Reviewed, UniProtKB/Swiss-Prot Q46AN5 (SYS2_METBF)

Names and origin

Protein names

Recommended name:
    Type-2 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:	serS2
Ordered Locus Names:	Mbar_A2126

Organism

Methanosarcina barkeri (strain Fusaro / DSM 804) [Complete proteome] [HAMAP]

Taxonomic identifier

269797 [NCBI]

Taxonomic lineage

Archaea › Euryarchaeota › Methanomicrobia › Methanosarcinales › Methanosarcinaceae › Methanosarcina

Protein attributes

Sequence length	502 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 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). Ref.2
Catalytic activity	ATP + L-serine + tRNA(Ser) = AMP + diphosphate + L-seryl-tRNA(Ser). HAMAP MF_01278 ATP + L-serine + tRNA(Sec) = AMP + diphosphate + L-seryl-tRNA(Sec). HAMAP MF_01278
Cofactor	Binds 1 Zn2+ ion per subunit. This ion is coordinated with 2 cysteines, 1 glutamate and a water molecule that dissociates from the zinc ion to allow the coordination of the amino group of the serine substrate, which is essential for catalysis. Ref.4 Binds 2 magnesium ions per subunit. One ion coordinates the alpha and beta phosphates of ATP, and the other coordinates the beta and gamma phosphates. Ref.4
Enzyme regulation	Inhibited by serinamide, unlike type-1 M.barkeri SerRS. Ref.3
Pathway	Aminoacyl-tRNA biosynthesis; selenocysteinyl-tRNA(Sec) biosynthesis; L-seryl-tRNA(Sec) from L-serine and tRNA(Sec): step 1/1. HAMAP MF_01278
Subunit structure	Homodimer. Ref.4
Subcellular location	Cytoplasm By similarity.
Domain	Consists of two distinct domains, a catalytic core and a N-terminal extension that is presumably involved in tRNA binding. HAMAP MF_01278
Sequence similarities	Belongs to the class-II aminoacyl-tRNA synthetase family. Type-2 seryl-tRNA synthetase subfamily.
Biophysicochemical properties	Kinetic parameters: Catalytic efficiency is similar with the tRNA(Ser CGA) and tRNA(Ser GGA) isoacceptors, but is 5-fold lower with tRNA(Ser GCU). KM=25 µM for L-serine Ref.2 KM=13.6 µM for ATP KM=3 µM for tRNA(Ser CGA) KM=4.7 µM for tRNA(Ser GGA) KM=5.3 µM for tRNA(Ser GCU)

Ontologies

Keywords
Biological process	Protein biosynthesis
Cellular component	Cytoplasm
Ligand	ATP-binding Magnesium Metal-binding Nucleotide-binding Zinc
Molecular function	Aminoacyl-tRNA synthetase Ligase
Technical term	3D-structure Complete proteome
Gene Ontology (GO)
Biological process	selenocysteine biosynthetic process Inferred from electronic annotation. Source: HAMAP seryl-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 magnesium ion binding Inferred from electronic annotation. Source: UniProtKB-KW serine-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 – 502

502

Type-2 seryl-tRNA synthetase HAMAP MF_01278

PRO_0000285289

Regions

Nucleotide binding

336 – 338

3

ATP HAMAP MF_01278

Nucleotide binding

347 – 348

2

ATP HAMAP MF_01278

Region

353 – 355

3

Serine binding HAMAP MF_01278

Sites

Metal binding

306

1

Zinc; catalytic HAMAP MF_01278

Metal binding

336

1

Magnesium 1 HAMAP MF_01278

Metal binding

338

1

Magnesium 1 HAMAP MF_01278

Metal binding

355

1

Zinc; catalytic HAMAP MF_01278

Metal binding

416

1

Magnesium 2 HAMAP MF_01278

Metal binding

432

1

Magnesium 2 HAMAP MF_01278

Metal binding

435

1

Magnesium 2 HAMAP MF_01278

Metal binding

461

1

Zinc; catalytic HAMAP MF_01278

Binding site

304

1

Serine; via carbonyl oxygen HAMAP MF_01278

Binding site

336

1

Serine HAMAP MF_01278

Binding site

400

1

Serine HAMAP MF_01278

Binding site

432

1

ATP HAMAP MF_01278

Binding site

435

1

Serine HAMAP MF_01278

Binding site

468

1

ATP HAMAP MF_01278

Experimental info

Mutagenesis

306

1

C → A: Loss of activity. Ref.4

Mutagenesis

355

1

E → A: Loss of activity. Ref.4

Mutagenesis

461

1

C → A: Loss of activity. Ref.4

Secondary structure

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502

Helix Strand Turn

Details...

Beta strand

4 – 10

7

Helix

25 – 28

4

Turn

29 – 36

8

Beta strand

40 – 43

4

Beta strand

45 – 47

3

Beta strand

66 – 68

3

Turn

70 – 72

3

Helix

76 – 80

5

Beta strand

97 – 106

10

Beta strand

119 – 124

6

Beta strand

126 – 133

8

Helix

137 – 141

5

Helix

144 – 158

15

Beta strand

168 – 173

6

Helix

185 – 191

7

Beta strand

194 – 197

4

Beta strand

204 – 206

3

Helix

208 – 224

17

Turn

225 – 230

6

Beta strand

238 – 241

4

Helix

242 – 248

7

Helix

250 – 252

3

Helix

255 – 257

3

Beta strand

260 – 262

3

Helix

269 – 282

14

Helix

287 – 293

7

Beta strand

299 – 301

3

Beta strand

303 – 306

4

Helix

307 – 312

6

Turn

313 – 315

3

Helix

320 – 322

3

Beta strand

324 – 329

6

Beta strand

331 – 335

5

Beta strand

349 – 360

12

Helix

362 – 382

21

Beta strand

388 – 394

7

Helix

396 – 400

5

Beta strand

408 – 411

4

Beta strand

413 – 419

7

Helix

422 – 424

3

Beta strand

431 – 440

10

Helix

442 – 447

6

Beta strand

458 – 465

8

Helix

466 – 477

12

Turn

481 – 483

3

Helix

486 – 492

7

Sequences

	Sequence		Length	Mass (Da)
	Q46AN5-1 [UniParc]. Last modified September 13, 2005. Version 1. Checksum: C1A6D21716C69A5A	FASTA	502	57,828
	10 20 30 40 50 60 MKLQFNLKAY FKTSADPTPA KDAIAALFEE ANSTLLTRGA PEGQGAKVTE WKLGEDRIEL 70 80 90 100 110 120 TLQSGRYVRV HDAIFRLRKQ LAEALGKKYK IGIRGIEVES FIIKVPADHE LRMLKVPYIK 130 140 150 160 170 180 SMENIEGGIQ LELEVGEAEM KNRVPDRILT LLEEKIEAAQ YGAKAEHWNL LWQREPMEHP 190 200 210 220 230 240 FKEDPTQAMM KEGWLKRGSS RGQWIHGPQS ARIFRTFEKI VLEELLEPLG YREMIFPKLV 250 260 270 280 290 300 TWEVWMKSGH AKGVYPEIYY VCPPQTRDPD YWEEVADYYK VTHEVPTKLI KEKIAEPIGG 310 320 330 340 350 360 MCYAQCPPFW MYVAGETLPN EEIPVKVFDR SGTSHRYESG GIHGIERVDE FHRIEIVWIG 370 380 390 400 410 420 TKEEVLKCAE ELHDRYMHIF NDILDIEWRK ARVTPWFMAQ EGLLGLAEEN TVGTTDYEAC 430 440 450 460 470 480 LPYRGPDGEW LEFQNVSING DKYPKGFNVK LQSGDELWSG CSGVGLERWA AVFLAQKGLD 490 500 PANWPEEFRN RVGEMPKGIR FL

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"The Methanosarcina barkeri genome: comparative analysis with Methanosarcina acetivorans and Methanosarcina mazei reveals extensive rearrangement within methanosarcinal genomes." Maeder D.L., Anderson I., Brettin T.S., Bruce D.C., Gilna P., Han C.S., Lapidus A., Metcalf W.W., Saunders E., Tapia R., Sowers K.R. J. Bacteriol. 188:7922-7931(2006) [PubMed: 16980466] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[2]	"Differential modes of transfer RNA(Ser) recognition in Methanosarcina barkeri." Korencic D., Polycarpo C., Weygand-Durasevic I., Soell D. J. Biol. Chem. 279:48780-48786(2004) [PubMed: 15364939] [Abstract] Cited for: FUNCTION, KINETIC PARAMETERS, TRNA(SER) RECOGNITION.
[3]	"Selective inhibition of divergent seryl-tRNA synthetases by serine analogues." Ahel D., Slade D., Mocibob M., Soell D., Weygand-Durasevic I. FEBS Lett. 579:4344-4348(2005) [PubMed: 16054140] [Abstract] Cited for: ENZYME REGULATION.
[4]	"Structure of the unusual seryl-tRNA synthetase reveals a distinct zinc-dependent mode of substrate recognition." Bilokapic S., Maier T., Ahel D., Gruic-Sovulj I., Soell D., Weygand-Durasevic I., Ban N. EMBO J. 25:2498-2509(2006) [PubMed: 16675947] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS) IN COMPLEXES WITH ZINC; ATP; SUBSTRATE AND SUBSTRATE ANALOG, COFACTOR, SUBUNIT, MUTAGENESIS OF CYS-306; GLU-355 AND CYS-461, SERINE RECOGNITION MECHANISM.

Cross-references

Sequence databases

EMBLGenBankDDBJ

CP000099 Genomic DNA. Translation: AAZ71057.1.

RefSeq

YP_305637.1.

3D structure databases

PDBPDBe

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
2CIM	X-ray	2.51	A/B	1-502	[»]
2CJ9	X-ray	2.30	A/B	1-502	[»]
2CJA	X-ray	2.20	A/B	1-502	[»]
2CJB	X-ray	2.70	A/B	1-502	[»]

ModBase

Search...

Genome annotation databases

GeneID

3626080.

GenomeReviews

Gene locus Mbar_A2126 in contig CP000099_GR.

KEGG

mba:Mbar_A2126.

NMPDR

fig|269797.3.peg.1604.

Organism-specific databases

CMR

Search...

Phylogenomic databases

HOGENOM

Q46AN5.

OMA

Q46AN5. PAQCEPF.

Enzyme and pathway databases

BioCyc

MBAR269797:MBAR_A2126-MON.

Family and domain databases

HAMAP

MF_01278.
[Tree]

InterPro

IPR002314. aa-tRNA-synt_IIb_cons-reg.
IPR006195. aa-tRNA-synth_II_cons-reg.
[Graphical view]

Pfam

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

PROSITE

PS50862. AA_TRNA_LIGASE_II. 1 hit.
[Graphical view]

ProtoNet

Search...

Entry information

Entry name

SYS2_METBF

Accession

Primary (citable) accession number: Q46AN5

Entry history

Integrated into UniProtKB/Swiss-Prot:	May 1, 2007
Last sequence update:	September 13, 2005
Last modified:	June 16, 2009
This is version 33 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)