Reviewed, UniProtKB/Swiss-Prot Q5SM28 (SYP_THET8)

Names and origin

Protein names

Recommended name:
    Prolyl-tRNA synthetase
    EC=6.1.1.15
Alternative name(s):
    Proline--tRNA ligase
      Short name=ProRS

Gene names

Name:	proS
Ordered Locus Names:	TTHA0115

Organism

Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) [Complete proteome] [HAMAP]

Taxonomic identifier

300852 [NCBI]

Taxonomic lineage

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

Protein attributes

Sequence length	477 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 proline to tRNA(Pro) in a two-step reaction: proline is first activated by ATP to form Pro-AMP and then transferred to the acceptor end of tRNA(Pro). Can inadvertently accommodate and process cysteine. HAMAP MF_01571
Catalytic activity	ATP + L-proline + tRNA(Pro) = AMP + diphosphate + L-prolyl-tRNA(Pro). HAMAP MF_01571
Subunit structure	Homodimer. Only one tRNA molecule binds per dimer. Ref.5 Ref.6
Subcellular location	Cytoplasm.
Domain	Consists of three domains: the N-terminal catalytic domain, the anticodon-binding domain and the C-terminal extension. The C-terminal extension binds a zinc ion, which probably plays a non-essential structural role in stabilizing the fold of C-terminal domain. HAMAP MF_01571
Sequence similarities	Belongs to the class-II aminoacyl-tRNA synthetase family. ProS type 3 subfamily.
Biophysicochemical properties	Kinetic parameters: KM=0.15 mM for proline (at 60 degrees Celsius) Ref.4 KM=0.02 mM for cysteine (at 60 degrees Celsius)

Ontologies

Keywords
Biological process	Protein biosynthesis
Cellular component	Cytoplasm
Ligand	ATP-binding Metal-binding Nucleotide-binding Zinc
Molecular function	Aminoacyl-tRNA synthetase Ligase
Technical term	3D-structure Complete proteome
Gene Ontology (GO)
Biological process	prolyl-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 proline-tRNA ligase activity Inferred from electronic annotation. Source: HAMAP zinc ion binding Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 477

477

Prolyl-tRNA synthetase HAMAP MF_01571

PRO_0000248229

Regions

Region

340 – 369

30

Interaction with tRNA HAMAP MF_01571

Sites

Metal binding

427

1

Zinc; structural HAMAP MF_01571

Metal binding

432

1

Zinc; structural HAMAP MF_01571

Metal binding

458

1

Zinc; structural HAMAP MF_01571

Metal binding

461

1

Zinc; structural HAMAP MF_01571

Binding site

111

1

Proline HAMAP MF_01571

Binding site

113

1

Proline HAMAP MF_01571

Binding site

142

1

ATP HAMAP MF_01571

Binding site

142

1

Proline HAMAP MF_01571

Binding site

153

1

ATP HAMAP MF_01571

Binding site

225

1

ATP HAMAP MF_01571

Binding site

228

1

ATP HAMAP MF_01571

Binding site

230

1

Proline HAMAP MF_01571

Binding site

262

1

ATP HAMAP MF_01571

Binding site

264

1

ATP HAMAP MF_01571

Experimental info

Mutagenesis

477

1

Y → A: Slightly reduces the aminoacylation activity. Ref.5

Mutagenesis

477

1

Y → F: Little change in the aminoacylation activity. Ref.5

Secondary structure

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477

Helix Strand Turn

Details...

Helix

10 – 24

15

Beta strand

27 – 30

4

Beta strand

37 – 39

3

Helix

41 – 60

20

Beta strand

70 – 74

5

Beta strand

92 – 108

17

Helix

113 – 123

11

Helix

127 – 129

3

Beta strand

132 – 141

10

Turn

149 – 151

3

Beta strand

154 – 167

14

Helix

168 – 190

23

Beta strand

195 – 198

4

Turn

201 – 203

3

Beta strand

208 – 217

10

Beta strand

223 – 233

11

Helix

235 – 239

5

Beta strand

243 – 245

3

Beta strand

251 – 253

3

Beta strand

255 – 262

8

Helix

264 – 273

10

Turn

283 – 285

3

Beta strand

289 – 294

6

Turn

298 – 300

3

Helix

301 – 317

17

Beta strand

322 – 324

3

Beta strand

328 – 330

3

Helix

332 – 341

10

Beta strand

345 – 350

6

Helix

352 – 356

5

Beta strand

359 – 364

6

Beta strand

371 – 373

3

Helix

374 – 376

3

Helix

377 – 402

26

Beta strand

404 – 406

3

Helix

410 – 416

7

Turn

417 – 419

3

Beta strand

420 – 424

5

Helix

430 – 440

11

Beta strand

443 – 451

9

Turn

459 – 461

3

Beta strand

471 – 474

4

Sequences

	Sequence		Length	Mass (Da)
	Q5SM28-1 [UniParc]. Last modified December 21, 2004. Version 1. Checksum: 6AA477F1EC4D12F5	FASTA	477	54,488
	10 20 30 40 50 60 MAKEKGLTPQ SQDFSEWYLE VIQKAELADY GPVRGTIVVR PYGYAIWENI QQVLDRMFKE 70 80 90 100 110 120 TGHQNAYFPL FIPMSFLRKE AEHVEGFSPE LAVVTHAGGE ELEEPLAVRP TSETVIGYMW 130 140 150 160 170 180 SKWIRSWRDL PQLLNQWGNV VRWEMRTRPF LRTSEFLWQE GHTAHATREE AEEEVRRMLS 190 200 210 220 230 240 IYARLAREYA AIPVIEGLKT EKEKFAGAVY TTTIEALMKD GKALQAGTSH YLGENFARAF 250 260 270 280 290 300 DIKFQDRDLQ VKYVHTTSWG LSWRFIGAII MTHGDDRGLV LPPRLAPIQV VIVPIYKDES 310 320 330 340 350 360 RERVLEAAQG LRQALLAQGL RVHLDDRDQH TPGYKFHEWE LKGVPFRVEL GPKDLEGGQA 370 380 390 400 410 420 VLASRLGGKE TLPLAALPEA LPGKLDAFHE ELYRRALAFR EDHTRKVDTY EAFKEAVQEG 430 440 450 460 470 FALAFHCGDK ACERLIQEET TATTRCVPFE AEPEEGFCVR CGRPSAYGKR VVFAKAY

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Aminoacyl-tRNA formation in the hyperthermophile Thermus thermophilus." Ahel I., Stathopoulos C., Hartsch T., Soell D. Submitted (MAY-2001) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]	"Complete genome sequence of Thermus thermophilus HB8." Masui R., Kurokawa K., Nakagawa N., Tokunaga F., Koyama Y., Shibata T., Oshima T., Yokoyama S., Yasunaga T., Kuramitsu S. Submitted (NOV-2004) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[3]	"Aminoacyl-tRNA formation in the extreme thermophile Thermus thermophilus." Feng L., Stathopoulos C., Ahel I., Mitra A., Tumbula-Hansen D., Hartsch T., Soell D. Extremophiles 6:167-174(2002) [PubMed: 12013438] [Abstract] Cited for: PROLINE AND CYSTEINE ACTIVATION.
[4]	"Cysteine activation is an inherent in vitro property of prolyl-tRNA synthetases." Ahel I., Stathopoulos C., Ambrogelly A., Sauerwald A., Toogood H., Hartsch T., Soell D. J. Biol. Chem. 277:34743-34748(2002) [PubMed: 12130657] [Abstract] Cited for: PROLINE AND CYSTEINE ACTIVATION, KINETIC PARAMETERS.
[5]	"Crystal structure of a eukaryote/archaeon-like prolyl-tRNA synthetase and its complex with tRNAPro(CGG)." Yaremchuk A., Cusack S., Tukalo M. EMBO J. 19:4745-4758(2000) [PubMed: 10970866] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.43 ANGSTROMS) OF APOENZYME AND IN COMPLEX WITH ZINC IONS AND TRNA, MUTAGENESIS OF TYR-477, SUBUNIT.
[6]	"A succession of substrate induced conformational changes ensures the amino acid specificity of Thermus thermophilus prolyl-tRNA synthetase: comparison with histidyl-tRNA synthetase." Yaremchuk A., Tukalo M., Groetli M., Cusack S. J. Mol. Biol. 309:989-1002(2001) [PubMed: 11399074] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.85 ANGSTROMS) IN COMPLEX WITH PROLINE; ZINC IONS, TRNA AND PRO-AMP ANALOGS, SUBUNIT.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBLGenBankDDBJ

AF384553 Genomic DNA. Translation: AAK62359.1.
AP008226 Genomic DNA. Translation: BAD69938.1.

RefSeq

YP_143381.1.

3D structure databases

PDBPDBe

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1H4Q	X-ray	3.00	A/B	1-477	[»]
1H4S	X-ray	2.85	A/B	1-477	[»]
1H4T	X-ray	2.90	A/B/C/D	1-477	[»]
1HC7	X-ray	2.43	A/B/C/D	1-477	[»]

ModBase

Search...

Protein-protein interaction databases

STRING

Q5SM28.

Genome annotation databases

GeneID

3169620.

GenomeReviews

Gene locus TTHA0115 in contig AP008226_GR.

KEGG

ttj:TTHA0115.

NMPDR

fig|300852.3.peg.146.

Organism-specific databases

CMR

Search...

Phylogenomic databases

HOGENOM

Q5SM28.

OMA

LIMVHSD

Enzyme and pathway databases

BioCyc

TTHE300852:TTHA0115-MON.

Family and domain databases

HAMAP

MF_01571.
[Tree]

InterPro

IPR002314. aa-tRNA-synt_IIb_cons-reg.
IPR006195. aa-tRNA-synth_II_cons-reg.
IPR004154. Anticodon_bd.
IPR002316. Pro-tRNA-synth_IIa_cons-reg.
IPR004499. Pro-tRNA-synth_IIa_pro-type.
IPR017449. Pro-tRNA_synth_II.
IPR016061. Pro-tRNA_synth_II_C.
[Graphical view]

Gene3D

G3DSA:3.40.50.800. Anticodon_bd. 1 hit.
G3DSA:3.30.110.30. Pro-tRNA-synth_II_C_arc/euk. 1 hit.

PANTHER

PTHR11451:SF6. ProS_fam_I. 1 hit.

Pfam

PF03129. HGTP_anticodon. 1 hit.
PF09180. ProRS-C_1. 1 hit.
PF00587. tRNA-synt_2b. 1 hit.
[Graphical view]

PRINTS

PR01046. TRNASYNTHPRO.

TIGRFAMs

TIGR00408. proS_fam_I. 1 hit.

PROSITE

PS50862. AA_TRNA_LIGASE_II. 1 hit.
[Graphical view]

ProtoNet

Search...

Entry information

Entry name

SYP_THET8

Accession

Primary (citable) accession number: Q5SM28
Secondary accession number(s): Q93N97

Entry history

Integrated into UniProtKB/Swiss-Prot:	September 5, 2006
Last sequence update:	December 21, 2004
Last modified:	November 24, 2009
This is version 46 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)