384

10

Helix

386 – 394

9

Helix

406 – 408

3

Helix

409 – 412

4

Beta strand

415 – 417

3

Sequences

	Sequence		Length	Mass (Da)
	P34945-1 [UniParc]. Last modified May 24, 2004. Version 2. Checksum: 5E89B0D131EFC209	FASTA	421	47,813
	10 20 30 40 50 60 MVDLKRLRQE PEVFHRAIRE KGVALDLEAL LALDREVQEL KKRLQEVQTE RNQVAKRVPK 70 80 90 100 110 120 APPEEKEALI ARGKALGEEA KRLEEALREK EARLEALLLQ VPLPPWPGAP VGGEEANREI 130 140 150 160 170 180 KRVGGPPEFS FPPLDHVALM EKNGWWEPRI SQVSGSRSYA LKGDLALYEL ALLRFAMDFM 190 200 210 220 230 240 ARRGFLPMTL PSYAREKAFL GTGHFPAYRD QVWAIAETDL YLTGTAEVVL NALHSGEILP 250 260 270 280 290 300 YEALPLRYAG YAPAFRSEAG SFGKDVRGLM RVHQFHKVEQ YVLTEASLEA SDRAFQELLE 310 320 330 340 350 360 NAEEILRLLE LPYRLVEVAT GDMGPGKWRQ VDIEVYLPSE GRYRETHSCS ALLDWQARRA 370 380 390 400 410 420 NLRYRDPEGR VRYAYTLNNT ALATPRILAM LLENHQLQDG RVRVPQALIP YMGKEVLEPC G

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"The genome sequence of the extreme thermophile Thermus thermophilus." Henne A., Brueggemann H., Raasch C., Wiezer A., Hartsch T., Liesegang H., Johann A., Lienard T., Gohl O., Martinez-Arias R., Jacobi C., Starkuviene V., Schlenczeck S., Dencker S., Huber R., Klenk H.-P., Kramer W., Merkl R., Gottschalk G., Fritz H.-J. Nat. Biotechnol. 22:547-553(2004) [PubMed: 15064768] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[2]	"Refined crystal structure of the seryl-tRNA synthetase from Thermus thermophilus at 2.5-A resolution." Fujinaga M., Berthet-Colominas C., Yaremchuk A.D., Tukalo M.A., Cusack S. J. Mol. Biol. 234:222-233(1993) [PubMed: 8230201] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS), SUBUNIT.
[3]	"Crystal structures at 2.5 angstrom resolution of seryl-tRNA synthetase complexed with two analogs of seryl adenylate." Belrhali H., Yaremchuk A.D., Tukalo M.A., Larsen K., Berthet-Colominas C., Leberman R., Beijer B., Sproat B., Als-Nielsen J., Gruebel G., Legrand J.-F., Lehmann M., Cusack S. Science 263:1432-1436(1994) [PubMed: 8128224] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS) IN COMPLEXES WITH SUBSTRATE ANALOGS.
[4]	"The 2.9 A crystal structure of T. thermophilus seryl-tRNA synthetase complexed with tRNA(Ser)." Biou V., Yaremchuk A.D., Tukalo M.A., Cusack S. Science 263:1404-1410(1994) [PubMed: 8128220] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.9 ANGSTROMS) IN COMPLEX WITH TRNA(SER), SUBUNIT.
[5]	"The crystal structure of the ternary complex of T.thermophilus seryl-tRNA synthetase with tRNA(Ser) and a seryl-adenylate analogue reveals a conformational switch in the active site." Cusack S., Yaremchuk A.D., Tukalo M.A. EMBO J. 15:2834-2842(1996) [PubMed: 8654381] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.7 ANGSTROMS) IN COMPLEX WITH TRNA(SER) AND SUBSTRATE ANALOG, SUBUNIT.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

AE017221 Genomic DNA. Translation: AAS80868.1.

RefSeq

YP_004495.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1SER	X-ray	2.90	A/B	1-421	[»]
1SES	X-ray	2.50	A/B	1-421	[»]
1SET	X-ray	2.55	A/B	1-421	[»]
1SRY	X-ray	2.50	A/B	1-421	[»]
3ERR	X-ray	2.27	A/B	1-419	[»]

ProteinModelPortal

P34945.

DisProt

DP00514.

ModBase

Search...

Protein-protein interaction databases

STRING

P34945.

Genome annotation databases

GeneID

2775083.

GenomeReviews

Gene locus TT_C0520 in contig AE017221_GR.

Organism-specific databases

CMR

Search...

Phylogenomic databases

eggNOG

COG0172.

HOGENOM

HBG629391.

OMA

NLRYRDP.

ProtClustDB

PRK05431.

Enzyme and pathway databases

BioCyc

TTHE262724:TT_C0520-MONOMER.

Family and domain databases

HAMAP

MF_00176. Ser_tRNA_synth_type1.
[Tree]

InterPro

IPR002314. aa-tRNA-synt_IIb_cons-dom.
IPR006195. aa-tRNA-synth_II_cons-dom.
IPR002317. Ser-tRNA-synth_IIa.
IPR018156. Ser-tRNA-synth_IIa_C.
IPR015866. Ser-tRNA-synth_IIa_N.
IPR010978. tRNA-bd_arm.
[Graphical view]

Gene3D

G3DSA:1.10.287.40. Ser-tRNA-synth_IIa_N. 1 hit.

PANTHER

PTHR11778. tRNA-synt_ser. 1 hit.

Pfam

PF02403. Seryl_tRNA_N. 1 hit.
PF00587. tRNA-synt_2b. 1 hit.
[Graphical view]

PIRSF

PIRSF001529. Ser-tRNA-synth_IIa. 1 hit.

PRINTS

PR00981. TRNASYNTHSER.

SUPFAM

SSF46589. tRNA_binding_arm. 1 hit.

TIGRFAMs

TIGR00414. serS. 1 hit.

PROSITE

PS50862. AA_TRNA_LIGASE_II. 1 hit.
[Graphical view]

ProtoNet

Search...

Other Resources

DrugBank

DB00131. Adenosine monophosphate.

Entry information

Entry name

SYS_THET2

Accession

Primary (citable) accession number: P34945

Entry history

Integrated into UniProtKB/Swiss-Prot:	February 1, 1994
Last sequence update:	May 24, 2004
Last modified:	August 10, 2010
This is version 83 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)