Reviewed, UniProtKB/Swiss-Prot O26708 (SYP_METTH)

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:	MTH_611

Organism

Methanobacterium thermoautotrophicum [Complete proteome] [HAMAP]

Taxonomic identifier

187420 [NCBI]

Taxonomic lineage

Archaea › Euryarchaeota › Methanobacteria › Methanobacteriales › Methanobacteriaceae › Methanothermobacter

Protein attributes

Sequence length	482 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. The dimer is functionally asymmetric: only one of the two active sites at a time is able to form prolyl-adenylate, and only one tRNA molecule binds per dimer. Interacts with LeuRS, which enhances tRNA(Pro) aminoacylation. Ref.4 Ref.3 Ref.5
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=0.26 mM for proline (at 60 degrees Celsius) Ref.2 Ref.4 KM=0.05 mM for cysteine (at 60 degrees Celsius) KM=4.1 µM for tRNA(Pro) (at 50 degrees Celsius) KM=2.2 µM for tRNA(Pro) (at 50 degrees Celsius in the presence of LeuRS)

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 – 482

482

Prolyl-tRNA synthetase HAMAP MF_01571

PRO_0000139352

Regions

Region

346 – 376

31

Interaction with tRNA By similarity

Sites

Metal binding

436

1

Zinc; structural HAMAP MF_01571

Metal binding

441

1

Zinc; structural HAMAP MF_01571

Metal binding

464

1

Zinc; structural HAMAP MF_01571

Metal binding

467

1

Zinc; structural HAMAP MF_01571

Binding site

117

1

Proline HAMAP MF_01571

Binding site

119

1

Proline HAMAP MF_01571

Binding site

148

1

ATP HAMAP MF_01571

Binding site

148

1

Proline HAMAP MF_01571

Binding site

150

1

ATP HAMAP MF_01571

Binding site

232

1

ATP HAMAP MF_01571

Binding site

235

1

ATP HAMAP MF_01571

Binding site

237

1

Proline HAMAP MF_01571

Binding site

269

1

ATP HAMAP MF_01571

Secondary structure

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482

Helix Strand Turn

Details...

Helix

20 – 30

11

Helix

48 – 65

18

Turn

66 – 68

3

Beta strand

76 – 79

4

Helix

80 – 83

4

Helix

87 – 92

6

Turn

93 – 96

4

Beta strand

98 – 103

6

Beta strand

106 – 114

9

Beta strand

116 – 118

3

Helix

119 – 129

11

Turn

133 – 135

3

Beta strand

138 – 147

10

Turn

156 – 158

3

Beta strand

161 – 175

15

Helix

176 – 196

21

Beta strand

202 – 205

4

Turn

208 – 210

3

Beta strand

216 – 224

9

Beta strand

230 – 240

11

Helix

242 – 247

6

Beta strand

250 – 252

3

Beta strand

258 – 260

3

Beta strand

262 – 268

7

Helix

271 – 279

9

Beta strand

283 – 287

5

Turn

290 – 292

3

Beta strand

296 – 301

6

Beta strand

304 – 307

4

Helix

308 – 323

16

Turn

324 – 326

3

Beta strand

329 – 331

3

Helix

338 – 347

10

Beta strand

351 – 356

6

Helix

358 – 361

4

Turn

362 – 364

3

Beta strand

365 – 373

9

Beta strand

376 – 380

5

Turn

381 – 383

3

Helix

384 – 408

25

Beta strand

411 – 413

3

Helix

417 – 427

11

Beta strand

429 – 435

7

Helix

439 – 449

11

Beta strand

452 – 458

7

Turn

465 – 467

3

Sequences

	Sequence		Length	Mass (Da)
	O26708-1 [UniParc]. Last modified January 1, 1998. Version 1. Checksum: 57D81ED7E9496BAA	FASTA	482	55,806
	10 20 30 40 50 60 MQKPIKKDPN RYHGEKMTEF SEWFHNILEE AEIIDQRYPV KGMHVWMPHG FMIRKNTLKI 70 80 90 100 110 120 LRRILDRDHE EVLFPLLVPE DELAKEAIHV KGFEDEVYWV THGGLSKLQR KLALRPTSET 130 140 150 160 170 180 VMYPMFALWV RSHTDLPMRF YQVVNTFRYE TKHTRPLIRV REITTFKEAH TIHATASEAE 190 200 210 220 230 240 EQVERAVEIY KEFFNSLGIP YLITRRPPWD KFPGSEYTVA FDTLMPDGKT LQIGTVHNLG 250 260 270 280 290 300 QTFARTFEIK FETPEGDHEY VHQTCYGLSD RVIASVIAIH GDESGLCLPP DVAAHQVVIV 310 320 330 340 350 360 PIIFKKAAEE VMEACRELRS RLEAAGFRVH LDDRDIRAGR KYYEWEMRGV PLRVEIGPRD 370 380 390 400 410 420 LEKGAAVISR RDTGEKVTAD LQGIEETLRE LMKDILENLR TRAWERMESE IREAETLEEA 430 440 450 460 470 480 SRIVDEKRGI ISFMWCGEEE CGMDVEEKVR VDILGIQEEG SGTCINCGRE APTGLTLPEH IS

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Complete genome sequence of Methanobacterium thermoautotrophicum deltaH: functional analysis and comparative genomics." Smith D.R., Doucette-Stamm L.A., Deloughery C., Lee H.-M., Dubois J., Aldredge T., Bashirzadeh R., Blakely D., Cook R., Gilbert K., Harrison D., Hoang L., Keagle P., Lumm W., Pothier B., Qiu D., Spadafora R., Vicare R. , Wang Y., Wierzbowski J., Gibson R., Jiwani N., Caruso A., Bush D., Safer H., Patwell D., Prabhakar S., McDougall S., Shimer G., Goyal A., Pietrovski S., Church G.M., Daniels C.J., Mao J.-I., Rice P., Noelling J., Reeve J.N. J. Bacteriol. 179:7135-7155(1997) [PubMed: 9371463] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: Delta H.
[2]	"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.
[3]	"Asymmetric behavior of archaeal prolyl-tRNA synthetase." Ambrogelly A., Kamtekar S., Stathopoulos C., Kennedy D., Soell D. FEBS Lett. 579:6017-6022(2005) [PubMed: 16226256] [Abstract] Cited for: SUBUNIT.
[4]	"Association between Archaeal prolyl- and leucyl-tRNA synthetases enhances tRNA(Pro) aminoacylation." Praetorius-Ibba M., Rogers T.E., Samson R., Kelman Z., Ibba M. J. Biol. Chem. 280:26099-26104(2005) [PubMed: 15917221] [Abstract] Cited for: INTERACTION WITH LEURS, KINETIC PARAMETERS.
[5]	"The structural basis of cysteine aminoacylation of tRNAPro by prolyl-tRNA synthetases." Kamtekar S., Kennedy W.D., Wang J., Stathopoulos C., Soell D., Steitz T.A. Proc. Natl. Acad. Sci. U.S.A. 100:1673-1678(2003) [PubMed: 12578991] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.55 ANGSTROMS) OF APOENZYME AND IN COMPLEX WITH AMINOACYL-ADENYLATE ANALOGS AND ZINC IONS, SUBUNIT.

Cross-references

Sequence databases

EMBLGenBankDDBJ

AE000666 Genomic DNA. Translation: AAB85117.1.

PIR

C69181.

RefSeq

NP_275754.1.

3D structure databases

PDBPDBe

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1NJ1	X-ray	2.55	A	1-472	[»]
1NJ2	X-ray	3.11	A	1-472	[»]
1NJ5	X-ray	2.80	A	1-472	[»]
1NJ6	X-ray	2.85	A	1-472	[»]

ModBase

Search...

Protein-protein interaction databases

STRING

O26708.

Genome annotation databases

GeneID

1470572.

GenomeReviews

Gene locus MTH_611 in contig AE000666_GR.

KEGG

mth:MTH611.

NMPDR

fig|187420.1.peg.609.

Organism-specific databases

CMR

Search...

Phylogenomic databases

HOGENOM

O26708.

OMA

LIMVHSD

Enzyme and pathway databases

BioCyc

MTHE187420:MTH611-MON.

BRENDA

6.1.1.15. 270.

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_METTH

Accession

Primary (citable) accession number: O26708

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 15, 1998
Last sequence update:	January 1, 1998
Last modified:	November 24, 2009
This is version 80 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)